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https://biorxiv.org/cgi/content/short/172494v1?rss=1"
Beausang, J. F.Wheeler, A. J.Chan, N. H.Hanft, V. R.Dirbas, F. M.Jeffrey, S. S.Quake, S. R.2017-08-04doi:10.1101/172494Cold Spring Harbor Laboratory Press2017-08-04
https://biorxiv.org/cgi/content/short/144436v1?rss=1"
Beyene, A.McFarlane, I. R.Pinals, R.Landry, M.2017-05-31doi:10.1101/144436Cold Spring Harbor Laboratory Press2017-05-31
https://biorxiv.org/cgi/content/short/120170v1?rss=1"
Boettcher, M.Tian, R.Blau, J.Markegard, E.Wu, D.Biton, A.Zaitlen, N.McCormick, F.Kampmann, M.McManus, M. T.2017-03-25doi:10.1101/120170Cold Spring Harbor Laboratory Press2017-03-25
https://biorxiv.org/cgi/content/short/196980v1?rss=1"
Branon, T. C.Bosch, J. A.Sanchez, A. D.Udeshi, N. D.Svinkina, T.Carr, S. A.Feldman, J. L.Perrimon, N.Ting, A. Y.2017-10-02doi:10.1101/196980Cold Spring Harbor Laboratory Press2017-10-02
https://biorxiv.org/cgi/content/short/173468v1?rss=1"
Brower, K.Puccinelli, R.Markin, C.Shimko, T.Longwell, S.Cruz, B.Gomez-Sjoberg, R.Fordyce, P. M.2017-08-13doi:10.1101/173468Cold Spring Harbor Laboratory Press2017-08-13
https://biorxiv.org/cgi/content/short/179804v1?rss=1"
Camunas-Soler, J.Lee, H.Hudgins, L.Hintz, S. R.Blumenfeld, Y. J.El-Sayed, Y. Y.Quake, S. R.2017-08-23doi:10.1101/179804Cold Spring Harbor Laboratory Press2017-08-23
https://biorxiv.org/cgi/content/short/149385v1?rss=1"
50 MY through a process analogous to Darwinian evolution of the genome.
]]>Catania, S.Dumesic, P. A.Stoddard, C.Cooke, S.Burke, J.Cuomo, C. A.Narlikar, G. J.Madhani, H. D.2017-06-13doi:10.1101/149385Cold Spring Harbor Laboratory Press2017-06-13
https://biorxiv.org/cgi/content/short/200204v1?rss=1"
Citron, Y. R.Fagerstrom, C. J.Keszthelyi, B.Huang, B.Rusan, N. M.Kelly, M. J. S.Agard, D. A.2017-10-10doi:10.1101/200204Cold Spring Harbor Laboratory Press2017-10-10
https://biorxiv.org/cgi/content/short/147017v1?rss=1"
Dao Duc, K.Saleem, Z. H.Song, Y. S.2017-06-07doi:10.1101/147017Cold Spring Harbor Laboratory Press2017-06-07
https://biorxiv.org/cgi/content/short/139758v1?rss=1"
de Bourcy, C. F. A.Dekker, C. L.Davis, M. M.Nicolls, M. R.Quake, S. R.2017-05-18doi:10.1101/139758Cold Spring Harbor Laboratory Press2017-05-18
https://biorxiv.org/cgi/content/short/169672v1?rss=1"
Deaton, J.Yu, F.Quake, S.2017-07-28doi:10.1101/169672Cold Spring Harbor Laboratory Press2017-07-28
https://biorxiv.org/cgi/content/short/145912v1?rss=1"
Del Bonis-O'Donnell, J. T.Page, R. H.Beyene, A. G.Tindall, E. G.McFarlane, I. R.Landry, M. P.2017-06-04doi:10.1101/145912Cold Spring Harbor Laboratory Press2017-06-04
https://biorxiv.org/cgi/content/short/179549v1?rss=1"
Demirer, G. S.Chang, R.Zhang, H.Chio, L.Landry, M. P.2017-08-22doi:10.1101/179549Cold Spring Harbor Laboratory Press2017-08-22
https://biorxiv.org/cgi/content/short/109686v1?rss=1"
Doan, T.Acharya, N.Pinsky, B.Sahoo, M.Chow, E.Banaei, N.Budvytiene, I.Cevallos, V.Zhong, L.Zhou, Z.Lietman, T.DeRisi, J. L.2017-02-18doi:10.1101/109686Cold Spring Harbor Laboratory Press2017-02-18
https://biorxiv.org/cgi/content/short/108043v1?rss=1"
Enge, M.Arda, H. E.Mignardi, M.Beausang, J.Bottino, R.Kim, S. K.Quake, S. R.2017-02-13doi:10.1101/108043Cold Spring Harbor Laboratory Press2017-02-13
https://biorxiv.org/cgi/content/short/137059v1?rss=1"
Feng, S.Sekine, S.Pessino, V.Li, H.Leonetti, M. D.Huang, B.2017-05-12doi:10.1101/137059Cold Spring Harbor Laboratory Press2017-05-12
https://biorxiv.org/cgi/content/short/179093v1?rss=1"
Gasch, A. P.Yu, F. B.Hose, J.Escalante, L. E.Place, M.Bacher, R.Kanbar, J.Ciobanu, D.Sandor, L.Grigoriev, I.Kendziorski, C.Quake, S. R.McClean, M. N.2017-08-21doi:10.1101/179093Cold Spring Harbor Laboratory Press2017-08-21
https://biorxiv.org/cgi/content/short/139873v1?rss=1"
Herman, N.Kim, S.-J.Li, J. S.Cai, W.Koshino, H.Zhang, W.2017-05-18doi:10.1101/139873Cold Spring Harbor Laboratory Press2017-05-18
https://biorxiv.org/cgi/content/short/145052v1?rss=1"
Horns, F.Vollmers, C.Dekker, C. L.Quake, S. R.2017-10-19doi:10.1101/145052Cold Spring Harbor Laboratory Press2017-10-19
https://biorxiv.org/cgi/content/short/164087v1?rss=1"
Hughes, A.Mornin, J. D.Biswas, S. K.Bauer, D. P.Bianco, S.Gartner, Z. J.2017-07-15doi:10.1101/164087Cold Spring Harbor Laboratory Press2017-07-15
https://biorxiv.org/cgi/content/short/205500v1?rss=1"
Hultquist, J. F.Hiatt, J.Schumann, K.McGregor, M. J.Roth, T. L.Haas, P.Doudna, J.Marson, A.Krogan, N. J.2017-10-19doi:10.1101/205500Cold Spring Harbor Laboratory Press2017-10-19
https://biorxiv.org/cgi/content/short/172809v1?rss=1"
Kalia, R.Wang, R. Y.- R.Yusuf, A.Thomas, P. V.Agard, D. A.Shaw, J. M.Frost, A.2017-08-04doi:10.1101/172809Cold Spring Harbor Laboratory Press2017-08-04
https://biorxiv.org/cgi/content/short/166462v1?rss=1"
100-fold enrichment of cells experiencing a specific GPCR-arrestin PPI during a short 10-minute light window over cells missing that PPI during the same time window. Due to its high specificity, sensitivity, and generality, PPI-FLARE should be a broadly useful tool for PPI analysis and discovery.
]]>Kim, M. W.Wang, W.Sanchez, M. I.Coukos, R.Von Zastrow, M.Ting, A.2017-07-21doi:10.1101/166462Cold Spring Harbor Laboratory Press2017-07-21
https://biorxiv.org/cgi/content/short/113746v1?rss=1"
Kowarsky, M. A.Camunas-Soler, J.Kertesz, M.De Vlaminck, I.Koh, L. C. W.Pan, W.Martin, L.Neff, N.Okamoto, J.Wong, R. J.Kharbanda, S.El-Sayed, Y.Blumenfeld, Y.Stevenson, D. K.Shaw, G. M.Wolfe, N. D.Quake, S. R.2017-03-04doi:10.1101/113746Cold Spring Harbor Laboratory Press2017-03-04
https://biorxiv.org/cgi/content/short/148528v1?rss=1"
Kronstad, L. M.Seiler, C.Vergara, R.Holmes, S. P.Blish, C. A.2017-06-10doi:10.1101/148528Cold Spring Harbor Laboratory Press2017-06-10
https://biorxiv.org/cgi/content/short/102798v1?rss=1"
Langelier, C.Zinter, M. S.Kalantar, K.Yank, G. A.Christenson, S.Odonovan, B.White, C.Wilson, M. R.Sapru, A.Dvorak, C. C.Miller, S.Chiu, C. Y.DeRisi, J. L.2017-01-24doi:10.1101/102798Cold Spring Harbor Laboratory Press2017-01-24
https://biorxiv.org/cgi/content/short/193904v1?rss=1"
Le, D. D.Shimko, T. C.Aditham, A. K.Keys, A. M.Orenstein, Y.Fordyce, P.2017-09-26doi:10.1101/193904Cold Spring Harbor Laboratory Press2017-09-26
https://biorxiv.org/cgi/content/short/178905v1?rss=1"
Li, H.Beckman, K. A.Pessino, V.Huang, B.Weissman, J. S.Leonetti, M. D.2017-08-21doi:10.1101/178905Cold Spring Harbor Laboratory Press2017-08-21
https://biorxiv.org/cgi/content/short/145045v1?rss=1"
Li, H.Horns, F.Wu, B.Xie, Q.Li, J.Li, T.Luginbuhl, D.Quake, S. R.Luo, L.2017-06-03doi:10.1101/145045Cold Spring Harbor Laboratory Press2017-06-03
https://biorxiv.org/cgi/content/short/155440v1?rss=1"
Luo, S.Yu, J. A.Li, H.Song, Y. S.2017-06-26doi:10.1101/155440Cold Spring Harbor Laboratory Press2017-06-26
https://biorxiv.org/cgi/content/short/139352v1?rss=1"
Mavor, D.Barlow, K.Asarnow, D.Birman, Y.Britain, D.Chen, W.Green, E. M.Kenner, L. R.Mensa, B.Morinishi, L. S.Nelson, C. A.Poss, E. M.Suresh, P.Tian, R.Arhar, T.Ary, B. E.Bauer, D. P.Bergman, I. D.Brunetti, R. M.Chio, C. M.Dai, S. A.Dickinson, M. S.Elledge, S.Hendel, N. L.Helsell, C. V. M.Kang, E.Kern, N.Khoroshkin, M. S.Kirkemo, L. L.Lewis, G. R.Lou, K.Marin, W. M.Maxwell, A. M.McTigue, P. F.Meyers-Turnbull, D.Nagy, T. L.Natale, A. M.Oltion, K.Pourmal, S.Reder, G. K.Rettko, N. J.Rohweder, P. J.Schwarz, D. M. C.2017-05-17doi:10.1101/139352Cold Spring Harbor Laboratory Press2017-05-17
https://biorxiv.org/cgi/content/short/140418v1?rss=1"
McGorty, R.Xie, D.Huang, B.2017-05-20doi:10.1101/140418Cold Spring Harbor Laboratory Press2017-05-20
https://biorxiv.org/cgi/content/short/131870v1?rss=1"
Milgrom, P.Horst, J. A.Ludwig, S.Rothen, M.Chaffee, B. W.Lyalina, S.Pollard, K.DeRisi, J. L.Mancl, L.2017-04-29doi:10.1101/131870Cold Spring Harbor Laboratory Press2017-04-29
https://biorxiv.org/cgi/content/short/204693v1?rss=1"
Mocciaro, A.Roth, T.Bennett, H.Soumillon, M.Shah, A.Hiatt, J.Chapman, K.Marson, A.Lavieu, G.2017-10-17doi:10.1101/204693Cold Spring Harbor Laboratory Press2017-10-17
https://biorxiv.org/cgi/content/short/178269v1?rss=1"
Mumbach, M. R.Satpathy, A. T.Boyle, E. A.Dai, C.Gowen, B. G.Cho, S. W.Nguyen, M. L.Rubin, A. J.Granja, J. M.Kazane, K. R.Wei, Y.Nguyen, T.Greenside, P. G.Corces, M. R.Tycko, J.Simeonov, D. R.Suliman, N.Li, R.Xu, J.Flynn, R. A.Kundaje, A.Khavari, P. A.Marson, A.Corn, J. E.Quertermous, T.Greenleaf, W. J.Chang, H. Y.2017-08-26doi:10.1101/178269Cold Spring Harbor Laboratory Press2017-08-26
https://biorxiv.org/cgi/content/short/119131v1?rss=1"
Nagy, T.Kampmann, M.2017-03-22doi:10.1101/119131Cold Spring Harbor Laboratory Press2017-03-22
https://biorxiv.org/cgi/content/short/125013v1?rss=1"
Pessino, V.Citron, Y. R.Feng, S.Huang, B.2017-04-06doi:10.1101/125013Cold Spring Harbor Laboratory Press2017-04-06
https://biorxiv.org/cgi/content/short/167874v1?rss=1"
Rauch, J.Chen, J. J.Sorum, A. W.Miller, G. M.Sharf, T.See, S. K.Hsieh-Wilson, L. C.Kampmann, M.Kosik, K. S.2017-07-24doi:10.1101/167874Cold Spring Harbor Laboratory Press2017-07-24
https://biorxiv.org/cgi/content/short/183418v1?rss=1"
1 kilobase) DNA sequences at specific sites in the genomes of primary human T cells while preserving cell viability and function. We successfully tested the potential therapeutic use of this approach in two settings. First, we corrected a pathogenic IL2RA mutation in primary T cells from multiple family members with monogenic autoimmune disease and demonstrated enhanced signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR redirecting T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized the tumour antigen, with concomitant cytokine release and tumour cell killing. Taken together, these studies provide preclinical evidence that non-viral genome targeting will enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells.
]]>Roth, T. L.Yu, R.Shifrut, E.Hiatt, J.Li, H.Schumann, K.Tobin, V.Ferris, A. M.Chen, J.Schickel, J.-N.Pellerin, L.Carmody, D.Alkorta-Aranburu, G.Del Gaudio, D.Cho, M.Matsumoto, H.Morell, M.Mao, Y.Nguyen, D.Quadros, R.Gurumurthy, C.Smith, B.Haugwitz, M.Hughes, S. H.Weissman, J.May, A. P.Kupfer, G.Greeley, S.Bacchetta, R.Meffre, E.Roncarolo, M. G.Romberg, N.Herold, K. C.Leonetti, M. D.Marson, A.2017-08-31doi:10.1101/183418Cold Spring Harbor Laboratory Press2017-08-31
https://biorxiv.org/cgi/content/short/125005v1?rss=1"
Schnitzbauer, J.Wang, Y.Bakalar, M.Chen, B.Nuwal, T.Zhao, S.Huang, B.2017-06-23doi:10.1101/125005Cold Spring Harbor Laboratory Press2017-06-23
https://biorxiv.org/cgi/content/short/152199v1?rss=1"
Seto, J.Horst, J. A.Parkinson, D. Y.Frachella, J. C.DeRisi, J. L.2017-06-19doi:10.1101/152199Cold Spring Harbor Laboratory Press2017-06-19
https://biorxiv.org/cgi/content/short/142042v1?rss=1"
Shi, X.Garcia, G.Van De Weghe, J. C.McGorty, R.Pazour, G. J.Doherty, D.Huang, B.Reiter, J. F.2017-05-25doi:10.1101/142042Cold Spring Harbor Laboratory Press2017-05-25
https://biorxiv.org/cgi/content/short/162081v1?rss=1"
Song, C.-X.Yin, S.Ma, L.Wheeler, A.Chen, Y.Zhang, Y.Liu, B.Xiong, J.Zhang, W.Hi, J.Zhou, Z.Dong, B.Tian, Z.Jeffrey, S. S.Chua, M.-S.So, S.Li, W.Wei, Y.Diao, J.Xie, D.Quake, S. R.2017-07-12doi:10.1101/162081Cold Spring Harbor Laboratory Press2017-07-12
https://biorxiv.org/cgi/content/short/195578v1?rss=1"
Walczak, M.Ganesan, S. M.Niles, J. C.Yeh, E.2017-10-02doi:10.1101/195578Cold Spring Harbor Laboratory Press2017-10-02
https://biorxiv.org/cgi/content/short/188615v1?rss=1"
White, J.Streets, A. M.2017-09-14doi:10.1101/188615Cold Spring Harbor Laboratory Press2017-09-14
https://biorxiv.org/cgi/content/short/114496v1?rss=1"
Yu, F.Blainey, P. C.Schulz, F.Woyke, T.Horowitz, M. A.Quake, S. R.2017-03-07doi:10.1101/114496Cold Spring Harbor Laboratory Press2017-03-07
https://biorxiv.org/cgi/content/short/203331v1?rss=1"
Zanini, F.Pu, S.-Y.Bekerman, E.Einav, S.Quake, S. R.2017-10-14doi:10.1101/203331Cold Spring Harbor Laboratory Press2017-10-14
https://biorxiv.org/cgi/content/short/184135v1?rss=1"
Zviran, A.Mor, N.Rais, Y.Gingold, H.Peles, S.Chomsky, E.Viukov, S.Buenrostro, J. D.Weinberger, L.Manor, Y. S.Krupalnik, V.Zerbib, M.Hezroni, H.Jaitin, D. A.Larastiaso, D.Gilad, S.Benjamin, S.Mousa, A.Ayyash, M.Sheban, D.Bayerl, J.Aguilera Castrejon, A.Massarwa, R.Maza, I.Hanna, S.Amit, I.Stelzer, Y.Ulitsky, I.Greenleaf, W. J.Pilpel, Y.Novershtern, N.Hanna, J. H.2017-09-07doi:10.1101/184135Cold Spring Harbor Laboratory Press2017-09-07
https://biorxiv.org/cgi/content/short/121202v1?rss=1"
Regev, A.Teichmann, S.Lander, E. S.Amit, I.Benoist, C.Birney, E.Bodenmiller, B.Campbell, P.Carninci, P.Clatworthy, M.Clevers, H.Deplancke, B.Dunham, I.Eberwine, J.Eils, R.Enard, W.Farmer, A.Fugger, L.Gottgens, B.Hacohen, N.Haniffa, M.Hemberg, M.Kim, S. K.Klenerman, P.Kriegstein, A.Lein, E.Linnarsson, S.Lundeberg, J.Majumder, P.Marioni, J.Merad, M.Mhlanga, M.Nawijn, M.Netea, M.Nolan, G.Pe'er, D.Philipakis, A.Ponting, C. P.Quake, S. R.Reik, W.Rozenblatt-Rosen, O.Sanes, J. R.Satija, R.Shumacher, T.Shalek, A. K2017-05-08doi:10.1101/121202Cold Spring Harbor Laboratory Press2017-05-08
https://biorxiv.org/cgi/content/short/202002v1?rss=1"
Kreimer, A.Yan, Z.Ahituv, N.Yosef, N.2017-10-11doi:10.1101/202002Cold Spring Harbor Laboratory Press2017-10-11
https://biorxiv.org/cgi/content/short/212910v1?rss=1"
Ngo, T. T.Moufarrej, M. N.Rasmussen, M.-L. H.Camunas-Soler, J.Pan, W.Okamoto, J.Neff, N.Liu, K.Wong, R. J.Downes, K.Tibshirani, R.Shaw, G. M.Skotte, L.Stevenson, D. K.Biggio, J. R.Elovitz, M. A.Melbye, M.Quake, S. R.2017-11-01doi:10.1101/212910Cold Spring Harbor Laboratory Press2017-11-01
https://biorxiv.org/cgi/content/short/210955v1?rss=1"
Garud, N. R.Good, B. H.Hallatschek, O.Pollard, K. S.2017-10-30doi:10.1101/210955Cold Spring Harbor Laboratory Press2017-10-30
https://biorxiv.org/cgi/content/short/213561v1?rss=1"
Wilson, M. R.O'Donovan, B. D.Gelfand, J. M.Sample, H. A.Chow, F. C.Betjemann, J. P.Shah, M. P.Richie, M. B.Gorman, M. P.Hajj-Ali, R. A.Calabrese, L. H.Zorn, K. C.Greenlee, J. E.Blum, J. H.Green, G.Khan, L. M.Banerji, D.Langelier, C.Bryson-Cahn, C.Harrington, W.Lingappa, J. R.Shanbhag, N. M.Green, A. J.Brew, B. J.Soldatos, A.Strnad, L.Doernberg, S. B.Jay, C. A.Douglas, V.Josephson, S. A.DeRisi, J. L.2017-11-07doi:10.1101/213561Cold Spring Harbor Laboratory Press2017-11-07
https://biorxiv.org/cgi/content/short/218164v1?rss=1"
McKitterick, A. C.Seed, K.2017-11-11doi:10.1101/218164Cold Spring Harbor Laboratory Press2017-11-11
https://biorxiv.org/cgi/content/short/221689v1?rss=1"
Barlow, K. A.O Conchuir, S.Thompson, S.Suresh, P.Lucas, J. E.Heinonen, M.Kortemme, T.2017-11-17doi:10.1101/221689Cold Spring Harbor Laboratory Press2017-11-17
https://biorxiv.org/cgi/content/short/220954v1?rss=1"
SoRelle, E. D.Yecies, D. W.Liba, O.Bennett, C. F.Graef, C.-M.Dutta, R.Mitra, S. S.Joubert, L.-M.Cheshier, S. H.Grant, G. A.de la Zerda, A.2017-11-17doi:10.1101/220954Cold Spring Harbor Laboratory Press2017-11-17
https://biorxiv.org/cgi/content/short/217968v1?rss=1"
Parsa, J.-Y.Boudoukha, S.Burke, J.Homer, C.Madhani, H.2017-11-11doi:10.1101/217968Cold Spring Harbor Laboratory Press2017-11-11
https://biorxiv.org/cgi/content/short/222257v1?rss=1"
Tsai, J. C.Miller-Vedam, L. E.Anand, A. A.Jaishankar, P.Nguyen, H. C.Renslo, A. R.Frost, A.Walter, P.2017-11-22doi:10.1101/222257Cold Spring Harbor Laboratory Press2017-11-22
https://biorxiv.org/cgi/content/short/224170v1?rss=1"
Burke, J.Longhurst, A.Merkurjev, D.Sales-Lee, J.Rao, B.Moresco, J.Yates, J.Li, J. J.Madhani, H. D.2017-11-22doi:10.1101/224170Cold Spring Harbor Laboratory Press2017-11-22
https://biorxiv.org/cgi/content/short/227660v1?rss=1"
Steinrücken, M.Spence, J. P.Kamm, J. A.Wieczorek, E.Song, Y. S.2017-12-01doi:10.1101/227660Cold Spring Harbor Laboratory Press2017-12-01
https://biorxiv.org/cgi/content/short/222307v1?rss=1"
Grabek, K. R.Cooke, T. F.Epperson, L. E.Spees, K. K.Cabral, G. F.Sutton, S. C.Merriman, D. K.Martin, S. L.Bustamante, C. D.2017-12-02doi:10.1101/222307Cold Spring Harbor Laboratory Press2017-12-02
https://biorxiv.org/cgi/content/short/228122v1?rss=1"
Bayas, C. A.Wang, J.Lee, M. K.Schrader, J. M.Shapiro, L.Moerner, W. E.2017-12-03doi:10.1101/228122Cold Spring Harbor Laboratory Press2017-12-03
https://biorxiv.org/cgi/content/short/228338v1?rss=1"
Delley, C. L.Liu, L.Sarhan, M. F.Abate, A. R.2017-12-03doi:10.1101/228338Cold Spring Harbor Laboratory Press2017-12-03
https://biorxiv.org/cgi/content/short/231266v1?rss=1"
Croote, D.Braslavsky, I.Quake, S. R.2017-12-12doi:10.1101/231266Cold Spring Harbor Laboratory Press2017-12-12
https://biorxiv.org/cgi/content/short/090837v1?rss=1"
Dao Duc, K.Song, Y. S.2016-12-01doi:10.1101/090837Cold Spring Harbor Laboratory Press2016-12-01
https://biorxiv.org/cgi/content/short/229245v1?rss=1"
Wang, M.Fischer, J.Song, Y. S.2017-12-05doi:10.1101/229245Cold Spring Harbor Laboratory Press2017-12-05
https://biorxiv.org/cgi/content/short/233908v1?rss=1"
Rosen, Z.Bhaskar, A.Roch, S.Song, Y. S.2017-12-13doi:10.1101/233908Cold Spring Harbor Laboratory Press2017-12-13
https://biorxiv.org/cgi/content/short/237446v1?rss=1"
The Tabula Muris Consortium,Quake, S. R.Wyss-Coray, T.Darmanis, S.2017-12-20doi:10.1101/237446Cold Spring Harbor Laboratory Press2017-12-20
https://biorxiv.org/cgi/content/short/220293v1?rss=1"
Lasker, K.von Diezmann, A.Ahrens, D. G.Mann, T. H.Moerner, W. E.Shapiro, L.2017-12-20doi:10.1101/220293Cold Spring Harbor Laboratory Press2017-12-20
https://biorxiv.org/cgi/content/short/239350v1?rss=1"
Winetraub, Y.Wu, C.Chu, S.de la Zerda, A.2017-12-24doi:10.1101/239350Cold Spring Harbor Laboratory Press2017-12-24
https://biorxiv.org/cgi/content/short/243345v1?rss=1"
Charlesworth, C. T.Deshpande, P. S.Dever, D. P.Dejene, B.Gomez-Ospina, N.Mantri, S.Pavel-Dinu, M.Camarena, J.Weinberg, K. I.Porteus, M. H.2018-01-05doi:10.1101/243345Cold Spring Harbor Laboratory Press2018-01-05
https://biorxiv.org/cgi/content/short/244020v1?rss=1"
Harrigan, P.Madhani, H.El-Samad, H.2018-01-07doi:10.1101/244020Cold Spring Harbor Laboratory Press2018-01-07
https://biorxiv.org/cgi/content/short/250373v1?rss=1"
10 nm from the target surface. Increasing antigen height allows for co-localization of Fc receptors and the inhibitory phosphatase CD45 at the cell-cell interface, which reduces Fc receptor phosphorylation, and inhibits phagocytosis. Our work shows that close contact between macrophage and target cell is a requirement for efficient phagocytosis, suggesting that therapeutic antibodies should target short antigens in order to trigger Fc receptor activation through size-dependent physical segregation.
]]>Bakalar, M. H.Joffe, A. M.Schmid, E.Son, S.Podolski, M.Fletcher, D. A.2018-01-19doi:10.1101/250373Cold Spring Harbor Laboratory Press2018-01-19
https://biorxiv.org/cgi/content/short/252080v1?rss=1"
Yecies, D.Liba, O.SoRelle, E.Dutta, R.Yuan, E.Vogel, H.Grant, G.de la Zerda, A.2018-01-22doi:10.1101/252080Cold Spring Harbor Laboratory Press2018-01-22
https://biorxiv.org/cgi/content/short/248419v1?rss=1"
nView larger version (28K):norg.highwire.dtl.DTLVardef@1cc6c8borg.highwire.dtl.DTLVardef@1ea1eb3org.highwire.dtl.DTLVardef@185a0b4org.highwire.dtl.DTLVardef@1f9c6b9_HPS_FORMAT_FIGEXP M_FIG Graphical abstractnnC_FIG
]]>Gomez-Schiavon, M.El-Samad, H.2018-01-16doi:10.1101/248419Cold Spring Harbor Laboratory Press2018-01-16
https://biorxiv.org/cgi/content/short/258814v1?rss=1"
Zitnik, M.Agrawal, M.Leskovec, J.2018-02-02doi:10.1101/258814Cold Spring Harbor Laboratory Press2018-02-02
https://biorxiv.org/cgi/content/short/258863v1?rss=1"
Zou, R.Zhu, X.Tu, Y.Wu, J.Landry, M. P.2018-02-01doi:10.1101/258863Cold Spring Harbor Laboratory Press2018-02-01
https://biorxiv.org/cgi/content/short/256313v1?rss=1"
Ryu, H.Inoue, F.Whalen, S.Williams, A.Kircher, M.Martin, B.Alvarado, B.Samee, M. A. H.Keough, K.Thomas, S.Kriegstein, A.Shendure, J.Pollen, A.Ahituv, N.Pollard, K.2018-01-29doi:10.1101/256313Cold Spring Harbor Laboratory Press2018-01-29
https://biorxiv.org/cgi/content/short/253450v1?rss=1"
nView larger version (108K):norg.highwire.dtl.DTLVardef@68f595org.highwire.dtl.DTLVardef@d33792org.highwire.dtl.DTLVardef@e56314org.highwire.dtl.DTLVardef@1cbbba2_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Jha, A. R.Davenport, E. R.Gautam, Y.Bhandari, D.Tandukar, S.Ng, K.Holmes, S.Gautam, G. P.Sherchand, J. B.Bustamante, C.Sonnenburg, J.2018-01-27doi:10.1101/253450Cold Spring Harbor Laboratory Press2018-01-27
https://biorxiv.org/cgi/content/short/260208v1?rss=1"
Ng, N.Shi, H.Colavin, A.Huang, K.2018-02-05doi:10.1101/260208Cold Spring Harbor Laboratory Press2018-02-05
https://biorxiv.org/cgi/content/short/252163v1?rss=1"
Martin, R.Ikeda, K.Uchida, N.Cromer, M. K.Nishimura, T.Dever, D. P.Camarena, J.Bak, R.Lausten, A.Jakobsen, M. R.Wiebking, V.Sebastiano, V.Nakauchi, H.Porteus, M. H.2018-01-23doi:10.1101/252163Cold Spring Harbor Laboratory Press2018-01-23
https://biorxiv.org/cgi/content/short/108910v1?rss=1"
Amberg-Johnson, K.Ganesan, S. M.Lorenzi, H. A.Niles, J. C.Yeh, E.2017-02-15doi:10.1101/108910Cold Spring Harbor Laboratory Press2017-02-15
https://biorxiv.org/cgi/content/short/134338v1?rss=1"
Gisselberg, J. E.Herrera, Z.Orchard, L.Llinas, M.Yeh, E.2017-05-04doi:10.1101/134338Cold Spring Harbor Laboratory Press2017-05-04
https://biorxiv.org/cgi/content/short/229286v1?rss=1"
Colavin, A.Shi, H.Huang, K. C.2017-12-04doi:10.1101/229286Cold Spring Harbor Laboratory Press2017-12-04
https://biorxiv.org/cgi/content/short/148692v1?rss=1"
Hueschen, C.Kenny, S. J.Xu, K.Dumont, S.2017-06-11doi:10.1101/148692Cold Spring Harbor Laboratory Press2017-06-11
https://biorxiv.org/cgi/content/short/168518v1?rss=1"
Ge, L.Zhang, M.Kenny, S.Liu, D.Maeda, M.Saito, K.Marthur, A.Xu, K.Schekman, R.2017-07-25doi:10.1101/168518Cold Spring Harbor Laboratory Press2017-07-25
https://biorxiv.org/cgi/content/short/280495v1?rss=1"
Chen, B.Zou, W.Huang, B.2018-03-12doi:10.1101/280495Cold Spring Harbor Laboratory Press2018-03-12
https://biorxiv.org/cgi/content/short/265967v1?rss=1"
Boucher, M. J.Ghosh, S.Zhang, L.Lal, A.Jang, S. W.Ju, A.Zhang, S.Wang, X.Ralph, S. A.Zou, J.Elias, J. E.Yeh, E.2018-02-14doi:10.1101/265967Cold Spring Harbor Laboratory Press2018-02-14
https://biorxiv.org/cgi/content/short/258103v1?rss=1"
Armon, S.Bull, M. S.Aranda-Diaz, A. J.Prakash, M.2018-02-16doi:10.1101/258103Cold Spring Harbor Laboratory Press2018-02-16
https://biorxiv.org/cgi/content/short/267211v1?rss=1"
Chan, J.Perrone, V.Spence, J. P.Jenkins, P. A.Mathieson, S.Song, Y. S.2018-02-18doi:10.1101/267211Cold Spring Harbor Laboratory Press2018-02-18
https://biorxiv.org/cgi/content/short/272245v1?rss=1"
Whalen, S.Pollard, K. S.2018-02-26doi:10.1101/272245Cold Spring Harbor Laboratory Press2018-02-26
https://biorxiv.org/cgi/content/short/273359v1?rss=1"
1.06. We demonstrated multicolor and fast volumetric imaging of live cells and single-molecule super-resolution microscopy using our system.
]]>Yang, B.Wang, Y.Feng, S.Pessino, V.Stuurman, N.Huang, B.2018-02-28doi:10.1101/273359Cold Spring Harbor Laboratory Press2018-02-28
https://biorxiv.org/cgi/content/short/278556v1?rss=1"
Tran, T. M.Kim, S. C.Abate, A. R.2018-03-07doi:10.1101/278556Cold Spring Harbor Laboratory Press2018-03-07
https://biorxiv.org/cgi/content/short/301341v1?rss=1"
Rendon, O. Z.Fredrickson, E. K.Howard, C. J.Vranken, J. V.Fogarty, S.Tolley, N. D.Kalia, R.Osuna, B. A.Shen, P. S.Hill, C. P.Frost, A.Rutter, J.2018-04-14doi:10.1101/301341Cold Spring Harbor Laboratory Press2018-04-14
https://biorxiv.org/cgi/content/short/299446v1?rss=1"
Greenhouse, B.Smith, D. L.Rodriguez-Barraquer, I.Mueller, I.Drakeley, C.2018-04-11doi:10.1101/299446Cold Spring Harbor Laboratory Press2018-04-11
https://biorxiv.org/cgi/content/short/293738v1?rss=1"
Zhou, X.Shapiro, L.2018-04-03doi:10.1101/293738Cold Spring Harbor Laboratory Press2018-04-03
https://biorxiv.org/cgi/content/short/292037v1?rss=1"
Lopez, R.Regier, J.Cole, M. B.Jordan, M.Yosef, N.2018-03-30doi:10.1101/292037Cold Spring Harbor Laboratory Press2018-03-30
https://biorxiv.org/cgi/content/short/291864v1?rss=1"
Zinter, M. S.Dvorak, C. C.Mayday, M. Y.Iwanaga, K.Ly, N. P.McGarry, M. E.Church, G. D.Faricy, L. E.Rowan, C. M.Hume, J. R.Steiner, M. E.Crawford, E. D.Langelier, C.Kalantar, K.Chow, E. D.Miller, S.Shimano, K.Melton, A.Yanik, G. A.Sapru, A.DeRisi, J. L.2018-03-29doi:10.1101/291864Cold Spring Harbor Laboratory Press2018-03-29
https://biorxiv.org/cgi/content/short/291195v1?rss=1"
Su, M.Zhu, X.Zhang, W.2018-03-29doi:10.1101/291195Cold Spring Harbor Laboratory Press2018-03-29
https://biorxiv.org/cgi/content/short/290122v1?rss=1"
Miller, M.Kenny, S.Mannowetz, N.Mansell, S.Wojcik, M.Mendoza, S.Zucker, R.Xu, K.Lishko, P. V.2018-03-27doi:10.1101/290122Cold Spring Harbor Laboratory Press2018-03-27
https://biorxiv.org/cgi/content/short/288290v1?rss=1"
Garcia, V. E.Liu, J.DeRisi, J.2018-03-25doi:10.1101/288290Cold Spring Harbor Laboratory Press2018-03-25
https://biorxiv.org/cgi/content/short/287268v1?rss=1"
Kamm, J. A.Terhorst, J.Durbin, R.Song, Y. S.2018-03-23doi:10.1101/287268Cold Spring Harbor Laboratory Press2018-03-23
https://biorxiv.org/cgi/content/short/285205v1?rss=1"
Fudenberg, G.Pollard, K.2018-03-19doi:10.1101/285205Cold Spring Harbor Laboratory Press2018-03-19
https://biorxiv.org/cgi/content/short/284992v1?rss=1"
Zylberberg, M.Van Hemert, C.Handel, C. M.DeRisi, J.2018-03-19doi:10.1101/284992Cold Spring Harbor Laboratory Press2018-03-19
https://biorxiv.org/cgi/content/short/289686v1?rss=1"
Kim, J.Wojcik, M.Wang, Y.Xu, K.Zhang, X.2018-03-27doi:10.1101/289686Cold Spring Harbor Laboratory Press2018-03-27
https://biorxiv.org/cgi/content/short/306779v1?rss=1"
Nguyen, H. Q.Roy, J.Harink, B.Damle, N.Baxter, B.Brower, K.Kortemme, T.Thorn, K.Cyert, M.Fordyce, P. M.2018-04-23doi:10.1101/306779Cold Spring Harbor Laboratory Press2018-04-23
https://biorxiv.org/cgi/content/short/304923v1?rss=1"
Hatori, M. N.Kim, S. C.Abate, A. R.2018-04-19doi:10.1101/304923Cold Spring Harbor Laboratory Press2018-04-19
https://biorxiv.org/cgi/content/short/303545v1?rss=1"
Chevalier, M.Gomez-Schiavon, M.Ng, A.El-Samad, H.2018-04-18doi:10.1101/303545Cold Spring Harbor Laboratory Press2018-04-18
https://biorxiv.org/cgi/content/short/301556v1?rss=1"
Retallack, H.Okihiro, M. S.Britton, E.Van Sommeran, S.DeRisi, J. L.2018-04-15doi:10.1101/301556Cold Spring Harbor Laboratory Press2018-04-15
https://biorxiv.org/cgi/content/short/309856v1?rss=1"
Belardi, B.Son, S.Vahey, M. D.Wang, J.Hou, J.Fletcher, D. A.2018-04-27doi:10.1101/309856Cold Spring Harbor Laboratory Press2018-04-27
https://biorxiv.org/cgi/content/short/308460v1?rss=1"
Harris, N. C.Born, D. A.Cai, W.Huang, Y.Martin, J.Khalaf, R.Drennan, C. L.Zhang, W.2018-04-25doi:10.1101/308460Cold Spring Harbor Laboratory Press2018-04-25
https://biorxiv.org/cgi/content/short/310284v1?rss=1"
Mezger, A.Klemm, S.Mann, I.Brower, K.Mir, A.Bostick, M.Farmer, A.Fordyce, P.Linnarsson, S.Greenleaf, W.2018-04-28doi:10.1101/310284Cold Spring Harbor Laboratory Press2018-04-28
https://biorxiv.org/cgi/content/short/313346v1?rss=1"
Angermeyer, A.Das, M. M.Singh, D. V.Seed, K. D.2018-05-02doi:10.1101/313346Cold Spring Harbor Laboratory Press2018-05-02
https://biorxiv.org/cgi/content/short/315903v1?rss=1"
Zitnik, M.Sosic, R.Leskovec, J.2018-05-07doi:10.1101/315903Cold Spring Harbor Laboratory Press2018-05-07
https://biorxiv.org/cgi/content/short/317941v1?rss=1"
Wang, B.Pourshafeie, A.Zitnik, M.Zhu, J.Bustamante, C.Batzoglou, S.Leskovec, J.2018-05-09doi:10.1101/317941Cold Spring Harbor Laboratory Press2018-05-09
https://biorxiv.org/cgi/content/short/317776v1?rss=1"
Hsieh, R. W.Kuo, A. H.Scheeren, F. A.Zarnegar, M. A.Sikandar, S. S.Antony, J.Heitink, L. S.Periyakoil, D.Kalisky, T.Sim, S.Qian, D.Malhotra, S. V.Somlo, G.Dirbas, F. M.Jadhav, A.Newman, A. M.Clarke, M. F.2018-05-10doi:10.1101/317776Cold Spring Harbor Laboratory Press2018-05-10
https://biorxiv.org/cgi/content/short/315499v1?rss=1"
Peters, J. M.Koo, B.-M.Patino, R.Heussler, G. E.Hearne, C. C.Inclan, Y.Hawkins, J. S.Lu, C. H. S.Harden, M. M.Osadnik, H.Peters, J. E.Engel, J. N.Dutton, R. J.Grossman, A. D.Gross, C. A.Rosenberg, O. S.2018-05-05doi:10.1101/315499Cold Spring Harbor Laboratory Press2018-05-05
https://biorxiv.org/cgi/content/short/168104v1?rss=1"
Rajniak, J.Giehl, R. F.Chang, E.Murgia, I.von Wiren, N.Sattely, E. S.2017-07-25doi:10.1101/168104Cold Spring Harbor Laboratory Press2017-07-25
https://biorxiv.org/cgi/content/short/288449v1?rss=1"
Chen, Y. C.Holmes, E.Rajniak, J.Kim, J.-G.Tang, S.Fischer, C.Mudgett, M. B.Sattely, E.2018-03-25doi:10.1101/288449Cold Spring Harbor Laboratory Press2018-03-25
https://biorxiv.org/cgi/content/short/128843v1?rss=1"
Street, K.Risso, D.Fletcher, R. B.Das, D.Ngai, J.Yosef, N.Purdom, E.Dudoit, S.2017-04-19doi:10.1101/128843Cold Spring Harbor Laboratory Press2017-04-19
https://biorxiv.org/cgi/content/short/235382v1?rss=1"
Cole, M. B.Risso, D.Wagner, A.DeTomaso, D.Ngai, J.Purdom, E.Dudoit, S.Yosef, N.2017-12-16doi:10.1101/235382Cold Spring Harbor Laboratory Press2017-12-16
https://biorxiv.org/cgi/content/short/300012v1?rss=1"
0, and that this bound is tight. Moving beyond the worst case, we explore a special set of instances where the reference graph grows monotonically between conditions, and show that this problem admits substantially improved approximation algorithms. We also developed an integer linear programming solver for the general problem and demonstrate its ability to reach optimality with instances from the human protein interaction network.nnConclusionOur results demonstrate that in contrast to most connectivity problems studied in computational biology, accounting for multiplicity of biological conditions adds considerable complexity, which we propose to address with a new solver. Importantly, our results extend to several network connectivity problems that are commonly used in computational biology, such as Prize-Collecting Steiner Tree, and provide insight into the theoretical guarantees for their applications in a multiple condition setting.nnAvailabilityOur solver for the general condition Steiner network problem is available at https://github.com/YosefLab/condition_connectivity_problems
]]>Wu, J.Khodaverdian, A.Weitz, B.Yosef, N.2018-04-13doi:10.1101/300012Cold Spring Harbor Laboratory Press2018-04-13
https://biorxiv.org/cgi/content/short/112599v1?rss=1"
Kohler, S.Wojcik, M.Xu, K.Dernburg, A. F.2017-02-28doi:10.1101/112599Cold Spring Harbor Laboratory Press2017-02-28
https://biorxiv.org/cgi/content/short/208462v1?rss=1"
Geller, R.Pechmann, S.Acevedo, A.Andino, R.Frydman, J.2017-10-24doi:10.1101/208462Cold Spring Harbor Laboratory Press2017-10-24
https://biorxiv.org/cgi/content/short/198721v1?rss=1"
Lopez Pineda, A.Rodriguez Moran, M. F.Alvarez Aguilar, C.Fuentes Valle, S. M.Acosta Rosales, R.Bustamante, C. D.2017-10-06doi:10.1101/198721Cold Spring Harbor Laboratory Press2017-10-06
https://biorxiv.org/cgi/content/short/191569v1?rss=1"
Fregel, R.Mendez, F. L.Bokbot, Y.Martin-Socas, D.Camalich-Massieu, M. D.Avila-Arcos, M. C.Underhill, P. A.Shapiro, B.Wojcik, G. L.Rasmussen, M.Soares, A. E. R.Kapp, J.Sockell, A.Rodriguez-Santos, F. J.Mikdad, A.Santana, J.Trujillo-Mederos, A.Bustamante, C. D.2017-09-21doi:10.1101/191569Cold Spring Harbor Laboratory Press2017-09-21
https://biorxiv.org/cgi/content/short/223438v1?rss=1"
Cornejo, O. E.Yee, M.-C.Dominguez, V.Andrews, M.Sockell, A.Strandberg, E.Livingstone, D.Stack, C.Romero, A.Umaharan, P.Royaert, S.Tawari, N. R.Pauline, N.Schnell, R.Wilbert, P.Mockaitis, K.Bustamante, C. D.Motamayor, J. C.2017-11-22doi:10.1101/223438Cold Spring Harbor Laboratory Press2017-11-22
https://biorxiv.org/cgi/content/short/320937v1?rss=1"
Massey, T. L.Santacruz, S. R.Hou, J. F.Pister, K. S.Carmena, J. M.Maharbiz, M. M.2018-05-13doi:10.1101/320937Cold Spring Harbor Laboratory Press2018-05-13
https://biorxiv.org/cgi/content/short/319673v1?rss=1"
Fragiadakis, G. K.Smits, S. A.Sonnenburg, E. D.Van Treuren, W.Reid, G.Knight, R.Manjurano, A.Changalucha, J.Dominguez-Bello, M. G.Leach, J.Sonnenburg, J. L.2018-05-15doi:10.1101/319673Cold Spring Harbor Laboratory Press2018-05-15
https://biorxiv.org/cgi/content/short/322511v1?rss=1"
Dougan, T.Quake, S. R.2018-05-15doi:10.1101/322511Cold Spring Harbor Laboratory Press2018-05-15
https://biorxiv.org/cgi/content/short/323105v1?rss=1"
10-fold dynamic range in response to two different small-molecule ligands. Since our system acts directly on each target-specific sgRNA, it enables new applications that require differential and opposing temporal control of multiple genes.
]]>Kundert, K.Lucas, J. E.Watters, K. E.Fellmann, C.Ng, A. H.Heineike, B. M.Fitzsimmons, C. M.Oakes, B. L.Savage, D. F.El-Samad, H.Doudna, J. A.Kortemme, T.2018-05-15doi:10.1101/323105Cold Spring Harbor Laboratory Press2018-05-15
https://biorxiv.org/cgi/content/short/323444v1?rss=1"
Mann, T. H.Shapiro, L.2018-05-16doi:10.1101/323444Cold Spring Harbor Laboratory Press2018-05-16
https://biorxiv.org/cgi/content/short/322545v1?rss=1"
Si, P.Yuan, E.Liba, O.Winetraub, Y.Yousefi, S.SoRelle, E.Yecies, D.Dutta, R.de la Zerda, A.2018-05-16doi:10.1101/322545Cold Spring Harbor Laboratory Press2018-05-16
https://biorxiv.org/cgi/content/short/324566v1?rss=1"
Olm, M. R.West, P. T.Brooks, B.Firek, B. A.Baker, R.Morowitz, M. J.Banfield, J. F.2018-05-17doi:10.1101/324566Cold Spring Harbor Laboratory Press2018-05-17
https://biorxiv.org/cgi/content/short/327866v1?rss=1"
Croote, D.Darmanis, S.Nadeau, K. C.Quake, S. R.2018-05-22doi:10.1101/327866Cold Spring Harbor Laboratory Press2018-05-22
https://biorxiv.org/cgi/content/short/329862v1?rss=1"
Mandel-Brehm, C.Retallack, H.Knudsen, G. M.Yamana, A.Hajj-Ali, R. A.Calabrese, L. H.Tihan, T.Sample, H. A.Zorn, K. C.Gorman, M. P.Madan Cohen, J.Sreih, A. G.Marcus, J. F.Josephson, S. A.Douglas, V. C.Gelfand, J. M.Wilson, M. R.DeRisi, J. L.2018-05-24doi:10.1101/329862Cold Spring Harbor Laboratory Press2018-05-24
https://biorxiv.org/cgi/content/short/328856v1?rss=1"
Matheus Carnevali, P. B.Schulz, F.Castelle, C. J.Kantor, R.Shih, P.Sharon, I.Santini, J.Olm, M.Amano, Y.Thomas, B. C.Anantharaman, K.Burstein, D.Becraft, E. D.Stepanauskas, R.Woyke, T.Banfield, J. F.2018-05-25doi:10.1101/328856Cold Spring Harbor Laboratory Press2018-05-25
https://biorxiv.org/cgi/content/short/332650v1?rss=1"
Vahey, M. D.Fletcher, D. A.2018-05-28doi:10.1101/332650Cold Spring Harbor Laboratory Press2018-05-28
https://biorxiv.org/cgi/content/short/342923v1?rss=1"
2,500 human genomes to identify optimized pairs of sgRNAs that can be used for human therapeutic editing in large populations in the future.
]]>Keough, K. C.Lyalina, S.Olvera, M. P.Whalen, S.Conklin, B. R.Pollard, K. S.2018-06-08doi:10.1101/342923Cold Spring Harbor Laboratory Press2018-06-08
https://biorxiv.org/cgi/content/short/381962v1?rss=1"
McKitterick, A.LeGault, K.Angermeyer, A.Alam, M.Seed, K.2018-08-01doi:10.1101/381962Cold Spring Harbor Laboratory Press2018-08-01
https://biorxiv.org/cgi/content/short/335083v1?rss=1"
Meheust, R.Burstein, D.Castelle, C. J.Banfield, J. F.2018-05-30doi:10.1101/335083Cold Spring Harbor Laboratory Press2018-05-30
https://biorxiv.org/cgi/content/short/341107v1?rss=1"
1500 tertiary assemblies with differing helical sequences and compared calculations to independent measurements from a high-throughput experimental platform. The blind predictions accounted for thermodynamic effects from changing helix sequence and length with unexpectedly tight accuracies (RMSD of 0.34 and 0.77 kcal/mol, respectively). These comparisons lead to a detailed picture of how RNA base pair steps fluctuate within complex assemblies and suggest a new route toward predicting RNA tertiary structure formation and energetics.
]]>Yesselman, J. D.Denny, S. K.Bisaria, N.Herschlag, D.Greenleaf, W. J.Das, R.2018-06-06doi:10.1101/341107Cold Spring Harbor Laboratory Press2018-06-06
https://biorxiv.org/cgi/content/short/331785v1?rss=1"
Laurie, M. T.White, C. V.Retallack, H.Wu, W.Moser, M. S.Sakanari, J.Ang, K.Wilson, C.Arkin, M. R.DeRisi, J. L.2018-06-06doi:10.1101/331785Cold Spring Harbor Laboratory Press2018-06-06
https://biorxiv.org/cgi/content/short/326272v1?rss=1"
Adorno, M.Nicolis di Robilant, B.Sikandar, S.Haro Acosta, V.Antony, J.Heller, C.Clarke, M.2018-06-08doi:10.1101/326272Cold Spring Harbor Laboratory Press2018-06-08
https://biorxiv.org/cgi/content/short/341149v1?rss=1"
Langelier, C.Kalantar, K. L.Moazed, F.Wilson, M. R.Crawford, E.Deiss, T.Belzer, A.Bolourchi, S.Caldera, S.Fung, M.Jauregui, A.Malcolm, K.Lyden, A.Khan, L.Vessel, K.Quan, J.Zinter, M.Chiu, C. Y.Chow, E. D.Wilson, J.Miller, S.Matthay, M. A.Pollard, K. S.Christenson, S.Calfee, C. S.DeRisi, J. L.2018-06-11doi:10.1101/341149Cold Spring Harbor Laboratory Press2018-06-11
https://biorxiv.org/cgi/content/short/349084v1?rss=1"
Le Gars, M.Seiler, C.Kay, A.Bayless, N.Starosvetsky, E.Moore, L.Shen-Orr, S.Aziz, N.Dekker, C.Khatri, P.Swan, G.Davis, M.Holmes, S.Blish, C.2018-06-16doi:10.1101/349084Cold Spring Harbor Laboratory Press2018-06-16
https://biorxiv.org/cgi/content/short/350538v1?rss=1"
Wang, W.Vilella, F.Moreno, I.Pan, W.Simon, C.Quake, S. R.2018-06-19doi:10.1101/350538Cold Spring Harbor Laboratory Press2018-06-19
https://biorxiv.org/cgi/content/short/351627v1?rss=1"
Beyene, A. G.Alizadehmojarad, A. A.Dorlhiac, G.Streets, A. M.Kral, P.Vukovic, L.Landry, M. P.2018-06-20doi:10.1101/351627Cold Spring Harbor Laboratory Press2018-06-20
https://biorxiv.org/cgi/content/short/356790v1?rss=1"
540 kb in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phage. We refer to these as Lak phage. CRISPR spacer targeting indicates that the Lak phage infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed, and up to 35 putative tRNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in relative abundance of phage sub-populations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phage are widespread in gut communities that contain Prevotella species, especially in individuals in the developing world, and conclude that megaphage, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
]]>Devoto, A. E.Santini, J. M.Olm, M. R.Anantharaman, K.Munk, P.Tung, J.Archie, E. A.Turnbaugh, P. J.Seed, K. D.Blekhman, R.Aarestrup, F. M.Thomas, B. C.Banfield, J. F.2018-06-27doi:10.1101/356790Cold Spring Harbor Laboratory Press2018-06-27
https://biorxiv.org/cgi/content/short/357970v1?rss=1"
Dao Duc, K.Batra, S. S.Bhattacharya, N.Cate, J. H. D.Song, Y. S.2018-06-28doi:10.1101/357970Cold Spring Harbor Laboratory Press2018-06-28
https://biorxiv.org/cgi/content/short/356543v1?rss=1"
Beyene, A. G.Delevich, K.Del Bonis ODonnell, J. T.Piekarski, D. J.Lin, W. C.Thomas, A. W.Yang, S. J.Kosillo, P.Yang, D.Wilbrecht, L.Landry, M. P.2018-07-03doi:10.1101/356543Cold Spring Harbor Laboratory Press2018-07-03
https://biorxiv.org/cgi/content/short/314377v1?rss=1"
200 versus 21 post-vaccination; 3,210 versus 286 transcripts with significant fold-change), but shared gene modules were induced in the same sequence. The abundance of 131 transcripts on days 8 and 9 post-vaccination was strongly correlated with NAb titers measured 6 weeks post-vaccination.nnConclusionsLAV dengue vaccination elicits early transcriptional responses that mirror those found in symptomatic natural infection and provide candidate early markers of protection against DENV infection.nnClinical Trial Registration Number: NCT00831012 (available at clinicaltrials.gov)nnSummary: Interferon- and cell cycle-associated gene transcript abundance levels in the peripheral blood of dengue vaccine recipients on days 8 and 9 post-vaccination were associated with dengue neutralizing antibody titers on day 42, and mirrored responses in primary dengue infection, suggesting the possibility of predicting protective immunity.
]]>Popper, S. J.Strouts, F. R.Lindow, J. C.Cheng, H. K.Montoya, M.Balmaseda, A.Durbin, A. P.Whitehead, S. S.Harris, E.Kirkpatrick, B. D.Relman, D. A.2018-05-06doi:10.1101/314377Cold Spring Harbor Laboratory Press2018-05-06
https://biorxiv.org/cgi/content/short/364265v1?rss=1"
Kim, T.Myers, F.Reber, C.Loury, P.Loumou, P.Webster, D.Echanique, C.Li, P.Davila, J.Maamari, R.Switz, N.Keenan, J.Woodward, M.Paulus, Y.Margolis, T.Fletcher, D.2018-07-07doi:10.1101/364265Cold Spring Harbor Laboratory Press2018-07-07
https://biorxiv.org/cgi/content/short/364166v1?rss=1"
Tarashansky, A. J.Xue, Y.Quake, S. R.Wang, B.2018-07-07doi:10.1101/364166Cold Spring Harbor Laboratory Press2018-07-07
https://biorxiv.org/cgi/content/short/366039v1?rss=1"
Lin, M. C.Hu, D.Marmor, M.Herfat, S. T.Bahney, C. S.Maharbiz, M. M.2018-07-10doi:10.1101/366039Cold Spring Harbor Laboratory Press2018-07-10
https://biorxiv.org/cgi/content/short/266700v1?rss=1"
Goltsman, D. S. A.Sun, C. L.Proctor, D. M.DiGiulio, D. B.Robaczewska, A.Thomas, B. C.Shaw, G. M.Stevenson, D. K.Holmes, S. P.Banfield, J. F.Relman, D. A.2018-02-18doi:10.1101/266700Cold Spring Harbor Laboratory Press2018-02-18
https://biorxiv.org/cgi/content/short/369322v1?rss=1"
Leung, K. K.Nguyen, A.Shi, T.Tang, L.Ni, X.Escoubet, L.MacBeth, K. J.DiMartino, J.Wells, J. A.2018-07-14doi:10.1101/369322Cold Spring Harbor Laboratory Press2018-07-14
https://biorxiv.org/cgi/content/short/369751v1?rss=1"
300 whole genome CRISPR screens, we report ~1 million pairs of correlated "co-functional" genes that provide finer-scale information about cell compartments, biological pathways, and protein complexes than traditional gene sets. Lastly, we employed a gene community detection approach to implicate core genes for cancer growth and compress signal from functionally related genes in the same community into a single score. This work establishes new algorithms for probing cancer cell networks and motivates the acquisition of further CRISPR screen data across diverse genotypes and cell types to further resolve the complexity of cell signaling processes.
]]>Boyle, E. A.Pritchard, J. K.Greenleaf, W. J.2018-07-16doi:10.1101/369751Cold Spring Harbor Laboratory Press2018-07-16
https://biorxiv.org/cgi/content/short/370452v1?rss=1"
Inoue, F.Kreimer, A.Ashuach, T.Ahituv, N.Yosef, N.2018-07-16doi:10.1101/370452Cold Spring Harbor Laboratory Press2018-07-16
https://biorxiv.org/cgi/content/short/357640v1?rss=1"
Bess, E. N.Bisanz, J. E.Spanogiannopoulos, P.Ang, Q. Y.Bustion, A.Kitamura, S.Alba, D. L.Wolan, D. W.Koliwad, S. K.Turnbaugh, P. J.2018-06-27doi:10.1101/357640Cold Spring Harbor Laboratory Press2018-06-27
https://biorxiv.org/cgi/content/short/370478v1?rss=1"
10 hours. We visualized algal migration within Aiptasia larvae and observed algal expulsion under an environmental stressor. To our knowledge, this device is the first to enable live imaging of cnidarian larvae and their algal symbionts and, in further implementation, could provide important insights into the cellular mechanisms of coral bleaching under different environmental stressors. The device is simple to use, requires minimal external equipment and no specialized training to operate, and can easily be adapted to study a variety of large, motile organisms.
]]>Van Treuren, W.Brower, K.Labanieh, L.Hunt, D.Lensch, S.Cruz, B.Cartwright, H. N.Tran, C.Fordyce, P. M.2018-07-19doi:10.1101/370478Cold Spring Harbor Laboratory Press2018-07-19
https://biorxiv.org/cgi/content/short/352484v1?rss=1"
McGinnis, C. S.Murrow, L. M.Gartner, Z. J.2018-06-20doi:10.1101/352484Cold Spring Harbor Laboratory Press2018-06-20
https://biorxiv.org/cgi/content/short/373878v1?rss=1"
Kim, T.Moon, S.Xu, K.2018-07-22doi:10.1101/373878Cold Spring Harbor Laboratory Press2018-07-22
https://biorxiv.org/cgi/content/short/375360v1?rss=1"
Kalantar, K.Moazed, F.Christenson, S.Wilson, J.Deiss, T.Belzer, A.Vessell, K.Jauregui, A.Boulourchi, S.DeRisi, J. L.Calfee, C.Langelier, C.2018-07-24doi:10.1101/375360Cold Spring Harbor Laboratory Press2018-07-24
https://biorxiv.org/cgi/content/short/378646v1?rss=1"
Zhang, X.Xu, C.Yosef, N.2018-07-28doi:10.1101/378646Cold Spring Harbor Laboratory Press2018-07-28
https://biorxiv.org/cgi/content/short/380006v1?rss=1"
Massey, T. L.Kuo, L. S.Fan, J. L.Maharbiz, M. M.2018-07-30doi:10.1101/380006Cold Spring Harbor Laboratory Press2018-07-30
https://biorxiv.org/cgi/content/short/384123v1?rss=1"
Amberg-Johnson, K.Yeh, E.2018-08-03doi:10.1101/384123Cold Spring Harbor Laboratory Press2018-08-03
https://biorxiv.org/cgi/content/short/384776v1?rss=1"
Shifrut, E.Carnevale, J.Tobin, V.Roth, T. L.Woo, J. M.Bui, C.Li, P. J.Diolaiti, M.Ashworth, A.Marson, A.2018-08-03doi:10.1101/384776Cold Spring Harbor Laboratory Press2018-08-03
https://biorxiv.org/cgi/content/short/385005v1?rss=1"
Ramesh, A.Nakielny, S.Hsu, J.Kyohere, M.Byaruhanga, O.de Bourcy, C.Egger, R.Dimitrov, B.Juan, Y.-F.Sheu, J.Wang, J.Kalantar, K.Langelier, C.Ruel, T.Mpimbaza, A.Wilson, M. R.Rosenthal, P. J.DeRisi, J. L.2018-08-04doi:10.1101/385005Cold Spring Harbor Laboratory Press2018-08-04
https://biorxiv.org/cgi/content/short/386532v1?rss=1"
Talledge, N.McCullough, J.Wenzel, D.Nguyen, H. C.Lalonde, M. S.Bajorek, M.Skalicky, J.Frost, A.Sundquist, W. I.2018-08-07doi:10.1101/386532Cold Spring Harbor Laboratory Press2018-08-07
https://biorxiv.org/cgi/content/short/387241v1?rss=1"
McGinnis, C. S.Patterson, D. M.Winkler, J.Hein, M. Y.Srivastava, V.Conrad, D. N.Murrow, L. M.Weissman, J. S.Werb, Z.Chow, E. D.Gartner, Z. J.2018-08-08doi:10.1101/387241Cold Spring Harbor Laboratory Press2018-08-08
https://biorxiv.org/cgi/content/short/388181v1?rss=1"
Zanini, F.Robinson, M.Croote, D.Sahoo, M. K.Sanz, A. M.Ortiz-Lasso, E.Albornoz, L. L.Suarez, F. R.Montoya, J. G.Pinsky, B. A.Quake, S.Einav, S.2018-08-09doi:10.1101/388181Cold Spring Harbor Laboratory Press2018-08-09
https://biorxiv.org/cgi/content/short/386292v1?rss=1"
Jaffe, A. L.Castelle, C. J.Dupont, C. L.Banfield, J. F.2018-08-07doi:10.1101/386292Cold Spring Harbor Laboratory Press2018-08-07
https://biorxiv.org/cgi/content/short/389999v1?rss=1"
Afik, S.Yosef, N.2018-08-10doi:10.1101/389999Cold Spring Harbor Laboratory Press2018-08-10
https://biorxiv.org/cgi/content/short/391417v1?rss=1"
Berghuis, B. A.Yu, F. B.Schulz, F.Blainey, P. C.Woyke, T.Quake, S.2018-08-14doi:10.1101/391417Cold Spring Harbor Laboratory Press2018-08-14
https://biorxiv.org/cgi/content/short/391433v1?rss=1"
Liu, R.Mignardi, M.Jones, R.Enge, M.Kim, S. K.Quake, S. R.Zou, J.2018-08-14doi:10.1101/391433Cold Spring Harbor Laboratory Press2018-08-14
https://biorxiv.org/cgi/content/short/404947v1?rss=1"
Leenay, R. T.Aghazadeh, A.Hiatt, J.Tse, D.Hulquist, J.Krogan, N.Wu, Z.Marson, A.May, A. P.Zou, J.2018-08-31doi:10.1101/404947Cold Spring Harbor Laboratory Press2018-08-31
https://biorxiv.org/cgi/content/short/400408v1?rss=1"
Strohman, M. J.Maeda, S.Hilger, D.Masureel, M.Du, Y.Kobilka, B. K.2018-08-25doi:10.1101/400408Cold Spring Harbor Laboratory Press2018-08-25
https://biorxiv.org/cgi/content/short/401489v1?rss=1"
Guo, C.-J.Allen, B.Hiam, K.Dodd, D.van Treuren, W.Higginbottom, S.Fischer, C.Sonnenburg, J.Spitzer, M.Fischbach, M.2018-08-27doi:10.1101/401489Cold Spring Harbor Laboratory Press2018-08-27
https://biorxiv.org/cgi/content/short/401570v1?rss=1"
Tang, Y.Meister, T. R.Walczak, M.Pulkoski-Gross, M.Hari, S. B.Sauer, R. T.Amberg-Johnson, K.Yeh, E.2018-08-27doi:10.1101/401570Cold Spring Harbor Laboratory Press2018-08-27
https://biorxiv.org/cgi/content/short/402560v1?rss=1"
Harink, B.Nguyen, H.Thorn, K.Fordyce, P.2018-08-28doi:10.1101/402560Cold Spring Harbor Laboratory Press2018-08-28
https://biorxiv.org/cgi/content/short/403527v1?rss=1"
Schafflick, D.Cole, M.Hartlehnert, M.Lautwein, T.Buscher, K.Wolbert, J.Meuth, S. G.Stettner, M.Kleinschnitz, C.Kuhlmann, T.Gross, C. C.Wiendl, H.Yosef, N.Meyer zu Horste, G.2018-08-29doi:10.1101/403527Cold Spring Harbor Laboratory Press2018-08-29
https://biorxiv.org/cgi/content/short/403055v1?rss=1"
DeTomaso, D.Jones, M.Subramaniam, M.Ashuach, T.Ye, C. J.Yosef, N.2018-08-29doi:10.1101/403055Cold Spring Harbor Laboratory Press2018-08-29
https://biorxiv.org/cgi/content/short/426338v1?rss=1"
Quan, J.Langelier, C.Kuchta, A.Batson, J.Teyssier, N.Lyden, A.Caldera, S.McGeever, A.Dimitrov, B.King, R.Wilheim, J.Murphy, M.Pesce Ares, L.Travisano, K. A.Sit, R.Amato, R.Mumbengegwi, D. R.Smith, J. L.Bennett, A.Gosling, R.Mourani, P. M.Calfee, C. S.Neff, N. F.Chow, E. D.Kim, P. S.Greenhouse, B.DeRisi, J. L.Crawford, E. D.2018-09-27doi:10.1101/426338Cold Spring Harbor Laboratory Press2018-09-27
https://biorxiv.org/cgi/content/short/167163v1?rss=1"
Cole, R. H.Tang, S.-Y.Siltanen, C. A.Shahi, P.Zhang, J. Q.Poust, S.Gartner, Z. J.Abate, A. R.2017-07-21doi:10.1101/167163Cold Spring Harbor Laboratory Press2017-07-21
https://biorxiv.org/cgi/content/short/416966v1?rss=1"
Liu, L.Dalal, C.Heineike, B.Abate, A.2018-09-15doi:10.1101/416966Cold Spring Harbor Laboratory Press2018-09-15
https://biorxiv.org/cgi/content/short/406595v1?rss=1"
Coyle, S. M.Flaum, E.Li, H.Krishnamurthy, D.Prakash, M.2018-09-03doi:10.1101/406595Cold Spring Harbor Laboratory Press2018-09-03
https://biorxiv.org/cgi/content/short/407650v1?rss=1"
Del Bonis-O Donnell, J. T.Pinals, R.Jeong, S.Thakrar, A.Wolfinger, R.Landry, M. P.2018-09-04doi:10.1101/407650Cold Spring Harbor Laboratory Press2018-09-04
https://biorxiv.org/cgi/content/short/412890v1?rss=1"
Sprockett, D.Fischer, N.Boneh, R. S.Turner, D.Kierkus, J.Sladek, M.Escher, J.Wine, E.Yerushalmi, B.Dias, J. A.Shaoul, R.Kori, M.Snapper, S.Holmes, S.Bousvaros, A.Levine, A.Relman, D. A.2018-09-10doi:10.1101/412890Cold Spring Harbor Laboratory Press2018-09-10
https://biorxiv.org/cgi/content/short/415513v1?rss=1"
Sheridan, C. M.Garcia, V. E.Ahyong, V.DeRisi, J. L.2018-09-12doi:10.1101/415513Cold Spring Harbor Laboratory Press2018-09-12
https://biorxiv.org/cgi/content/short/422618v1?rss=1"
Boucher, M. J.Yeh, E.2018-09-21doi:10.1101/422618Cold Spring Harbor Laboratory Press2018-09-21
https://biorxiv.org/cgi/content/short/425231v1?rss=1"
Bradley, P. H.Pollard, K. S.2018-09-24doi:10.1101/425231Cold Spring Harbor Laboratory Press2018-09-24
https://biorxiv.org/cgi/content/short/428573v1?rss=1"
Mathijssen, A.Culver, J.Bhamla, M. S.Prakash, M.2018-09-26doi:10.1101/428573Cold Spring Harbor Laboratory Press2018-09-26
https://biorxiv.org/cgi/content/short/430561v1?rss=1"
Isakova, A.Quake, S.2018-09-29doi:10.1101/430561Cold Spring Harbor Laboratory Press2018-09-29
https://biorxiv.org/cgi/content/short/430611v1?rss=1"
Murrow, L. M.Weber, R. J.Caruso, J.McGinnis, C. S.Borowsky, A. D.Desai, T. A.Thomson, M.Tlsty, T. D.Gartner, Z. J.2018-09-29doi:10.1101/430611Cold Spring Harbor Laboratory Press2018-09-29
https://biorxiv.org/cgi/content/short/440156v1?rss=1"
Mayday, M. Y.Khan, L. M.Chow, E. D.Zinter, M. S.DeRisi, J. L.2018-10-10doi:10.1101/440156Cold Spring Harbor Laboratory Press2018-10-10
https://biorxiv.org/cgi/content/short/440693v1?rss=1"
Erdmann-Pham, D. D.Dao Duc, K.Song, Y. S.2018-10-11doi:10.1101/440693Cold Spring Harbor Laboratory Press2018-10-11
https://biorxiv.org/cgi/content/short/450544v1?rss=1"
Lai, A.Altemose, N.White, J. A.Streets, A. M.2018-10-23doi:10.1101/450544Cold Spring Harbor Laboratory Press2018-10-23
https://biorxiv.org/cgi/content/short/454041v1?rss=1"
Feng, S.Varshney, A.Coto Villa, D.Modavi, C.Kohler, J.Farah, F.Ali, N.Mueller, J. D.VanHoven, M.Huang, B.2018-10-25doi:10.1101/454041Cold Spring Harbor Laboratory Press2018-10-25
https://biorxiv.org/cgi/content/short/454033v1?rss=1"
Zitnik, M.Sosic, R.Feldman, M. W.Leskovec, J.2018-10-26doi:10.1101/454033Cold Spring Harbor Laboratory Press2018-10-26
https://biorxiv.org/cgi/content/short/454470v1?rss=1"
Fazal, F. M.Han, S.Kaewsapsak, P.Parker, K. R.Xu, J.Boettiger, A. N.Chang, H. Y.Ting, A. Y.2018-10-26doi:10.1101/454470Cold Spring Harbor Laboratory Press2018-10-26
https://biorxiv.org/cgi/content/short/452888v1?rss=1"
Han, Y.Martell, J.Branon, T.Boassa, D.Shechner, D.Ellisman, M.Ting, A.2018-10-25doi:10.1101/452888Cold Spring Harbor Laboratory Press2018-10-25
https://biorxiv.org/cgi/content/short/460063v1?rss=1"
Gordon, C. K. L.Eisenstein, M.Soh, H. T.2018-11-01doi:10.1101/460063Cold Spring Harbor Laboratory Press2018-11-01
https://biorxiv.org/cgi/content/short/459974v1?rss=1"
Shi, H.Quint, D.Gopinathan, A.Huang, K. C.2018-11-01doi:10.1101/459974Cold Spring Harbor Laboratory Press2018-11-01
https://biorxiv.org/cgi/content/short/458869v1?rss=1"
Wang, Y.Yang, B.Feng, S.Pessino, V.Huang, B.2018-11-01doi:10.1101/458869Cold Spring Harbor Laboratory Press2018-11-01
https://biorxiv.org/cgi/content/short/461913v1?rss=1"
Shi, X.Garcia, G.Wang, Y.Reiter, J. F.Huang, B.2018-11-05doi:10.1101/461913Cold Spring Harbor Laboratory Press2018-11-05
https://biorxiv.org/cgi/content/short/154831v1?rss=1"
Duan, R.Kim, J. H.Shilagardi, K.Schiffhauer, E.Son, S.Lee, D.Li, S.Thomas, C.Luo, T.Fletcher, D. A.Robinson, D. N.Chen, E. H.2017-06-23doi:10.1101/154831Cold Spring Harbor Laboratory Press2017-06-23
https://biorxiv.org/cgi/content/short/164020v1?rss=1"
Hughes, A. J.Miyazaki, H.Coyle, M. C.Zhang, J.Laurie, M. T.Chu, D.Vavrusova, Z.Schneider, R. A.Klein, O. D.Gartner, Z. J.2017-07-15doi:10.1101/164020Cold Spring Harbor Laboratory Press2017-07-15
https://biorxiv.org/cgi/content/short/191197v1?rss=1"
Rodriguez-Barraquer, I.Arinaitwe, E.Jagannathan, P.Kamya, M.Rosenthal, P.Rek, J.Dorsey, G.Nankabirwa, J.Staedke, S. G.Kilama, M.Drakeley, C.Ssewanyan, I.Smith, D. L.Greenhouse, B.2017-09-20doi:10.1101/191197Cold Spring Harbor Laboratory Press2017-09-20
https://biorxiv.org/cgi/content/short/342808v1?rss=1"
Layton, C. J.McMahon, P. L.Greenleaf, W. J.2018-06-08doi:10.1101/342808Cold Spring Harbor Laboratory Press2018-06-08
https://biorxiv.org/cgi/content/short/314112v1?rss=1"
Moskowitz, D. M.Greenleaf, W. J.2018-05-04doi:10.1101/314112Cold Spring Harbor Laboratory Press2018-05-04
https://biorxiv.org/cgi/content/short/357731v1?rss=1"
Rosas, E.Modzelewski, A. J.He, L.Herr, A. E.2018-06-28doi:10.1101/357731Cold Spring Harbor Laboratory Press2018-06-28
https://biorxiv.org/cgi/content/short/461293v1?rss=1"
Takagi, J.Singh-Babak, S. D.Lohse, M. B.Dalal, C. K.Johnson, A. D.2018-11-07doi:10.1101/461293Cold Spring Harbor Laboratory Press2018-11-07
https://biorxiv.org/cgi/content/short/301234v1?rss=1"
Sorrells, T. R.Johnson, A. N.Howard, C. J.Britton, C. S.Fowler, K. R.Feigerle, J. T.Weil, P. A.Johnson, A. D.2018-04-14doi:10.1101/301234Cold Spring Harbor Laboratory Press2018-04-14
https://biorxiv.org/cgi/content/short/409672v1?rss=1"
Alexander, J. M.Guan, J.Huang, B.Lomvardas, S.Weiner, O. D.2018-09-05doi:10.1101/409672Cold Spring Harbor Laboratory Press2018-09-05
https://biorxiv.org/cgi/content/short/241083v1?rss=1"
Sepulveda, G.Antkowiak, M.Brust-Mascher, I.Mahe, K.Ou, T.Castro, N.Christensen, L. N.Cheung, L.Yoon, D.Huang, B.Jao, L.-E.2017-12-30doi:10.1101/241083Cold Spring Harbor Laboratory Press2017-12-30
https://biorxiv.org/cgi/content/short/101444v1?rss=1"
Guan, J.Liu, H.Shi, X.Feng, S.Huang, B.2017-01-18doi:10.1101/101444Cold Spring Harbor Laboratory Press2017-01-18
https://biorxiv.org/cgi/content/short/408757v1?rss=1"
Gomez-Ospina, N.Scharenberg, S. G.Mostrel, N.Bak, R. O.Mantri, S.Quadros, R. M.Gurumurthy, C. B.Lee, C.Bao, G.Aurelian, L.Porteus, M.2018-09-04doi:10.1101/408757Cold Spring Harbor Laboratory Press2018-09-04
https://biorxiv.org/cgi/content/short/397463v1?rss=1"
Pavel-Dinu, M.Wiebking, V.Dejene, B. T.Srifa, W.Mantri, S.Nicolas, C.Lee, C.Bao, G.Kildebeck, E. J.Punjya, N.Sindhu, C.Inlay, M. A.Saxena, N.DeRavin, S. S.Malech, H.Roncarolo, M. G.Weinberg, K. I.Porteus, M.2018-08-22doi:10.1101/397463Cold Spring Harbor Laboratory Press2018-08-22
https://biorxiv.org/cgi/content/short/460055v1?rss=1"
Aidukas, T.Eckert, R.Harvey, A. R.Waller, L.Konda, P. C.2018-11-02doi:10.1101/460055Cold Spring Harbor Laboratory Press2018-11-02
https://biorxiv.org/cgi/content/short/543231v1?rss=1"
Mahdessian, D.Sullivan, D.Danielsson, F.Arif, M.Zhang, C.Akesson, L.Gnann, C.Schutten, R.Thul, P.Carja, O.Ayoglu, B.Mardinoglu, A.Ponten, F.Uhen, M.Lindskog, C.Lundberg, E.2019-02-07doi:10.1101/543231Cold Spring Harbor Laboratory Press2019-02-07
https://biorxiv.org/cgi/content/short/607416v1?rss=1"
Pan, L.Zhang, P.Hu, F.Yan, R.He, M.Li, W.Xu, J.Xu, K.2019-04-13doi:10.1101/607416Cold Spring Harbor Laboratory Press2019-04-13
https://biorxiv.org/cgi/content/short/604561v1?rss=1"
Roth, T. L.Li, P. J.Nies, J.Yu, R.Nguyen, M. L. T.Lee, Y.Apathy, R.Truong, A.Hiatt, J.Wu, D.Nguyen, D. N.Goodman, D.Bluestone, J. A.Roybal, K.Shifrut, E.Marson, A.2019-04-12doi:10.1101/604561Cold Spring Harbor Laboratory Press2019-04-12
https://biorxiv.org/cgi/content/short/466524v1?rss=1"
Carja, O.Creanza, N.2018-11-09doi:10.1101/466524Cold Spring Harbor Laboratory Press2018-11-09
https://biorxiv.org/cgi/content/short/481093v1?rss=1"
Kowarsky, M.De Vlaminck, I.Okamoto, J.Neff, N. F.LeBreton, M.Nwobegabay, J.Tamoufe, U.Ledoux, J. D.Tafon, B.Kiyang, J.Saylors, K.Wolfe, N. D.Quake, S. R.2018-11-29doi:10.1101/481093Cold Spring Harbor Laboratory Press2018-11-29
https://biorxiv.org/cgi/content/short/504654v1?rss=1"
Anand, A. A.Kenner, L. R.Nguyen, H. C.Myasnikov, A. G.Klose, C. J.McGeever, L. A.Tsai, J. C.Miller-Vedam, L. E.Walter, P.Frost, A.2018-12-22doi:10.1101/504654Cold Spring Harbor Laboratory Press2018-12-22
https://biorxiv.org/cgi/content/short/506188v1?rss=1"
Fonseca, J. P.Bonny, A. R.Kumar, G. R.Ng, A. H.Town, J.Wu, Q. C.Aslankoohi, E.Chen, S. Y.Harrigan, P.Osimiri, L. C.Kistler, A. L.El-Samad, H.2018-12-26doi:10.1101/506188Cold Spring Harbor Laboratory Press2018-12-26
https://biorxiv.org/cgi/content/short/527887v1?rss=1"
Ashuach, T.Fischer, D. S.Kreimer, A.Ahituv, N.Theis, F. J.Yosef, N.2019-01-23doi:10.1101/527887Cold Spring Harbor Laboratory Press2019-01-23
https://biorxiv.org/cgi/content/short/530204v1?rss=1"
Li, Z.-R.Li, J.Cai, W.Lai, J.McKinnie, S.Zhang, W.-P.Moore, B.Zhang, W.Qian, P.-Y.2019-01-24doi:10.1101/530204Cold Spring Harbor Laboratory Press2019-01-24
https://biorxiv.org/cgi/content/short/532168v1?rss=1"
Spence, J. P.Song, Y. S.2019-01-28doi:10.1101/532168Cold Spring Harbor Laboratory Press2019-01-28
https://biorxiv.org/cgi/content/short/532895v1?rss=1"
Xu, C.Lopez, R.Mehlman, E.Regier, J.Jordan, M. I.Yosef, N.2019-01-29doi:10.1101/532895Cold Spring Harbor Laboratory Press2019-01-29
https://biorxiv.org/cgi/content/short/534586v1?rss=1"
Romanov, V.McCullough, J.Sharma, A.Vershinin, M.Gale, B. K.Frost, A.2019-01-29doi:10.1101/534586Cold Spring Harbor Laboratory Press2019-01-29
https://biorxiv.org/cgi/content/short/538132v1?rss=1"
Aranda-Diaz, A.Obadia, B.Thomsen, T.Hallberg, Z. F.Guvener, Z. T.Huang, K. C.Ludington, W. B.2019-02-01doi:10.1101/538132Cold Spring Harbor Laboratory Press2019-02-01
https://biorxiv.org/cgi/content/short/538397v1?rss=1"
Comerci, C. J.Herrmann, J.Yoon, J.Jabbarpour, F.Zhou, X.Nomellini, J. F.Smit, J.Shapiro, L.Wakatsuki, S.Moerner, W. E.2019-02-01doi:10.1101/538397Cold Spring Harbor Laboratory Press2019-02-01
https://biorxiv.org/cgi/content/short/538678v1?rss=1"
Zhang, H.Demirer, G. S.Zhang, H.Ye, T.Goh, N. S.Aditham, A. J.Cunningham, F. J.Fan, C.Landry, M.2019-02-02doi:10.1101/538678Cold Spring Harbor Laboratory Press2019-02-02
https://biorxiv.org/cgi/content/short/541052v1?rss=1"
Proctor, D.Shelef, K.Gonzalez, A.Long, C.Dethlefsen, L.Burns, A.Loomer, P.Armitage, G.Ryder, M.Millman, M.Knight, R.Holmes, S.Relman, D. A.2019-02-08doi:10.1101/541052Cold Spring Harbor Laboratory Press2019-02-08
https://biorxiv.org/cgi/content/short/541797v1?rss=1"
Bisanz, J. E.Upadhyay, V.Turnbaugh, J. A.Ly, K.Turnbaugh, P. J.2019-02-05doi:10.1101/541797Cold Spring Harbor Laboratory Press2019-02-05
https://biorxiv.org/cgi/content/short/548255v1?rss=1"
Chen, S. Y.Osimiri, L. C.Chevalier, M. W.Bugaj, L. J.Ng, A. H.Stewart-Ornstein, J.Neves, L. T.El-Samad, H.2019-02-13doi:10.1101/548255Cold Spring Harbor Laboratory Press2019-02-13
https://biorxiv.org/cgi/content/short/551978v1?rss=1"
Lind, A.Lai, Y. Y. Y.Mostovoy, Y.Holloway, A. K.Iannucci, A.Mak, A. C.Fondi, M.Orlandini, V.Eckalbar, W. L.Milan, M.Rovatsos, M.Kichigin, I. G.Makunin, A. I.Trifonov, V.Schijlen, E.Kratochvil, L.Fani, R.Jessop, T. S.Patarnello, T.Hicks, J. W.Ryder, O. A.Mendelson, J. R.Ciofi, C.Kwok, P.-Y. A.Pollard, K. S.Bruneau, B.2019-02-15doi:10.1101/551978Cold Spring Harbor Laboratory Press2019-02-15
https://biorxiv.org/cgi/content/short/552224v1?rss=1"
Wilson, B. D.Eisenstein, M.Soh, H. T.2019-02-16doi:10.1101/552224Cold Spring Harbor Laboratory Press2019-02-16
https://biorxiv.org/cgi/content/short/555110v1?rss=1"
Camunas-Soler, J.Dai, X.Hang, Y.Bautista, A.Lyon, J.Suzuki, K.Kim, S. K.Quake, S. R.MacDonald, P. E.2019-02-20doi:10.1101/555110Cold Spring Harbor Laboratory Press2019-02-20
https://biorxiv.org/cgi/content/short/555169v1?rss=1"
Schmidt, S. T.Yu, F. B.Blainey, P. C.May, A. P.Quake, S. R.2019-02-20doi:10.1101/555169Cold Spring Harbor Laboratory Press2019-02-20
https://biorxiv.org/cgi/content/short/557769v1?rss=1"
Waltari, E.McGeever, A.Kim, P. S.McCutcheon, K. M.2019-02-22doi:10.1101/557769Cold Spring Harbor Laboratory Press2019-02-22
https://biorxiv.org/cgi/content/short/558676v1?rss=1"
Olm, M. R.Bhattacharya, N.Crits-Christoph, A.Firek, B. A.Baker, R.Song, Y. S.Morowitz, M. J.Banfield, J. F.2019-02-22doi:10.1101/558676Cold Spring Harbor Laboratory Press2019-02-22
https://biorxiv.org/cgi/content/short/559484v1?rss=1"
Xiang, L.Chen, K.Yan, R.Li, W.Xu, K.2019-02-25doi:10.1101/559484Cold Spring Harbor Laboratory Press2019-02-25
https://biorxiv.org/cgi/content/short/564427v1?rss=1"
Demirer, G. S.Zhang, H.Goh, N. S.Chang, R.Landry, M. P.2019-03-01doi:10.1101/564427Cold Spring Harbor Laboratory Press2019-03-01
https://biorxiv.org/cgi/content/short/565259v1?rss=1"
Thulin, N. K.Brewer, R. C.Sherwood, R.Bournazos, S.Edwards, K. G.Ramadoss, N. S.Taubenberger, J. K.Memoli, M.Jagannathan, P.Zhang, S.Libraty, D. H.Wang, T. T.2019-03-06doi:10.1101/565259Cold Spring Harbor Laboratory Press2019-03-06
https://biorxiv.org/cgi/content/short/571588v1?rss=1"
Becker, W. R.Jarmoskaite, I.Kappel, K.Vaidyanathan, P. P.Denny, S. K.Das, R.Greenleaf, W. J.Herschlag, D.2019-03-08doi:10.1101/571588Cold Spring Harbor Laboratory Press2019-03-08
https://biorxiv.org/cgi/content/short/572362v1?rss=1"
Al-Shayeb, B.Sachdeva, R.Chen, L.-X.Ward, F.Munk, P.Devoto, A.Castelle, C. J.Olm, M. R.Bouma-Gregson, K.Amano, Y.He, C.Meheust, R.Brooks, B.Thomas, A.Lavy, A.Matheus-Carnevali, P.Sun, C.Goltsman, D.Borton, M. A.Nelson, T. C.Kantor, R.Jaffe, A. L.Keren, R.Farag, I. F.Lei, S.Finstad, K.Amundson, R.Anantharaman, K.Zhou, J.Probst, A. J.Power, M. E.Tringe, S. G.Li, W.-J.Wrighton, K.Harrison, S.Morowitz, M.Relman, D. A.Doudna, J. A.Lehours, A.-C.Warren, L.Cate, J. H.Santini, J. M.Banfield, J. F.2019-03-11doi:10.1101/572362Cold Spring Harbor Laboratory Press2019-03-11
https://biorxiv.org/cgi/content/short/572602v1?rss=1"
Ngo, A. M.Shurtleff, M. J.Popova, K. D.Kulsuptrakul, J.Weissman, J. S.Puschnik, A. S.2019-03-09doi:10.1101/572602Cold Spring Harbor Laboratory Press2019-03-09
https://biorxiv.org/cgi/content/short/577460v1?rss=1"
von Appen, A.Lajoie, D.Johnson, I. E.Trnka, M.Pick, S. M.Burlingame, A. L.Ullman, K. S.Frost, A.2019-03-14doi:10.1101/577460Cold Spring Harbor Laboratory Press2019-03-14
https://biorxiv.org/cgi/content/short/577924v1?rss=1"
Burke, J. E.Longhurst, A. D.Natarajan, P.Rao, B.Liu, S. J.Sales-Lee, J.Mortensen, Y.Moresco, J.Diedrich, J. K.Yates, J. R.Madhani, H. D.2019-03-14doi:10.1101/577924Cold Spring Harbor Laboratory Press2019-03-14
https://biorxiv.org/cgi/content/short/578542v1?rss=1"
Hanson, T. L.Diaz-Botia, C. A.Kharazia, V.Maharbiz, M. M.Sabes, P. N.2019-03-14doi:10.1101/578542Cold Spring Harbor Laboratory Press2019-03-14
https://biorxiv.org/cgi/content/short/579532v1?rss=1"
99% identical to each other and to a Bangladeshi strain only previously recognized to cause systemic illness in 2017. CHIKV qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital (n=472) revealed 17 additional CHIKV meningitis cases. Orthogonal molecular confirmation of each mNGS-identified infection, case-based clinical data, and follow-up of patients substantiated the key findings.nnUsing mNGS, we obtained a microbiological diagnosis for 40% of idiopathic meningitis cases and identified a previous unappreciated pediatric CHIKV meningitis outbreak. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis and facilitate informed policy decisions.
]]>Saha, S.Ramesh, A.Kalantar, K. L.Malaker, R.Hasanuzzaman, M.Khan, L. M.Mayday, M. Y.Sajib, M. S. I.Li, L. M.Langelier, C.Rahman, H.Crawford, E. D.Tato, C. M.Islam, M.Juan, Y.-F.Bourcy, C. d.Dimitrov, B.Wang, J.Tang, J.Sheu, J.Egger, R.Carvalho, T. R. D.Wilson, M. R.Saha, S.DeRisi, J.2019-03-15doi:10.1101/579532Cold Spring Harbor Laboratory Press2019-03-15
https://biorxiv.org/cgi/content/short/580233v1?rss=1"
Gumuscu, B.Herr, A.2019-03-16doi:10.1101/580233Cold Spring Harbor Laboratory Press2019-03-16
https://biorxiv.org/cgi/content/short/580845v1?rss=1"
Kim, C. K.Cho, K. F.Kim, M. W.Ting, A. Y.2019-03-18doi:10.1101/580845Cold Spring Harbor Laboratory Press2019-03-18
https://biorxiv.org/cgi/content/short/581447v1?rss=1"
Fay, A.Czudnochowski, N.Rock, J.Johnson, J.Krogan, N.Rosenberg, O.Glickman, M.2019-03-27doi:10.1101/581447Cold Spring Harbor Laboratory Press2019-03-27
https://biorxiv.org/cgi/content/short/583153v1?rss=1"
Pierson, E.Althoff, T.Thomas, D.Hillard, P.Leskovec, J.2019-03-20doi:10.1101/583153Cold Spring Harbor Laboratory Press2019-03-20
https://biorxiv.org/cgi/content/short/583252v1?rss=1"
Seidel, J. A.Miao, Y.Porterfield, W.Cai, W.Zhu, X.Kim, S.-J.Hu, F.Bhattarai-Kline, S.Min, W.Zhang, W.2019-03-21doi:10.1101/583252Cold Spring Harbor Laboratory Press2019-03-21
https://biorxiv.org/cgi/content/short/587485v1?rss=1"
Pinkard, H.Phillips, Z.Babakhani, A.Fletcher, D. A.Waller, L.2019-03-23doi:10.1101/587485Cold Spring Harbor Laboratory Press2019-03-23
https://biorxiv.org/cgi/content/short/591396v1?rss=1"
Stanley, G.Gokce, O.Malenka, R. C.Sudhof, T. C.Quake, S. R.2019-03-27doi:10.1101/591396Cold Spring Harbor Laboratory Press2019-03-27
https://biorxiv.org/cgi/content/short/591719v1?rss=1"
Nguyen, D. N.Roth, T. L.Li, J.Chen, P. A.Mamedov, M. M.Vo, L. T.Tobin, V.Apathy, R.Goodman, D.Shifrut, E.Bluestone, J. A.Puck, J. M.Szoka, F. C.Marson, A.2019-03-28doi:10.1101/591719Cold Spring Harbor Laboratory Press2019-03-28
https://biorxiv.org/cgi/content/short/594895v1?rss=1"
Li, H.Li, T.Horns, F.Li, J.Xie, Q.Xu, C.Wu, B.Kebschull, J.Vacek, D.Xie, A.Luginbuhl, D.Quake, S.Luo, L.2019-03-31doi:10.1101/594895Cold Spring Harbor Laboratory Press2019-03-31
https://biorxiv.org/cgi/content/short/595074v1?rss=1"
Sieber, C. M. K.Paul, B. G.Castelle, C. J.Hu, P.Tringe, S. G.Valentine, D. L.Andersen, G. L.Banfield, J. F.2019-04-01doi:10.1101/595074Cold Spring Harbor Laboratory Press2019-04-01
https://biorxiv.org/cgi/content/short/597468v1?rss=1"
Starr, E. P.Nuccio, E. E.Pett-Ridge, J.Banfield, J. F.Firestone, M. K.2019-04-04doi:10.1101/597468Cold Spring Harbor Laboratory Press2019-04-04
https://biorxiv.org/cgi/content/short/598359v1?rss=1"
Harris, A. R.Belardi, B.Jreij, P.Wei, K.Bausch, A.Fletcher, D. A.2019-04-04doi:10.1101/598359Cold Spring Harbor Laboratory Press2019-04-04
https://biorxiv.org/cgi/content/short/599795v1?rss=1"
Sanderlin, A.Vondrak, C.Scricco, A.Fedrigo, I.Ahyong, V.Lamason, R.2019-04-04doi:10.1101/599795Cold Spring Harbor Laboratory Press2019-04-04
https://biorxiv.org/cgi/content/short/600064v1?rss=1"
Xie, Q.Wu, B.Li, J.Li, H.Luginbuhl, D.Xu, C.Wang, X.Luo, L.2019-04-04doi:10.1101/600064Cold Spring Harbor Laboratory Press2019-04-04
https://biorxiv.org/cgi/content/short/600155v1?rss=1"
Nayak, R. R.Alexander, M.Stapleton-Grey, K.Ubeda, C.Scher, J. U.Turnbaugh, P. J.2019-04-05doi:10.1101/600155Cold Spring Harbor Laboratory Press2019-04-05
https://biorxiv.org/cgi/content/short/601559v1?rss=1"
Woodworth, M. H.Dynerman, D.Crawford, E. D.Li, L. M.Doernberg, S. B.Ramirez, L.Serpa, P. H.Nichols, A.Lyden, A.Tato, C. M.Miller, S.Derisi, J. L.Langelier, C.2019-04-12doi:10.1101/601559Cold Spring Harbor Laboratory Press2019-04-12
https://biorxiv.org/cgi/content/short/610246v1?rss=1"
Krishnamurthy, D.Li, H.Benoit du Rey, F.Cambournac, P.Larson, A.Prakash, M.2019-04-15doi:10.1101/610246Cold Spring Harbor Laboratory Press2019-04-15
https://biorxiv.org/cgi/content/short/631101v1?rss=1"
Guo, S.-M.Krishnan, A. P.Folkesson, J.Ivanov, I.Chhun, B.Cho, N.Leonetti, M.Mehta, S. B.2019-05-09doi:10.1101/631101Cold Spring Harbor Laboratory Press2019-05-09
https://biorxiv.org/cgi/content/short/635185v1?rss=1"
Hoarfrost, A.Nayfach, S.Ladau, J.Yooseph, S.Arnosti, C.Dupont, C. L.Pollard, K.2019-05-10doi:10.1101/635185Cold Spring Harbor Laboratory Press2019-05-10
https://biorxiv.org/cgi/content/short/626713v1?rss=1"
Rudina, S. S.Smolke, C. D.2019-05-03doi:10.1101/626713Cold Spring Harbor Laboratory Press2019-05-03
https://biorxiv.org/cgi/content/short/626572v1?rss=1"
Gordon, C. K. L.Wu, D. T.Feagin, T. A.Pusuluri, A.Csordas, A. T.Eisenstein, M.Hawker, C. J.Niu, J.Soh, H. T.2019-05-03doi:10.1101/626572Cold Spring Harbor Laboratory Press2019-05-03
https://biorxiv.org/cgi/content/short/618637v1?rss=1"
Rosenberg, O.Qu, J.-X.Prasad, N. K.Peters, J.Looney, M.Yu, M.Lyden, A.Chen, S.Crawford, E.Silvis, M.2019-04-25doi:10.1101/618637Cold Spring Harbor Laboratory Press2019-04-25
https://biorxiv.org/cgi/content/short/617258v1?rss=1"
Chen, M. B.Yousef, H.Yang, A. C.Lee, D.Lehallier, B.Schaum, N.Quake, S. R.Wyss-Coray, T.2019-04-24doi:10.1101/617258Cold Spring Harbor Laboratory Press2019-04-24
https://biorxiv.org/cgi/content/short/339630v1?rss=1"
Fries, J. A.Varma, P.Chen, V.Xiao, K.Tejeda, H.Priyanka, S.Dunnmon, J.Chubb, H.Maskatia, S.Fiterau, M.Delp, S.Ashley, E.Re, C.Priest, J.2018-06-05doi:10.1101/339630Cold Spring Harbor Laboratory Press2018-06-05
https://biorxiv.org/cgi/content/short/637785v1?rss=1"
Chen, J. J.Nathaniel, D. L.Raghavan, P.Nelson, M.Tian, R.Tse, E.Hong, J. Y.See, S. K.Mok, S.-A.Southworth, D. R.Grinberg, L. T.Gestwicki, J. E.Leonetti, M. D.Kampmann, M.2019-05-15doi:10.1101/637785Cold Spring Harbor Laboratory Press2019-05-15
https://biorxiv.org/cgi/content/short/639039v1?rss=1"
Barth, Z.Silvas, T.Angermeyer, A.Seed, K.2019-05-17doi:10.1101/639039Cold Spring Harbor Laboratory Press2019-05-17
https://biorxiv.org/cgi/content/short/640169v1?rss=1"
Rumachik, N. G.Malaker, S. A.Poweleit, N.Maynard, L. H.Adams, C. M.Leib, R. D.Cirolia, G.Thomas, D.Stamnes, S.Holt, K.Sinn, P.May, A. P.Paulk, N. K.2019-05-17doi:10.1101/640169Cold Spring Harbor Laboratory Press2019-05-17
https://biorxiv.org/cgi/content/short/648485v1?rss=1"
Glasgow, A. A.Huang, Y.-M.Mandell, D. J.Thompson, M.Ritterson, R.Loshbaugh, A. L.Pellegrino, J.Krivacic, C.Pache, R. A.Barlow, K. A.Ollikainen, N.Jeon, D.Kelly, M. J. S.Fraser, J. S.Kortemme, T.2019-05-24doi:10.1101/648485Cold Spring Harbor Laboratory Press2019-05-24
https://biorxiv.org/cgi/content/short/647511v1?rss=1"
Olm, M. R.Crits-Christoph, A.Diamond, S.Lavy, A.Matheus Carnevali, P. B.Banfield, J. F.2019-05-24doi:10.1101/647511Cold Spring Harbor Laboratory Press2019-05-24
https://biorxiv.org/cgi/content/short/650895v1?rss=1"
Wilkinson, M.Darmanis, S.Pisco, A. O.Huber, G.2019-05-27doi:10.1101/650895Cold Spring Harbor Laboratory Press2019-05-27
https://biorxiv.org/cgi/content/short/642868v1?rss=1"
Moon, S.Li, W.Xu, K.2019-05-27doi:10.1101/642868Cold Spring Harbor Laboratory Press2019-05-27
https://biorxiv.org/cgi/content/short/656744v1?rss=1"
Si, P.Shevidi, S.Yuan, E.Yuan, K.Lautman, Z.Jeffrey, S. S.Sledge, G. W.de la Zerda, A.2019-05-31doi:10.1101/656744Cold Spring Harbor Laboratory Press2019-05-31
https://biorxiv.org/cgi/content/short/655324v1?rss=1"
Longwell, S. A.Fordyce, P. M.2019-06-02doi:10.1101/655324Cold Spring Harbor Laboratory Press2019-06-02
https://biorxiv.org/cgi/content/short/656165v1?rss=1"
5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
]]>Xue, Y.Theisen, T. C.Ferrel, A.Rastogi, S.Quake, S. R.Boothroyd, J. C.2019-06-03doi:10.1101/656165Cold Spring Harbor Laboratory Press2019-06-03
https://biorxiv.org/cgi/content/short/660837v1?rss=1"
Hilger, D.Krishna Kumar, K.Hu, H.Pedersen, M. F.Giehm, L.Mathiesen, J. M.Skiniotis, G.Kobilka, B. K.2019-06-05doi:10.1101/660837Cold Spring Harbor Laboratory Press2019-06-05
https://biorxiv.org/cgi/content/short/662254v1?rss=1"
Schaum, N.Lehallier, B.Hahn, O.Hosseinzadeh, S.Lee, S. E.Sit, R.Lee, D. P.Losada, P. M.Zardeneta, M. E.Palovics, R.Fehlmann, T.Webber, J.McGeever, A.Zhang, H.Berdnik, D.Tan, W.Zee, A.Tan, M.The Tabula Muris Consortium,Pisco, A.Karkanias, J.Neff, N. F.Keller, A.Darmanis, S.Quake, S. R.Wyss-Coray, T.2019-06-07doi:10.1101/662254Cold Spring Harbor Laboratory Press2019-06-07
https://biorxiv.org/cgi/content/short/653337v1?rss=1"
Crawford, E. D.Kamm, J.Miller, S.Li, L.Caldera, S.Lyden, A. D.Yokoe, D.Nichols, A.Ramirez-Avila, L.Tran, N. K.Barnhard, S.Conner, P. M.Nambiar, A.Zinter, M. S.Moayeri, M.Hayakawa Serpa, P.Prince, B. C.Quan, J.Sit, R.Tan, M.Phelps, M.DeRisi, J. S.Tato, C. M.Langelier, C.2019-05-30doi:10.1101/653337Cold Spring Harbor Laboratory Press2019-05-30
https://biorxiv.org/cgi/content/short/661728v1?rss=1"
The Tabula Muris Consortium,Pisco, A. O.Schaum, N.McGeever, A.Karkanias, J.Neff, N. F.Darmanis, S.Wyss-Coray, T.Quake, S. R.2019-06-08doi:10.1101/661728Cold Spring Harbor Laboratory Press2019-06-08
https://biorxiv.org/cgi/content/short/664656v1?rss=1"
Chen, Y. E.Bouladoux, N.Hurabielle, C.Mattke, A.Belkaid, Y. A.Fischbach, M. A.2019-06-10doi:10.1101/664656Cold Spring Harbor Laboratory Press2019-06-10
https://biorxiv.org/cgi/content/short/666230v1?rss=1"
Schubert, R. D.Hawes, I.Ramachandran, P. S.Ramesh, A.Crawford, E. D.Pak, J. E.Wu, W.Cheung, C. K.O'Donovan, B. D.Tato, C. M.Lyden, A.Tan, M.Sit, R.Sowa, G.Sample, H. A.Zorn, K. C.Banerji, D.Khan, L. M.Bove, R.Hauser, S. L.Gelfand, A. A.Johnson-Kerner, B.Nash, K.Krishnamoorthy, K. S.Chitnis, T.Ding, J. Z.McMillan, H. J.Chiu, C. Y.Briggs, B.Glaser, C. A.Yen, C.Chu, V.Wadford, D. A.Dominguez, S. R.Ng, T. F. F.Marine, R. L.Lopez, A. S.Nix, W. A.Soldatos, A.Gorman, M.Benson, L.Messacar, K.Konopka-Anstadt, J. L.Ob2019-06-10doi:10.1101/666230Cold Spring Harbor Laboratory Press2019-06-10
https://biorxiv.org/cgi/content/short/675165v1?rss=1"
Huber, G.Wilkinson, M.2019-06-19doi:10.1101/675165Cold Spring Harbor Laboratory Press2019-06-19
https://biorxiv.org/cgi/content/short/673152v1?rss=1"
Jeong, S.Yang, D.Beyene, A. G.Best, A.Landry, M.2019-06-18doi:10.1101/673152Cold Spring Harbor Laboratory Press2019-06-18
https://biorxiv.org/cgi/content/short/674291v1?rss=1"
Loshbaugh, A. L.Kortemme, T.2019-06-17doi:10.1101/674291Cold Spring Harbor Laboratory Press2019-06-17
https://biorxiv.org/cgi/content/short/676866v1?rss=1"
Prakash, V.Bull, M. S.Prakash, M.2019-06-19doi:10.1101/676866Cold Spring Harbor Laboratory Press2019-06-19
https://biorxiv.org/cgi/content/short/676825v1?rss=1"
Rao, R.Bhattacharya, N.Thomas, N.Duan, Y.Chen, X.Canny, J.Abbeel, P.Song, Y. S.2019-06-20doi:10.1101/676825Cold Spring Harbor Laboratory Press2019-06-20
https://biorxiv.org/cgi/content/short/026591v1?rss=1"
Matthias SteinrückenJohn A. KammYun S. Song2015-09-16doi:10.1101/026591Cold Spring Harbor Laboratory Press2015-09-16
https://biorxiv.org/cgi/content/short/672428v1?rss=1"
Chen, L.-X.Zhao, Y.McMahon, K. D.Mori, J. F.Jessen, G. L.Nelson, T. C.Warren, L. A.Banfield, J. F.2019-06-15doi:10.1101/672428Cold Spring Harbor Laboratory Press2019-06-15
https://biorxiv.org/cgi/content/short/671271v1?rss=1"
McKitterick, A.Hays, S.Alam, M.Seed, K.2019-06-14doi:10.1101/671271Cold Spring Harbor Laboratory Press2019-06-14
https://biorxiv.org/cgi/content/short/681676v1?rss=1"
Ghorbani, A.Ouyang, D.Abid, A.He, B.Chen, J. H.Harrington, R. A.Liang, D. H.Ashley, E. A.Zou, J. Y.2019-06-24doi:10.1101/681676Cold Spring Harbor Laboratory Press2019-06-24
https://biorxiv.org/cgi/content/short/678060v1?rss=1"
Gate, R. E.Kim, M. C.Lu, A.Lee, D.Shifrut, E.Subramaniam, M.Marson, A.Ye, C. J.2019-06-21doi:10.1101/678060Cold Spring Harbor Laboratory Press2019-06-21
https://biorxiv.org/cgi/content/short/684670v1?rss=1"
Jeong, S.Pinals, R. L.Dharmadhikari, B.Song, H.Kalluri, A.Debnath, D.Qi, W.Ham, M.-H.Patra, P.Landry, M.2019-06-27doi:10.1101/684670Cold Spring Harbor Laboratory Press2019-06-27
https://biorxiv.org/cgi/content/short/688275v1?rss=1"
Wilson, B. D.Hariri, A. A.Thompson, I. A. P.Eisenstein, M.Soh, H. T.2019-07-02doi:10.1101/688275Cold Spring Harbor Laboratory Press2019-07-02
https://biorxiv.org/cgi/content/short/687954v1?rss=1"
Shi, X.Li, Q.Dai, Z.Tran, A.Feng, S.Ramirez, A. D.Lin, Z.Wang, X.Chow, T. T.Seiple, I. B.Huang, B.2019-07-01doi:10.1101/687954Cold Spring Harbor Laboratory Press2019-07-01
https://biorxiv.org/cgi/content/short/513309v1?rss=1"
Tian, R.Gachechiladze, M. A.Ludwig, C. H.Laurie, M. T.Hong, J. Y.Nathaniel, D.Prabhu, A. V.Fernandopulle, M. S.Patel, R.Ward, M. E.Kampmann, M.2019-01-07doi:10.1101/513309Cold Spring Harbor Laboratory Press2019-01-07
https://biorxiv.org/cgi/content/short/695429v1?rss=1"
Stojkovic, V.Myasnikov, A.Young, I.Frost, A.Fraser, J.Fujmori, D.2019-07-07doi:10.1101/695429Cold Spring Harbor Laboratory Press2019-07-07
https://biorxiv.org/cgi/content/short/696724v1?rss=1"
Qiu, X.Zhang, Y.Yang, D.Hosseinzadeh, S.Wang, L.Yuan, R.Xu, S.Ma, Y.Replogle, J.Darmanis, S.Xing, J.Weissman, J.2019-07-09doi:10.1101/696724Cold Spring Harbor Laboratory Press2019-07-09
https://biorxiv.org/cgi/content/short/696328v1?rss=1"
Granja, J. M.Klemm, S.McGinnis, L. M.Kathiria, A. S.Mezger, A.Parks, B.Gars, E.Liedtke, M.Zheng, G. X.Chang, H. Y.Majeti, R.Greenleaf, W. J.2019-07-09doi:10.1101/696328Cold Spring Harbor Laboratory Press2019-07-09
https://biorxiv.org/cgi/content/short/698803v1?rss=1"
McKechnie, J. L.Beltran, D.Pitti, A.Saenz, L.Arauz, A. B.Vergara, R.Harris, E.Lanier, L. L.Blish, C. A.Lopez-Verges, S.2019-07-11doi:10.1101/698803Cold Spring Harbor Laboratory Press2019-07-11
https://biorxiv.org/cgi/content/short/704312v1?rss=1"
Tulpule, A.Guan, J.Neel, D. S.Lin, Y. P.Heslin, A.Allegakoan, H.Perati, S.Ramirez, A. D.Shi, X.Yang, B.Feng, S.Huang, B.Bivona, T. G.2019-07-16doi:10.1101/704312Cold Spring Harbor Laboratory Press2019-07-16
https://biorxiv.org/cgi/content/short/706903v1?rss=1"
Altemose, N.Maslan, A.Lai, A.White, J. A.Streets, A. M.2019-07-18doi:10.1101/706903Cold Spring Harbor Laboratory Press2019-07-18
https://biorxiv.org/cgi/content/short/709337v1?rss=1"
Horns, F.Dekker, C. L.Quake, S. R.2019-07-22doi:10.1101/709337Cold Spring Harbor Laboratory Press2019-07-22
https://biorxiv.org/cgi/content/short/720292v1?rss=1"
Willis, L.Jonsson, H.Huang, K. C.2019-07-30doi:10.1101/720292Cold Spring Harbor Laboratory Press2019-07-30
https://biorxiv.org/cgi/content/short/720532v1?rss=1"
100-fold less viable than 3610. We discovered that the higher viability in 3610 was due to its ability to produce the antibacterial compound surfactin, as surfactin addition rescued 168 viability and also increased yield in aerobic growth. We further demonstrate that surfactin strongly depolarizes the B. subtilis membrane, and that other known membrane-potential disruptors restore viability to 168. These findings highlight the importance of surfactin for survival during oxygen-depleted conditions and demonstrate that antimicrobials normally considered harmful can instead benefit cells in stressful conditions when the terminal electron acceptor in respiration is limiting.
]]>Arjes, H. A.Vo, L.Dunn, C. M.Willis, L.DeRosa, C. A.Fraser, C. L.Kearns, D. B.Huang, K.2019-07-30doi:10.1101/720532Cold Spring Harbor Laboratory Press2019-07-30
https://biorxiv.org/cgi/content/short/717686v1?rss=1"
Ng, K. M.Aranda-Diaz, A.Tropini, C.Frankel, M. R.Van Treuren, W. W.O'Laughlin, C.Merrill, B. D.Yu, F. B.Pruss, K. M.Oliveira, R. A.Higginbottom, S. K.Neff, N. F.Fischbach, M. A.Xavier, K. B.Sonnenburg, J. L.Huang, K. C.2019-08-08doi:10.1101/717686Cold Spring Harbor Laboratory Press2019-08-08
https://biorxiv.org/cgi/content/short/711853v1?rss=1"
Huang, Y.Cai, W.Del Rio Flores, A.Twiff, F. F.Zhang, W.2019-07-26doi:10.1101/711853Cold Spring Harbor Laboratory Press2019-07-26
https://biorxiv.org/cgi/content/short/712828v1?rss=1"
Kenny, S.Chen, X.Ge, L.Xu, K.2019-07-31doi:10.1101/712828Cold Spring Harbor Laboratory Press2019-07-31
https://biorxiv.org/cgi/content/short/715896v1?rss=1"
Guo, X.Aviles, G.Liu, Y.Tian, R.Unger, B. A.Lin, Y.-H. T.Wiita, A. P.Xu, K.Correia, M. A.Kampmann, M.2019-07-26doi:10.1101/715896Cold Spring Harbor Laboratory Press2019-07-26
https://biorxiv.org/cgi/content/short/748160v1?rss=1"
Elledge, S. K.Tran, H. L.Christian, A. H.Steri, V.Hann, B.Toste, F. D.Chang, C. J.Wells, J. A.2019-08-28doi:10.1101/748160Cold Spring Harbor Laboratory Press2019-08-28
https://biorxiv.org/cgi/content/short/747030v1?rss=1"
Fonseca, J. P.Aslankoohi, E.El-Samad, H.2019-08-28doi:10.1101/747030Cold Spring Harbor Laboratory Press2019-08-28
https://biorxiv.org/cgi/content/short/742320v1?rss=1"
Travaglini, K. J.Nabhan, A. N.Penland, L.Sinha, R.Gillich, A.Sit, R. V.Chang, S.Conley, S. D.Mori, Y.Seita, J.Berry, G. J.Shrager, J. B.Metzger, R. J.Kuo, C. S.Neff, N.Weissman, I. L.Quake, S. R.Krasnow, M. A.2019-08-27doi:10.1101/742320Cold Spring Harbor Laboratory Press2019-08-27
https://biorxiv.org/cgi/content/short/758557v1?rss=1"
Funabashi, M.Grove, T.Pascal, V.Varma, Y.McFadden, M.Brown, L.Guo, C.Medema, M. H.Almo, S.Fischbach, M. A.2019-09-05doi:10.1101/758557Cold Spring Harbor Laboratory Press2019-09-05
https://biorxiv.org/cgi/content/short/761890v1?rss=1"
3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.
]]>DeRisi, J. L.Huber, G.Kistler, A.Retallack, H.Wilkinson, M.Yllanes, D.2019-09-09doi:10.1101/761890Cold Spring Harbor Laboratory Press2019-09-09
https://biorxiv.org/cgi/content/short/748616v1?rss=1"
0.79) predictive accuracies on multiple sequence-activity prediction tasks. We developed model-guided design strategies which yielded large, sequence-diverse sets of novel promoters exhibiting activities similar to current best-in-class sequences. In addition to providing large sets of new promoters, our results show the value of model-guided design as an approach for generating useful DNA parts.
]]>Smolke, C.Kotopka, B.2019-08-28doi:10.1101/748616Cold Spring Harbor Laboratory Press2019-08-28
https://biorxiv.org/cgi/content/short/761296v1?rss=1"
Pinals, R. L.Yang, D.Lui, A.Cao, W.Landry, M. P.2019-09-08doi:10.1101/761296Cold Spring Harbor Laboratory Press2019-09-08
https://biorxiv.org/cgi/content/short/760280v1?rss=1"
Ramadoss, N. S.Zhao, N. Q.Richardson, B. A.Grant, P. M.Kim, P. S.Blish, C. A.2019-09-08doi:10.1101/760280Cold Spring Harbor Laboratory Press2019-09-08
https://biorxiv.org/cgi/content/short/761502v1?rss=1"
10 nm) ectodomains that undergo conformational changes to bring apposing membranes in close contact prior to fusion. Here we report that a viral fusogen with a short (<2 nm) ectodomain, the reptilian orthoreovirus p14, accomplishes the same task by hijacking the actin cytoskeleton. We show that the cytoplasmic domain of p14 triggers N-WASP-mediated assembly of a branched actin network, directly coupling local force generation with a short membrane-disruptive ectodomain. This work reveals that overcoming energetic barriers to cell-cell fusion does not require conformational changes of tall fusogens but can instead be driven by harnessing the host cytoskeleton.nnImpact StatementA viral fusogen drives cell-cell fusion by hijacking the actin machinery to directly couple actin assembly with a short fusogenic ectodomain.
]]>Chan, K. M. C.Son, S.Schmid, E. M.Fletcher, D. A.2019-09-08doi:10.1101/761502Cold Spring Harbor Laboratory Press2019-09-08
https://biorxiv.org/cgi/content/short/779074v1?rss=1"
Sprockett, D. D.Martin, M.Costello, E. K.Burns, A. R.Holmes, S. P.Gurven, M.Relman, D. A.2019-09-23doi:10.1101/779074Cold Spring Harbor Laboratory Press2019-09-23
https://biorxiv.org/cgi/content/short/772343v1?rss=1"
Mudd, A. B.Bredeson, J. V.Baum, R.Hockemeyer, D.Rokhsar, D. S.2019-09-18doi:10.1101/772343Cold Spring Harbor Laboratory Press2019-09-18
https://biorxiv.org/cgi/content/short/766683v1?rss=1"
Zhang, J. Q.Siltanen, C. A.Liu, L.Chang, K.-C.Gartner, Z. J.Abate, A. R.2019-09-12doi:10.1101/766683Cold Spring Harbor Laboratory Press2019-09-12
https://biorxiv.org/cgi/content/short/766899v1?rss=1"
Alexander, M.Ang, Q. Y.Turnbaugh, P. J.2019-09-12doi:10.1101/766899Cold Spring Harbor Laboratory Press2019-09-12
https://biorxiv.org/cgi/content/short/786319v1?rss=1"
Tang, S.Kim, P. S.2019-09-29doi:10.1101/786319Cold Spring Harbor Laboratory Press2019-09-29
https://biorxiv.org/cgi/content/short/790642v1?rss=1"
Durham, N. D.Agrawal, A.Waltari, E.Croote, D.Zanini, F.Fouch, M.Davidson, E.Smith, O.Carabajal, E.Pak, J. E.Doranz, B. J.Robinson, M.Sanz, A. M.Albornoz, L. L.Rosso, F.Einav, S.Quake, S. R.McCutcheon, K. M.Goo, L.2019-10-02doi:10.1101/790642Cold Spring Harbor Laboratory Press2019-10-02
https://biorxiv.org/cgi/content/short/843631v1?rss=1"
Carroll, E. C.Greene, E. R.Martin, A.Marqusee, S.2019-11-15doi:10.1101/843631Cold Spring Harbor Laboratory Press2019-11-15
https://biorxiv.org/cgi/content/short/780593v1?rss=1"
Shiver, A. L.Culver, R.Deutschbauer, A. M.Huang, K.2019-09-30doi:10.1101/780593Cold Spring Harbor Laboratory Press2019-09-30
https://biorxiv.org/cgi/content/short/784413v1?rss=1"
Chen, M. B.Jiang, X.Quake, S. R.Sudhof, T. C.2019-09-26doi:10.1101/784413Cold Spring Harbor Laboratory Press2019-09-26
https://biorxiv.org/cgi/content/short/785964v1?rss=1"
Jerison, E. R.Quake, S. R.2019-09-27doi:10.1101/785964Cold Spring Harbor Laboratory Press2019-09-27
https://biorxiv.org/cgi/content/short/786269v1?rss=1"
Batson, J.Royer, L. A.Webber, J. T.2019-09-30doi:10.1101/786269Cold Spring Harbor Laboratory Press2019-09-30
https://biorxiv.org/cgi/content/short/790493v1?rss=1"
Hays, S. G.Seed, K.2019-10-02doi:10.1101/790493Cold Spring Harbor Laboratory Press2019-10-02
https://biorxiv.org/cgi/content/short/791947v1?rss=1"
Gayoso, A.Lopez, R.Steier, Z. R.Regier, J.Streets, A. M.Yosef, N.2019-10-07doi:10.1101/791947Cold Spring Harbor Laboratory Press2019-10-07
https://biorxiv.org/cgi/content/short/792994v1?rss=1"
Hickey, K. L.Dickson, K.Cogan, J. Z.Replogle, J. M.Schoof, M.D'Orazio, K. N.Sinha, N. K.Frost, A.Green, R.Kostova, K. K.Weissman, J. S.2019-10-03doi:10.1101/792994Cold Spring Harbor Laboratory Press2019-10-03
https://biorxiv.org/cgi/content/short/794875v1?rss=1"
Clivio, O.Lopez, R.Regier, J.Gayoso, A.Jordan, M. I.Yosef, N.2019-10-07doi:10.1101/794875Cold Spring Harbor Laboratory Press2019-10-07
https://biorxiv.org/cgi/content/short/798181v1?rss=1"
Nguyen, H. C.Talledge, N.McCullough, J.Sharma, A.Moss, F. R.Iwasa, J. H.Vershinin, M. D.Sundquist, W. I.Frost, A.2019-10-11doi:10.1101/798181Cold Spring Harbor Laboratory Press2019-10-11
https://biorxiv.org/cgi/content/short/800060v1?rss=1"
Fudenberg, G.Kelley, D. R.Pollard, K. S.2019-10-10doi:10.1101/800060Cold Spring Harbor Laboratory Press2019-10-10
https://biorxiv.org/cgi/content/short/800078v1?rss=1"
Jones, M. G.Khodaverdian, A.Quinn, J. J.Chan, M. M.Hussmann, J. A.Wang, R.Xu, C.Weissman, J. S.Yosef, N.2019-10-10doi:10.1101/800078Cold Spring Harbor Laboratory Press2019-10-10
https://biorxiv.org/cgi/content/short/800169v1?rss=1"
Poweleit, N.Czudnochowski, N.Nakagawa, R.Murphy, K. C.Sassetti, C. M.Rosenberg, O.2019-10-10doi:10.1101/800169Cold Spring Harbor Laboratory Press2019-10-10
https://biorxiv.org/cgi/content/short/801589v1?rss=1"
Kowarsky, M.Anselmi, C.Hotta, K.Burighel, P.Zaniolo, G.Caicci, F.Rosental, B.Neff, N. F.Ishizuka, K. J.Palmeri, K. J.Okamoto, J.Gordon, T.Weissman, I. L.Quake, S. R.Manni, L.Voskoboynik, A.2019-10-14doi:10.1101/801589Cold Spring Harbor Laboratory Press2019-10-14
https://biorxiv.org/cgi/content/short/803460v1?rss=1"
70% efficiency. In addition, we establish complete downstream recovery of nucleic acids from single, sorted double emulsion droplets, an advance in droplet sorting comparable with the capabilities of single-cell FACS. This work resolves several hurdles in the field of high-throughput droplet analysis and paves the way for a variety of new droplet assays, including rare variant isolation and multiparameter single-cell analysis, marrying the full power of flow cytometry with droplet microfluidics.
]]>Brower, K. K.Carswell-Crumpton, C.Klemm, S.Cruz, B.Kim, G.Calhoun, S. G.Nichols, L.Fordyce, P. M.2019-10-15doi:10.1101/803460Cold Spring Harbor Laboratory Press2019-10-15
https://biorxiv.org/cgi/content/short/804138v1?rss=1"
Lourenco, R.Saurabh, S.Herrmann, J.Wakatsuki, S.Shapiro, L.2019-10-13doi:10.1101/804138Cold Spring Harbor Laboratory Press2019-10-13
https://biorxiv.org/cgi/content/short/805473v1?rss=1"
Allen, B. M.Hiam, K. J.Burnett, C. E.Venida, A.DeBarge, R.Carmi, Y.Spitzer, M. H.2019-10-16doi:10.1101/805473Cold Spring Harbor Laboratory Press2019-10-16
https://biorxiv.org/cgi/content/short/805689v1?rss=1"
Belardi, B.Hamkins-Indik, T.Harris, A. R.Fletcher, D. A.2019-10-16doi:10.1101/805689Cold Spring Harbor Laboratory Press2019-10-16
https://biorxiv.org/cgi/content/short/805770v1?rss=1"
2.5 cells/s (70X faster than serial sampling) and perform 25 immunoblots/mm2 device area (>10X increase over previous immunoblots). A straightforward device for parallel single-cell immunoblotting, projection electrophoresis promises to advance integration of protein-level profiles into the emerging single-cell atlas of genomic and transcriptomic profiles.
]]>Grist, S. M.Mourdoukoutas, A. P.Herr, A. E.2019-10-16doi:10.1101/805770Cold Spring Harbor Laboratory Press2019-10-16
https://biorxiv.org/cgi/content/short/806885v1?rss=1"
Shi, H.Hu, Y.Huang, K. C.2019-10-17doi:10.1101/806885Cold Spring Harbor Laboratory Press2019-10-17
https://biorxiv.org/cgi/content/short/808410v1?rss=1"
Chen, L.-X.Anantharaman, K.Shaiber, A.Eren, A. M.Banfield, J. F.2019-10-17doi:10.1101/808410Cold Spring Harbor Laboratory Press2019-10-17
https://biorxiv.org/cgi/content/short/810234v1?rss=1"
Wang, S.Pisco, A. O.Karkanias, J.Altman, R. B.2019-10-20doi:10.1101/810234Cold Spring Harbor Laboratory Press2019-10-20
https://biorxiv.org/cgi/content/short/811570v1?rss=1"
Sanchez Lopez, M. I.Ting, A. Y.2019-10-21doi:10.1101/811570Cold Spring Harbor Laboratory Press2019-10-21
https://biorxiv.org/cgi/content/short/811620v1?rss=1"
Markenscoff-Papadimitriou, E.Whalen, S.Przytycki, P.Thomas, R.Binyameen, F.Nowakowski, T. J.Sanders, S. J.State, M. W.Pollard, K. S.Rubenstein, J. L.2019-10-21doi:10.1101/811620Cold Spring Harbor Laboratory Press2019-10-21
https://biorxiv.org/cgi/content/short/819037v1?rss=1"
Li, J.Han, S.Li, H.Udeshi, N. D.Svinkina, T.Mani, D. R.Xu, C.Guajardo, R.Xie, Q.Li, T.Luginbuhl, D. J.Wu, B.McLaughlin, C. N.Xie, A.Kaewsapsak, P.Quake, S. R.Carr, S. A.Ting, A. Y.Luo, L.2019-10-25doi:10.1101/819037Cold Spring Harbor Laboratory Press2019-10-25
https://biorxiv.org/cgi/content/short/820084v1?rss=1"
Spanogiannopoulos, P.Bradley, P. H.Melamed, J.Malig, Y. N. A.Lam, K. N.Gerona, R. R.Pollard, K. S.Turnbaugh, P.2019-10-25doi:10.1101/820084Cold Spring Harbor Laboratory Press2019-10-25
https://biorxiv.org/cgi/content/short/820928v1?rss=1"
Zanini, F.Berghuis, B. A.Jones, R. C.Nicolis di Robilant, B.Nong, R. Y.Norton, J.Clarke, M. F.Quake, S. R.2019-10-27doi:10.1101/820928Cold Spring Harbor Laboratory Press2019-10-27
https://biorxiv.org/cgi/content/short/821132v1?rss=1"
Zou, L.Spanogiannopoulos, P.Chien, H.-C.Pieper, L. M.Cai, W.Khuri, N.Pottel, J.Vora, B.Ni, Z.Tsakalozou, E.Zhang, W.Shoichet, B. K.Giacomini, K. M.Turnbaugh, P. J.2019-10-28doi:10.1101/821132Cold Spring Harbor Laboratory Press2019-10-28
https://biorxiv.org/cgi/content/short/824086v1?rss=1"
Wang, S.Ma, J.Fong, S.Rensi, S.Han, J.Peng, J.Pratt, D.Altman, R.Ideker, T.2019-11-13doi:10.1101/824086Cold Spring Harbor Laboratory Press2019-11-13
https://biorxiv.org/cgi/content/short/833707v1?rss=1"
Ramkumar, P.Tian, R.Seyler, M.Leong, J. T.Choudhry, P.Hechler, T.Shah, N.Wong, S. W.Martin, T. G.Wolf, J. L.Roybal, K. T.Pahl, A.Taunton, J.Wiita, A. P.Kampmann, M.2019-11-07doi:10.1101/833707Cold Spring Harbor Laboratory Press2019-11-07
https://biorxiv.org/cgi/content/short/836312v1?rss=1"
Shen, K.Maharbiz, M. M.2019-11-11doi:10.1101/836312Cold Spring Harbor Laboratory Press2019-11-11
https://biorxiv.org/cgi/content/short/837278v1?rss=1"
Chio, L.Pinals, R. L.Goh, N. S.Murali, A.Landry, M. P.2019-11-12doi:10.1101/837278Cold Spring Harbor Laboratory Press2019-11-12
https://biorxiv.org/cgi/content/short/841098v1?rss=1"
Canaj, H.Hussmann, J. A.Li, H.Beckman, K. A.Goodrich, L.Cho, N. H.Li, Y. J.Santos, D. A.McGeever, A.Stewart, E. M.Pessino, V.Mandegar, M. A.Huang, C.Gan, L.Panning, B.Huang, B.Weissman, J. S.Leonetti, M. D.2019-11-13doi:10.1101/841098Cold Spring Harbor Laboratory Press2019-11-13
https://biorxiv.org/cgi/content/short/848010v1?rss=1"
Thompson, S.Zhang, Y.Ingle, C.Reynolds, K. A.Kortemme, T.2019-11-20doi:10.1101/848010Cold Spring Harbor Laboratory Press2019-11-20
https://biorxiv.org/cgi/content/short/846170v1?rss=1"
Yuan, E.Si, P.Shevidi, S.de la Zerda, A.2019-11-18doi:10.1101/846170Cold Spring Harbor Laboratory Press2019-11-18
https://biorxiv.org/cgi/content/short/847657v1?rss=1"
Przytycki, P. F.Pollard, K. S.2019-11-19doi:10.1101/847657Cold Spring Harbor Laboratory Press2019-11-19
https://biorxiv.org/cgi/content/short/2019.12.08.868828v1?rss=1"
Maynard, A.McCoach, C. E.Rotow, J. K.Harris, L.Haderk, F.Kerr, L. D.Yu, E. A.Schenk, E. L.Tan, W.Zee, A.Tan, M.Gui, P.Lea, T.Wu, W.Urisman, A.Jones, K.Sit, R.Kolli, P. K.Seeley, E.Gesthalter, Y.Le, D. D.Yamauchi, K. A.Naeger, D. M.Thomas, N. J.Gupta, A.Gonzalez, M.Do, H.Tan, L.Gomez-Sjoberg, R.Gubens, M.Jahan, T.Kratz, J. R.Jablons, D.Neff, N.Doebele, R. C.Weissman, J.Blakely, C. M.Darmanis, S.Bivona, T. G.2019-12-13doi:10.1101/2019.12.08.868828Cold Spring Harbor Laboratory Press2019-12-13
https://biorxiv.org/cgi/content/short/860999v1?rss=1"
Csorgo, B.Leon, L. M.Chau-Ly, I. J.Vasquez-Rifo, A.Berry, J. D.Mahendra, C.Crawford, E.Lewis, J. D.Bondy-Denomy, J.2019-12-03doi:10.1101/860999Cold Spring Harbor Laboratory Press2019-12-03
https://biorxiv.org/cgi/content/short/854182v1?rss=1"
Cheng, H. K.Tan, S. K.Sweeney, T. E.Jeganathan, P.Briese, T.Khadka, V.Strouts, F.Thair, S.Dalai, S.Hitchcock, M.Multani, A.Aronson, J.Andermann, T.Yu, A.Yang, S.Holmes, S.Lipkin, W. I.Khatri, P.Relman, D. A.2019-11-25doi:10.1101/854182Cold Spring Harbor Laboratory Press2019-11-25
https://biorxiv.org/cgi/content/short/865477v1?rss=1"
Ranganath, T.Simpson, L. J.Seiler, C.Ferreira, A.-M.Vendrame, E.Zhao, N. Q.Fontenot, J. D.Holmes, S. P.Blish, C. A.2019-12-05doi:10.1101/865477Cold Spring Harbor Laboratory Press2019-12-05
https://biorxiv.org/cgi/content/short/860981v1?rss=1"
Heineike, B. M.El-Samad, H.2019-12-02doi:10.1101/860981Cold Spring Harbor Laboratory Press2019-12-02
https://biorxiv.org/cgi/content/short/858118v1?rss=1"
Huang, X.Shi, X.Hansen, M. E.Nemeth, C. L.Celli, A.Huang, B.Mauro, T.Koval, M.Desai, T.2019-11-28doi:10.1101/858118Cold Spring Harbor Laboratory Press2019-11-28
https://biorxiv.org/cgi/content/short/2019.12.15.877100v1?rss=1"
Puschnik, A. S.Kulsuptrakul, J.Wang, R.Meyers, N. L.Ott, M.2019-12-16doi:10.1101/2019.12.15.877100Cold Spring Harbor Laboratory Press2019-12-16
https://biorxiv.org/cgi/content/short/2019.12.16.877183v1?rss=1"
Andreasson, J.Gotrik, M.Wu, M. J.Wayment-Steele, H.Kladwang, W.Portela, F.Wellington-Oguri, R.Players, E.Das, R.Greenleaf, W.2019-12-16doi:10.1101/2019.12.16.877183Cold Spring Harbor Laboratory Press2019-12-16
https://biorxiv.org/cgi/content/short/2019.12.15.877126v1?rss=1"
Benthall, K. N.Cording, K. R.Agopyan-Miu, A. H. C. W.Chen, E. Y.Bateup, H. S.2019-12-16doi:10.1101/2019.12.15.877126Cold Spring Harbor Laboratory Press2019-12-16
https://biorxiv.org/cgi/content/short/2019.12.30.891549v1?rss=1"
75,000 cells from eight distinct areas of developing human forebrain using single cell ATAC-seq (scATACseq). We identified thousands of loci that undergo extensive cell type-specific changes in accessibility during corticogenesis. Chromatin state profiling also reveals novel distinctions between neural progenitor cells from different cortical areas not seen in transcriptomic profiles and suggests a role for retinoic acid signaling in cortical arealization. Comparison of the cell type-specific chromatin landscape of cerebral organoids to primary developing cortex found that organoids establish broad cell type-specific enhancer accessibility patterns similar to the developing cortex, but lack many putative regulatory elements identified in homologous primary cell types. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.
]]>Ziffra, R. S.Kim, C. N.Wilfert, A.Haeussler, M.Casella, A. M.Przytycki, P. F.Kreimer, A.Pollard, K. S.Ament, S. A.Eichler, E. E.Ahituv, N.Nowakowski, T. J.2019-12-31doi:10.1101/2019.12.30.891549Cold Spring Harbor Laboratory Press2019-12-31
https://biorxiv.org/cgi/content/short/2020.01.10.902155v1?rss=1"
Mendoza, P.Jackson, J. R.Oliveira, T.Gaebler, C.Ramos, V.Caskey, M.Jankovic, M.Nussenzweig, M. C.Cohn, L. B.2020-01-11doi:10.1101/2020.01.10.902155Cold Spring Harbor Laboratory Press2020-01-11
https://biorxiv.org/cgi/content/short/2020.01.06.895466v1?rss=1"
Anand, N.Eguchi, R. R.Derry, A.Altman, R. B.Huang, P.2020-01-07doi:10.1101/2020.01.06.895466Cold Spring Harbor Laboratory Press2020-01-07
https://biorxiv.org/cgi/content/short/2020.01.05.895227v1?rss=1"
Dumesic, P. A.Stoddard, C. I.Catania, S.Narlikar, G. J.Madhani, H.2020-01-06doi:10.1101/2020.01.05.895227Cold Spring Harbor Laboratory Press2020-01-06
https://biorxiv.org/cgi/content/short/2020.01.04.893909v1?rss=1"
Perica, T.Mathy, C. J. P.Xu, J.Jang, G. M.Zhang, Y.Kaake, R.Ollikainen, N.Braberg, H.Swaney, D. L.Kelly, M. J. S.Krogan, N. J.Kortemme, T.2020-01-06doi:10.1101/2020.01.04.893909Cold Spring Harbor Laboratory Press2020-01-06
https://biorxiv.org/cgi/content/short/2019.12.23.878207v1?rss=1"
Wallach, T.Srivastava, V.Reyes, E.Klein, O. D.Gartner, Z. J.2019-12-26doi:10.1101/2019.12.23.878207Cold Spring Harbor Laboratory Press2019-12-26
https://biorxiv.org/cgi/content/short/2019.12.18.881540v1?rss=1"
Jaffe, A. L.Castelle, C. J.Matheus Carnevali, P. B.Gribaldo, S.Banfield, J.2019-12-19doi:10.1101/2019.12.18.881540Cold Spring Harbor Laboratory Press2019-12-19
https://biorxiv.org/cgi/content/short/2019.12.19.883256v1?rss=1"
Buen Abad Najar, C. F.Yosef, N.Lareau, L. F.2019-12-20doi:10.1101/2019.12.19.883256Cold Spring Harbor Laboratory Press2019-12-20
https://biorxiv.org/cgi/content/short/2019.12.21.886093v1?rss=1"
Roodgar, M.Good, B. H.Garud, N. R.Martis, S.Avula, M.Zhou, W.Lancaster, S.Lee, H.Babveyh, A.Nesamoney, S.Pollard, K. S.Snyder, M. P.2019-12-23doi:10.1101/2019.12.21.886093Cold Spring Harbor Laboratory Press2019-12-23
https://biorxiv.org/cgi/content/short/2019.12.23.887604v1?rss=1"
Zhang, M. J.Pisco, A. O.Darmanis, S.Zou, J.2019-12-27doi:10.1101/2019.12.23.887604Cold Spring Harbor Laboratory Press2019-12-27
https://biorxiv.org/cgi/content/short/2019.12.20.885285v1?rss=1"
Waltari, E.Carabajal, E.Sanyal, M.Friedland, N.McCutcheon, K. M.2019-12-23doi:10.1101/2019.12.20.885285Cold Spring Harbor Laboratory Press2019-12-23
https://biorxiv.org/cgi/content/short/2019.12.31.892075v1?rss=1"
Son, S.Takatori, S.Belardi, B.Podolski, M.Bakalar, M. H.Fletcher, D. A.2020-01-01doi:10.1101/2019.12.31.892075Cold Spring Harbor Laboratory Press2020-01-01
https://biorxiv.org/cgi/content/short/2020.01.13.905356v1?rss=1"
Pinals, R. L.Yang, D.Rosenberg, D. J.Chaudhary, T.Crothers, A. R.Iavarone, A. T.Hammel, M.Landry, M. P.2020-01-14doi:10.1101/2020.01.13.905356Cold Spring Harbor Laboratory Press2020-01-14
https://biorxiv.org/cgi/content/short/2020.01.20.913186v1?rss=1"
Vazquez, S. E.Ferre, E. M. N.Scheel, D. W.Sunshine, S.Miao, B.Mandel-Brehm, C.Quandt, Z.Chan, A. Y.Cheng, M.German, M. S.Lionakis, M. S.DeRisi, J. L.Anderson, M. S.2020-01-21doi:10.1101/2020.01.20.913186Cold Spring Harbor Laboratory Press2020-01-21
https://biorxiv.org/cgi/content/short/2020.01.21.911545v1?rss=1"
Levine, L. S.Hiam, K. J.Marquez, D. M.Tenvooren, I.Contreras, D. C.Rathmell, J. C.Spitzer, M. H.2020-01-22doi:10.1101/2020.01.21.911545Cold Spring Harbor Laboratory Press2020-01-22
https://biorxiv.org/cgi/content/short/2020.01.22.915579v1?rss=1"
1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born via cesarean section harbored Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital versus maternal microbiomes. Genomic loci showing diversity within an infant included variants found in other infants, possibly reflecting inoculation from diverse hospital-associated sources. InStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.
]]>Olm, M. R.Crits-Christoph, A.Bouma-Gregson, K.Firek, B.Morowitz, M.Banfield, J.2020-01-23doi:10.1101/2020.01.22.915579Cold Spring Harbor Laboratory Press2020-01-23
https://biorxiv.org/cgi/content/short/2020.01.22.916106v1?rss=1"
Poudineh, M.Maikawa, C. L.Yue Ma, E.Pan, J.Mamerow, D.Han, Y.Baker, S. w.Beirami, A.Eisenstein, M.Kim, S.Vuckovic, J.Appel, E. A.Soh, H. T.2020-01-23doi:10.1101/2020.01.22.916106Cold Spring Harbor Laboratory Press2020-01-23
https://biorxiv.org/cgi/content/short/2020.01.23.912717v1?rss=1"
Wagner, A.Wang, C.DeTomaso, D.Avila-Pacheco, J.Zaghouani, S.Fessler, J.Akama-Garren, E.Pierce, K.Ron-Harel, N.Douglas, V. P.Haigis, M.Sobel, R. A.Clish, C.Regev, A.Kuchroo, V. K.Yosef, N.2020-01-24doi:10.1101/2020.01.23.912717Cold Spring Harbor Laboratory Press2020-01-24
https://biorxiv.org/cgi/content/short/2020.01.24.917971v1?rss=1"
Chen, T.-C.Tallo-Parra, M.Kadener, S.Böttcher, R.Perez-Vilaro, G.Boonchuen, P.Somboonwiwat, K.Diez, J.Sarnow, P.2020-01-24doi:10.1101/2020.01.24.917971Cold Spring Harbor Laboratory Press2020-01-24
https://biorxiv.org/cgi/content/short/2020.01.28.923235v1?rss=1"
99.9% purity) results in qualitatively indistinguishable phenotypes as treatment with commercially obtained rigosertib across multiple assays. The two compounds have indistinguishable chemical-genetic interactions with genes involved in modulating the microtubule network (KIF2C and TACC3), both destabilize microtubules in cells and in vitro, and both show substantially reduced toxicity in cell lines expressing a rationally-designed mutant of tubulin (L240F TUBB mutant), in which the rigosertib binding site in tubulin is mutated. Importantly, the specificity of the L240F TUBB mutant for microtubule-destabilizing agents, which is disputed by Reddy and co-workers, was recently confirmed by an independent research group (Patterson et al., 2019). We conclude that rigosertib kills cancer cells by destabilizing microtubules, in agreement with our original findings.
]]>Jost, M.Chen, Y.Gilbert, L. A.Horlbeck, M. A.Krenning, L.Menchon, G.Rai, A.Cho, M. Y.Stern, J. J.Prota, A. E.Kampmann, M.Akhmanova, A.Steinmetz, M. O.Tanenbaum, M. E.Weissman, J. S.2020-01-29doi:10.1101/2020.01.28.923235Cold Spring Harbor Laboratory Press2020-01-29
https://biorxiv.org/cgi/content/short/2020.01.30.923003v1?rss=1"
Stenstrom, L.Mahdessian, D.Gnann, C.Leonetti, M.Uhlen, M.Cuylen-Haering, S.Thul, P.Lundberg, E.2020-01-30doi:10.1101/2020.01.30.923003Cold Spring Harbor Laboratory Press2020-01-30
https://biorxiv.org/cgi/content/short/2020.02.03.927442v1?rss=1"
Zylberberg, M.Van Hemert, C.Handel, C. M.Liu, R.DeRisi, J.2020-02-04doi:10.1101/2020.02.03.927442Cold Spring Harbor Laboratory Press2020-02-04
https://biorxiv.org/cgi/content/short/2020.02.03.932392v1?rss=1"
Wilson, B. D.Soh, H. T.2020-02-03doi:10.1101/2020.02.03.932392Cold Spring Harbor Laboratory Press2020-02-03
https://biorxiv.org/cgi/content/short/684357v1?rss=1"
McInnes, G.Dalton, R.Sangkuhl, K.Whirl-Carrillo, M.Lee, S.-b.Altman, R. B.Woodahl, E. L.2019-06-27doi:10.1101/684357Cold Spring Harbor Laboratory Press2019-06-27
https://biorxiv.org/cgi/content/short/2020.02.04.934570v1?rss=1"
Rastogi, S.Xue, Y.Quake, S. R.Boothroyd, J. C.2020-02-05doi:10.1101/2020.02.04.934570Cold Spring Harbor Laboratory Press2020-02-05
https://biorxiv.org/cgi/content/short/2020.02.06.937805v1?rss=1"
DeTomaso, D.Yosef, N.2020-02-07doi:10.1101/2020.02.06.937805Cold Spring Harbor Laboratory Press2020-02-07
https://biorxiv.org/cgi/content/short/2020.02.08.939918v1?rss=1"
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org.highwire.dtl.DTLVardef@6483e6org.highwire.dtl.DTLVardef@10f9e60org.highwire.dtl.DTLVardef@66c8c3org.highwire.dtl.DTLVardef@68ff4_HPS_FORMAT_FIGEXP M_FIG C_FIG
]]>Alizadehmojarad, A.Zhou, X.Beyene, A. G.Chacon, K.Sung, Y.Landry, M. P.Vukovic, L.2020-02-10doi:10.1101/2020.02.08.939918Cold Spring Harbor Laboratory Press2020-02-10
https://biorxiv.org/cgi/content/short/2020.02.10.941203v1?rss=1"
Qu, H.Ma, Q.Wang, L.Mao, Y.Eisenstein, M.Soh, H. T.Zheng, L.2020-02-10doi:10.1101/2020.02.10.941203Cold Spring Harbor Laboratory Press2020-02-10
https://biorxiv.org/cgi/content/short/2020.02.10.942359v1?rss=1"
Domingo-Gonzalez, R.Zanini, F.Che, X.Liu, M.Jones, R. C.Swift, M. A.Quake, S. R.Cornfield, D. N.Alvira, C. M.2020-02-11doi:10.1101/2020.02.10.942359Cold Spring Harbor Laboratory Press2020-02-11
https://biorxiv.org/cgi/content/short/2020.01.23.911966v1?rss=1"
Wang, C.Wagner, A.Fessler, J.Avila-Pacheco, J.Karminski, J.Thakore, P.Zaghouani, S.Pierce, K.Bod, L.Schnell, A.DeTomaso, D.Ron-Harel, N.Haigis, M.Puleston, D.Pearce, E.Soleimani, M.Sobel, R.Clish, C.Regev, A.Yosef, N.Kuchroo, V.2020-01-23doi:10.1101/2020.01.23.911966Cold Spring Harbor Laboratory Press2020-01-23
https://biorxiv.org/cgi/content/short/2020.02.10.942854v1?rss=1"
Batson, J.Kistler, A.Dudas, G.Li, L.Ratnasari, K.Haas-Stapleton, E.Logan, P.Retallack, H.2020-02-13doi:10.1101/2020.02.10.942854Cold Spring Harbor Laboratory Press2020-02-13
https://biorxiv.org/cgi/content/short/2020.02.12.946509v1?rss=1"
McGinnis, C. S.Siegel, D. A.Xie, G.Stone, M.Gartner, Z. J.Roan, N. R.Lee, S. A.2020-02-13doi:10.1101/2020.02.12.946509Cold Spring Harbor Laboratory Press2020-02-13
https://biorxiv.org/cgi/content/short/2020.02.13.942896v1?rss=1"
90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contribute to growth on methane. Transcriptomics data from one system showed that the phage-associated pmoC genes are actively expressed in situ. Augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this powerful greenhouse gas into the environment.
]]>Chen, L.-X.Meheust, R.Crits-Christoph, A.McMahon, K. D.Colenbrander Nelson, T.Warren, L. A.Banfield, J.2020-02-14doi:10.1101/2020.02.13.942896Cold Spring Harbor Laboratory Press2020-02-14
https://biorxiv.org/cgi/content/short/2020.02.16.947804v1?rss=1"
Köhler, S.Wojcik, M.Xu, K.Dernburg, A.2020-02-16doi:10.1101/2020.02.16.947804Cold Spring Harbor Laboratory Press2020-02-16
https://biorxiv.org/cgi/content/short/2020.02.18.954974v1?rss=1"
Chen, T. N.Gupta, A. N.Zalavadia, M. D.Streets, A.2020-02-20doi:10.1101/2020.02.18.954974Cold Spring Harbor Laboratory Press2020-02-20
https://biorxiv.org/cgi/content/short/2020.02.18.955393v1?rss=1"
Yao, Z.Zanini, F.Kumar, S.Panpradist, N.Muniz, A.Quake, S. R.Einav, S.2020-02-19doi:10.1101/2020.02.18.955393Cold Spring Harbor Laboratory Press2020-02-19
https://biorxiv.org/cgi/content/short/2020.02.21.959791v1?rss=1"
Harris, A. R.Jreij, P.Belardi, B.Bausch, A.Fletcher, D. A.2020-02-22doi:10.1101/2020.02.21.959791Cold Spring Harbor Laboratory Press2020-02-22
https://biorxiv.org/cgi/content/short/2020.02.23.961904v1?rss=1"
Weeks, A. M.Byrnes, J. R.Lui, I.Wells, J. A.2020-02-24doi:10.1101/2020.02.23.961904Cold Spring Harbor Laboratory Press2020-02-24
https://biorxiv.org/cgi/content/short/2020.02.25.960302v1?rss=1"
Brbic, M.Zitnik, M.Wang, S.Pisco, A. O.Altman, R. B.Darmanis, S.Leskovec, J.2020-02-26doi:10.1101/2020.02.25.960302Cold Spring Harbor Laboratory Press2020-02-26
https://biorxiv.org/cgi/content/short/2020.02.25.964536v1?rss=1"
Tessema, S. K.Hathaway, N. J.Teyssier, N. B.Murphy, M.Aydemir, O.Duarte, E. M.Simone, W.Colborn, J.Saute, F.Crawford, E.Aide, P.Bailey, J. A.Greenhouse, B.2020-02-26doi:10.1101/2020.02.25.964536Cold Spring Harbor Laboratory Press2020-02-26
https://biorxiv.org/cgi/content/short/2020.02.26.966911v1?rss=1"
Cortez, J. T.Montauti, E.Shifrut, E.Zhang, Y.Shaked, O.Xu, Y.Roth, T.Simeonov, D.Zhang, Y.Chen, S.Li, Z.Vogel, I. A.Prator, G. Y.Zhang, B.Lee, Y.Sun, Z.Ifergan, I.Van Gool, F.Bluestone, J. A.Marson, A.Fang, D.2020-02-27doi:10.1101/2020.02.26.966911Cold Spring Harbor Laboratory Press2020-02-27
https://biorxiv.org/cgi/content/short/2020.02.26.967133v1?rss=1"
Demaree, B.Delley, C. L.Vasudevan, H. N.Peretz, C. A. C.Ruff, D.Smith, C. C.Abate, A. R.2020-02-28doi:10.1101/2020.02.26.967133Cold Spring Harbor Laboratory Press2020-02-28
https://biorxiv.org/cgi/content/short/2020.02.27.968297v1?rss=1"
Han, S.Zhao, B. S.Myers, S. A.Carr, S. A.He, C.Ting, A. Y.2020-02-28doi:10.1101/2020.02.27.968297Cold Spring Harbor Laboratory Press2020-02-28
https://biorxiv.org/cgi/content/short/2020.02.28.970491v1?rss=1"
Wilk, A. J.Benner, N. L.Vergara, R.Haabeth, O. A. W.Levy, R.Waymouth, R. M.Wender, P. A.Blish, C. A.2020-03-03doi:10.1101/2020.02.28.970491Cold Spring Harbor Laboratory Press2020-03-03
https://biorxiv.org/cgi/content/short/2020.03.02.968818v1?rss=1"
Manning, J. E.Bohl, J. A.Lay, S.Chea, S.Ly, S.Sengdoeurn, Y.Heng, S.Vuthy, C.Kalantar, K.Ahyong, V.Tan, M.Sheu, J.Tato, C. M.DeRisi, J.Baril, L.Dussart, P.Duong, V.Karlsson, E. A.2020-03-05doi:10.1101/2020.03.02.968818Cold Spring Harbor Laboratory Press2020-03-05
https://biorxiv.org/cgi/content/short/2020.03.02.973008v1?rss=1"
Ponting, C. P.Baran-Gale, J.Morgan, M. D.Maio, S.Dhalla, F.Calvo-Asensio, I.Deadman, M.Handel, A. E.Maynard, A.Chen, S.Green, F.Sit, R.Neff, N.Darmanis, S.Tan, W.May, A. P.Marioni, J. C.Holländer, G. A.2020-03-03doi:10.1101/2020.03.02.973008Cold Spring Harbor Laboratory Press2020-03-03
https://biorxiv.org/cgi/content/short/2020.03.04.977157v1?rss=1"
Hryckowian, A. J.Merrill, B. D.Porter, N. T.Van Treuren, W.Nelson, E. J.Garlena, R. A.Russell, D. A.Martens, E. C.Sonnenburg, J. L.2020-03-05doi:10.1101/2020.03.04.977157Cold Spring Harbor Laboratory Press2020-03-05
https://biorxiv.org/cgi/content/short/2020.03.05.976068v1?rss=1"
Vonk, W. I. M.Rainbolt, T. K.Dolan, P. T.Webb, A. E.Brunet, A.Frydman, J.2020-03-06doi:10.1101/2020.03.05.976068Cold Spring Harbor Laboratory Press2020-03-06
https://biorxiv.org/cgi/content/short/2020.03.05.979708v1?rss=1"
Loewke, A. C.Minerva, A. R.Nelson, A. B.Kreitzer, A. C.Gunaydin, L. A.2020-03-06doi:10.1101/2020.03.05.979708Cold Spring Harbor Laboratory Press2020-03-06
https://biorxiv.org/cgi/content/short/2020.03.06.976126v1?rss=1"
1,000 different families of putative metabolic gene clusters. Analysis of the enzyme content of these gene clusters suggests that they encode pathways with a wide range of predicted substrate classes, including saccharides, amino acids/peptides and lipids. Altogether, these results indicate a potentially important role of this protein superfamily in the human gut, and our dataset provides significant opportunities for the discovery of novel pathways that may have significant effects on human health.
]]>Pascal Andreu, V.Fischbach, M. A.Medema, M. H.2020-03-06doi:10.1101/2020.03.06.976126Cold Spring Harbor Laboratory Press2020-03-06
https://biorxiv.org/cgi/content/short/2020.03.06.981712v1?rss=1"
Gonzalez, C. G.Wastyk, H. C.Topf, M.Gardner, C. D.Sonnenburg, J. L.Elias, J. E.2020-03-08doi:10.1101/2020.03.06.981712Cold Spring Harbor Laboratory Press2020-03-08
https://biorxiv.org/cgi/content/short/2020.03.11.988022v1?rss=1"
100 endogenous proteins, including many not previously linked to ER-mitochondria contacts. We validated eight novel candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially-specific proximity labeling in cells.
]]>Cho, K. F.Branon, T. C.Rajeev, S.Svinkina, T.Udeshi, N. D.Thoudam, T.Kwak, C.Rhee, H.-W.Lee, I.-K.Carr, S. A.Ting, A. Y.2020-03-12doi:10.1101/2020.03.11.988022Cold Spring Harbor Laboratory Press2020-03-12
https://biorxiv.org/cgi/content/short/2020.03.12.988147v1?rss=1"
Barth, Z. K.Netter, Z.Angermeyer, A.Bhardwaj, P.Seed, K.2020-03-12doi:10.1101/2020.03.12.988147Cold Spring Harbor Laboratory Press2020-03-12
https://biorxiv.org/cgi/content/short/2020.03.13.991414v1?rss=1"
Hiatt, J.Cavero, D. A.McGregor, M. J.Gordon, D. E.Zheng, W.Budzik, J. M.Roth, T. L.Haas, K. M.Rathore, U.Meyer-Franke, A.Bouzidi, M. S.Hultquist, J. F.Wojcechowskyj, J. A.Fontaine, K. A.Pillai, S. K.Cox, J. S.Ernst, J. D.Krogan, N. J.Marson, A.2020-03-15doi:10.1101/2020.03.13.991414Cold Spring Harbor Laboratory Press2020-03-15
https://biorxiv.org/cgi/content/short/2020.03.14.991018v1?rss=1"
Lui, J. H.Nguyen, N. D.Grutzner, S. M.Darmanis, S.Peixoto, D.Wagner, M. J.Allen, W. E.Kebschull, J. M.Richman, E. B.Ren, J.Newsome, W. T.Quake, S. R.Luo, L.2020-03-14doi:10.1101/2020.03.14.991018Cold Spring Harbor Laboratory Press2020-03-14
https://biorxiv.org/cgi/content/short/2020.03.14.992040v1?rss=1"
Thompson, I. A. P.Zheng, L.Eisenstein, M.Soh, H. T.2020-03-16doi:10.1101/2020.03.14.992040Cold Spring Harbor Laboratory Press2020-03-16
https://biorxiv.org/cgi/content/short/2020.03.16.992958v1?rss=1"
Blum, J.Nakayama, L.Klemm, S.Kathiria, A.Guttenplan, K.Hoang, P.Shadrach, J.Kaltschmidt, J.Greenleaf, W.Gitler, A. D.2020-03-17doi:10.1101/2020.03.16.992958Cold Spring Harbor Laboratory Press2020-03-17
https://biorxiv.org/cgi/content/short/2020.03.20.000133v1?rss=1"
Chamier, L. v.Jukkala, J.Spahn, C.Lerche, M.Hernandez-perez, S.Mattila, P.Karinou, E.Holden, S.Can Solak, A.Krull, A.Buchholz, T.-O.Jug, F.Royer, L. A.Heilemann, M.Laine, R. F.Jacquemet, G.Henriques, R.2020-03-20doi:10.1101/2020.03.20.000133Cold Spring Harbor Laboratory Press2020-03-20
https://biorxiv.org/cgi/content/short/2020.03.22.002386v1?rss=1"
Gordon, D. E.Jang, G. M.Bouhaddou, M.Xu, J.Obernier, K.O'Meara, M. J.Guo, J. Z.Swaney, D. L.Tummino, T. A.Huttenhain, R.Kaake, R.Richards, A. L.Tutuncuoglu, B.Foussard, H.Batra, J.Haas, K.Modak, M.Kim, M.Haas, P.Polacco, B. J.Braberg, H.Fabius, J. M.Eckhardt, M.Soucheray, M.Brewer, M.Cakir, M.McGregor, M. J.Li, Q.Naing, Z. Z. C.Zhou, Y.Peng, S.Kirby, I. T.Melnyk, J. E.Chorba, J. S.Lou, K.Dai, S. A.Shen, W.Shi, Y.Zhang, Z.Barrio-Hernandez, I.Memon, D.Hernandez-Armenta, C.Mathy, C. J. P.Perica, T.Pilla, K. B.2020-03-22doi:10.1101/2020.03.22.002386Cold Spring Harbor Laboratory Press2020-03-22
https://biorxiv.org/cgi/content/short/2020.03.22.999243v1?rss=1"
Borghi, S.Bournazos, S.Thulin, N.Li, C.Gajewski, A.Sherwood, R.Zhang, S.Harris, E.Jagannathan, P.Wang, L.-X.Ravetch, J. V.Wang, T. T.2020-03-25doi:10.1101/2020.03.22.999243Cold Spring Harbor Laboratory Press2020-03-25
https://biorxiv.org/cgi/content/short/2020.03.23.004093v1?rss=1"
West, P. T.Peters, S. L.Olm, M. R.Yu, F. B.Lou, Y. C.Firek, B. A.Baker, R.Johnson, A. D.Morowitz, M. J.Hettich, R. L.Banfield, J. F.2020-03-25doi:10.1101/2020.03.23.004093Cold Spring Harbor Laboratory Press2020-03-25
https://biorxiv.org/cgi/content/short/2020.03.24.006874v1?rss=1"
Schmunk, G.Chang, K. N.Soliman, S. S.Keefe, M. G.Bogdanoff, D.Tejera, D.Ziffra, R. S.Shin, D.Allen, D. E.Chhun, B. B.McGinnis, C. S.Winkler, E. A.Abla, A. A.Chang, E. F.Gartner, Z. J.Mehta, S. B.Piao, X.Hengen, K. B.Nowakowski, T. J.2020-03-25doi:10.1101/2020.03.24.006874Cold Spring Harbor Laboratory Press2020-03-25
https://biorxiv.org/cgi/content/short/2020.03.26.009217v1?rss=1"
Saha, P.Shumate, J. L.Caldwell, J. G.Elghobashi-Meinhardt, N.Lu, A.Zhang, L.Olsson, N.Elias, J. E.Pfeffer, S. R.2020-03-29doi:10.1101/2020.03.26.009217Cold Spring Harbor Laboratory Press2020-03-29
https://biorxiv.org/cgi/content/short/2020.03.27.012633v1?rss=1"
Hwang, B.Lee, D. S.Tamaki, W.Sun, Y.Ogorodnikov, A.Hartoularos, G.Winters, A.Song, Y. S.Chow, E. D.Spitzer, M. H.Ye, C. J.2020-03-30doi:10.1101/2020.03.27.012633Cold Spring Harbor Laboratory Press2020-03-30
https://biorxiv.org/cgi/content/short/2020.03.30.016329v1?rss=1"
Summers, D. K.Perry, D. S.Rao, B.Madhani, H. D.2020-03-30doi:10.1101/2020.03.30.016329Cold Spring Harbor Laboratory Press2020-03-30
https://biorxiv.org/cgi/content/short/2020.05.01.072884v1?rss=1"
Newberry, R. W.Arhar, T.Costello, J.Hartoularos, G. C.Maxwell, A. M.Naing, Z. Z. C.Pittman, M.Reddy, N. R.Schwarz, D. M. C.Wassarman, D. R.Wu, T. S.Barrero, D.Caggiano, C.Catching, A.Cavazos, T. B.Estes, L. S.Faust, B.Fink, E. A.Goldman, M. A.Gomez, Y. K.Gordon, M. G.Gunsalus, L. M.Hoppe, N.Jaime-Garza, M.Johnson, M. C.Jones, M. G.Kung, A. F.Lopez, K. E.Lumpe, J.Martyn, C.McCarthy, E. E.Miller-Vedam, L. E.Navarro, E. J.Palar, A.Pellegrino, J.Saylor, W.Stephens, C. A.Strickland, J.Torosyan, H.Wankowicz, S. A.Wong, D2020-05-03doi:10.1101/2020.05.01.072884Cold Spring Harbor Laboratory Press2020-05-03
https://biorxiv.org/cgi/content/short/2020.04.30.069690v1?rss=1"
Ruiz, C.Zitnik, M.Leskovec, J.2020-05-02doi:10.1101/2020.04.30.069690Cold Spring Harbor Laboratory Press2020-05-02
https://biorxiv.org/cgi/content/short/2020.04.28.066498v1?rss=1"
Granja, J. M.Corces, M. R.Pierce, S. E.Bagdatli, S. T.Choudhry, H.Chang, H.Greenleaf, W.2020-04-29doi:10.1101/2020.04.28.066498Cold Spring Harbor Laboratory Press2020-04-29
https://biorxiv.org/cgi/content/short/2020.04.28.065615v1?rss=1"
Theil, T.Hasenpusch-Theil, K.Laclef, C.Colligan, M.Fitzgerald, E.Howe, K.Carroll, E.Abrams, S.Reiter, J. F.Schneider-Maunoury, S.2020-04-28doi:10.1101/2020.04.28.065615Cold Spring Harbor Laboratory Press2020-04-28
https://biorxiv.org/cgi/content/short/2020.04.23.056978v1?rss=1"
Pollina, T.Larson, A.Lombard, F.Li, H.Colin, S.Vargas, C. d.Prakash, M.2020-04-23doi:10.1101/2020.04.23.056978Cold Spring Harbor Laboratory Press2020-04-23
https://biorxiv.org/cgi/content/short/2020.04.19.049254v1?rss=1"
Muus, C.Luecken, M. D.Eraslan, G.Waghray, A.Heimberg, G.Sikkema, L.Kobayashi, Y.Vaishnav, E. D.Subramanian, A.Smillie, C.Jagadeesh, K.Duong, E. T.Fiskin, E.Torlai Triglia, E.Ansari, M.Cai, P.Lin, B.Buchanan, J.Chen, S.Shu, J.Haber, A. L.Chung, H.Montoro, D. T.Adams, T.Aliee, H.Allon, S. J.Andrusivova, Z.Angelidis, I.Ashenberg, O.Bassler, K.Becavin, C.Benhar, I.Bergenstrahle, J.Bergenstrahle, L.Bolt, L.Braun, E.Bui, L. T.Chaffin, M.Chichelnitskiy, E.Chiou, J.Conlon, T. M.Cuoco, M. S.Deprez, M.Fischer, D. S.G2020-04-20doi:10.1101/2020.04.19.049254Cold Spring Harbor Laboratory Press2020-04-20
https://biorxiv.org/cgi/content/short/2020.04.16.045302v1?rss=1"
Damas, J.Hughes, G. M.Keough, K. C.Painter, C. A.Persky, N. S.Corbo, M.Hiller, M.Koepfli, K.-P.Pfenning, A. R.Zhao, H.Genereux, D. P.Swofford, R.Pollard, K. S.Ryder, O. A.Nweeia, M. T.Lindblad-Toh, K.Teeling, E. C.Karlsson, E. K.Lewin, H. A.2020-04-18doi:10.1101/2020.04.16.045302Cold Spring Harbor Laboratory Press2020-04-18
https://biorxiv.org/cgi/content/short/2020.04.16.045245v1?rss=1"
Quinn, J. J.Jones, M. G.Okimoto, R. A.Yosef, N.Bivona, T. G.Weissman, J. S.2020-04-17doi:10.1101/2020.04.16.045245Cold Spring Harbor Laboratory Press2020-04-17
https://biorxiv.org/cgi/content/short/2020.04.16.044867v1?rss=1"
Jensen, M. K.Samelson, A. J.Steward, A.Clarke, J.Marqusee, S.2020-04-18doi:10.1101/2020.04.16.044867Cold Spring Harbor Laboratory Press2020-04-18
https://biorxiv.org/cgi/content/short/2020.04.14.041772v1?rss=1"
Pan, X.Thompson, M.Zhang, Y.Lin, L.Fraser, J. S.Kelly, M. J. S.Kortemme, T.2020-04-15doi:10.1101/2020.04.14.041772Cold Spring Harbor Laboratory Press2020-04-15
https://biorxiv.org/cgi/content/short/2020.04.14.041525v1?rss=1"
Pompura, S. L.Wagner, A.Kitz, A.LaPerche, J.Yosef, N.Dominguez-Villar, M.Hafler, D. A.2020-04-15doi:10.1101/2020.04.14.041525Cold Spring Harbor Laboratory Press2020-04-15
https://biorxiv.org/cgi/content/short/2020.04.12.038604v1?rss=1"
Zhao, N. Q.Ferreira, A.-M.Grant, P. M.Holmes, S.Blish, C. A.2020-04-13doi:10.1101/2020.04.12.038604Cold Spring Harbor Laboratory Press2020-04-13
https://biorxiv.org/cgi/content/short/2020.04.10.036442v1?rss=1"
Chen, Z.Shaw, A.Wilson, H.Woringer, M.Darzacq, X.Marqusee, S.Wang, Q.Bustamante, C.2020-04-11doi:10.1101/2020.04.10.036442Cold Spring Harbor Laboratory Press2020-04-11
https://biorxiv.org/cgi/content/short/2020.04.10.036376v1?rss=1"
Hayes, B. M.Radkov, A. D.Yarza, F.Flores, S.Kim, J. R.Zhao, Z.Lexa, K. W.Marnin, L.Biboy, J.Bowcutt, V.Vollmer, W.Pedra, J. H.Chou, S.2020-04-11doi:10.1101/2020.04.10.036376Cold Spring Harbor Laboratory Press2020-04-11
https://biorxiv.org/cgi/content/short/2020.04.08.033035v1?rss=1"
Bonny, A. R.Kochanowski, K.Diether, M.El-Samad, H.2020-04-10doi:10.1101/2020.04.08.033035Cold Spring Harbor Laboratory Press2020-04-10
https://biorxiv.org/cgi/content/short/2020.04.07.030569v1?rss=1"
Sapoznik, E.Chang, B.-J.Ju, R. J.Welf, E. S.Broadbent, D.Carisey, A. F.Stehbens, S. J.Lee, K.-m.Marin, A.Hanker, A. B.Schmidt, J. C.Arteaga, C. L.Yang, B.Kruithoff, R.Millett-Sikking, A.York, A. G.Dean, K. M.Fiolka, R. P.2020-04-08doi:10.1101/2020.04.07.030569Cold Spring Harbor Laboratory Press2020-04-08
https://biorxiv.org/cgi/content/short/2020.04.07.030551v1?rss=1"
Kalantar, K. L.Carvalho, T.de Bourcy, C. F. A.Dimitrov, B.Dingle, G.Egger, R.Han, J.Holmes, O. B.Juan, Y.King, R.Kislyuk, A.Mariano, M.Reyenoso, L. V.Rissato Cruz, D.Sheu, J.Tang, J.Wang, J.Zhang, M. A.Zhong, E.Ahyong, V.Lay, S.Chea, S.Bohl, J. A.Manning, J. E.Tato, C. M.DeRisi, J. L.2020-04-09doi:10.1101/2020.04.07.030551Cold Spring Harbor Laboratory Press2020-04-09
https://biorxiv.org/cgi/content/short/2020.04.05.026567v1?rss=1"
Krishnan, A. P.Belthangady, C.Nyby, C.Lange, M.Yang, B.Royer, L. A.2020-04-06doi:10.1101/2020.04.05.026567Cold Spring Harbor Laboratory Press2020-04-06
https://biorxiv.org/cgi/content/short/2020.04.05.026559v1?rss=1"
Kaplan, C.Kenny, S. J.Chen, S.Schoeneberg, J.Sitarska, E.Diz-Munoz, A.Xu, K.Drubin, D. G.2020-04-06doi:10.1101/2020.04.05.026559Cold Spring Harbor Laboratory Press2020-04-06
https://biorxiv.org/cgi/content/short/2020.04.04.025825v1?rss=1"
Leng, K.Li, E.Eser, R.Piergies, A.Sit, R.Tan, M.Neff, N.Li, S. H.Diehl Rodriguez, R.Suemoto, C. K.Paraizo Leite, R. E.Pasqualucci, C. A.Seeley, W. W.Spina, S.Heinsen, H.Grinberg, L. T.Kampmann, M. T.2020-04-05doi:10.1101/2020.04.04.025825Cold Spring Harbor Laboratory Press2020-04-05
https://biorxiv.org/cgi/content/short/2020.03.31.017434v1?rss=1"
Tan, C.Hiwa, R.Mueller, J. L.Vykunta, V.Hibiya, K.Noviski, M.Huizar, J.Brooks, J. F.Garcia, J.Heyn, C.Li, Z.Marson, A.Zikherman, J.2020-04-01doi:10.1101/2020.03.31.017434Cold Spring Harbor Laboratory Press2020-04-01
https://biorxiv.org/cgi/content/short/2020.05.07.081752v1?rss=1"
Cesar, S.Anjur-Dietrich, M.Yu, B.Li, E.Rojas, E.Neff, N.Cooper, T. F.Huang, K. C.2020-05-08doi:10.1101/2020.05.07.081752Cold Spring Harbor Laboratory Press2020-05-08
https://biorxiv.org/cgi/content/short/2020.05.08.083337v1?rss=1"
Gayoso, A.Steier, Z.Lopez, R.Regier, J.Nazor, K. L.Streets, A.Yosef, N.2020-05-10doi:10.1101/2020.05.08.083337Cold Spring Harbor Laboratory Press2020-05-10
https://biorxiv.org/cgi/content/short/2020.05.09.086264v1?rss=1"
Zhou, J.Li, S.Leung, K. K.ODonovan, B. K.Zou, J.DeRisi, J.Wells, J. A.2020-05-10doi:10.1101/2020.05.09.086264Cold Spring Harbor Laboratory Press2020-05-10
https://biorxiv.org/cgi/content/short/2020.05.13.092619v1?rss=1"
1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as single digit ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.
]]>Robbiani, D. F.Gaebler, C.Muecksch, F.Cetrulo Lorenzi, J.Wang, Z.Cho, A.Agudelo, M.Barnes, C.Finkin, S.Hagglof, T.Oliveira, T.Viant, C.Hurley, A.Millard, K.Kost, R.Cipolla, M.Gazumyan, A.Gordon, K.Bianchini, F.Chen, S.Ramos, V.Patel, R.Dizon, J.Shimeliovich, I.Mendoza, P.Hartweger, H.Nogueira, L.Pack, M.Horowitz, J.Schmidt, F.Weisblum, Y.Hoffmann, H.-H.Michailidis, E.Ashbrook, A.Waltari, E. F.Pak, J.Huey-Tubman, K.Koranda, N.Hoffman, P.West, A.Rice, C.Hatziioannou, T.Bjorkman, P.Bieniasz, P.Caskey, M.Nuss2020-05-15doi:10.1101/2020.05.13.092619Cold Spring Harbor Laboratory Press2020-05-15
https://biorxiv.org/cgi/content/short/2020.05.14.086363v1?rss=1"
Matheus Carnevali, P. B.Lavy, A.Thomas, A. D.Crits-Christoph, A.Diamond, S.Meeheust, R.Olm, M. R.Sharrar, A.Lei, S.Dong, W.Falco, N.Bouskill, N.Newcomer, M.Nico, P.Wainwright, H.Dwivedi, D.Williams, K. H.Hubbard, S.Banfield, J. F.2020-05-15doi:10.1101/2020.05.14.086363Cold Spring Harbor Laboratory Press2020-05-15
https://biorxiv.org/cgi/content/short/2020.05.14.094862v1?rss=1"
He, C. Y.Keren, R.Whittaker, M.Farag, I. F.Doudna, J. A.Cate, J. H.Banfield, J. F.2020-05-15doi:10.1101/2020.05.14.094862Cold Spring Harbor Laboratory Press2020-05-15
https://biorxiv.org/cgi/content/short/2020.05.15.098012v1?rss=1"
Zhao, X.Tong, K.Chen, x.Yang, B.Li, Q.Dai, Z.Shi, X.Seiple, I.Huang, B.Guo, S.2020-05-16doi:10.1101/2020.05.15.098012Cold Spring Harbor Laboratory Press2020-05-16
https://biorxiv.org/cgi/content/short/2020.05.21.109157v1?rss=1"
Lui, I.Zhou, X. X.Lim, S. A.Elledge, S.Solomon, P.Rettko, N. J.Zha, B. S.Kirkemo, L. L.Gramespacher, J. A.Liu, J.Muecksch, F.Lorenzi, J. C. C.Schmidt, F.Weisblum, Y.Robbiani, D. F.Nussenzweig, M. C.Hatziioannou, T.Bieniasz, P. D.Rosenberg, O.Leung, K. K.Wells, J. A.2020-05-21doi:10.1101/2020.05.21.109157Cold Spring Harbor Laboratory Press2020-05-21
https://biorxiv.org/cgi/content/short/2020.05.23.112979v1?rss=1"
Bonny, A. R.Fonseca, J. P.Park, J. E.El-Samad, H.2020-05-24doi:10.1101/2020.05.23.112979Cold Spring Harbor Laboratory Press2020-05-24
https://biorxiv.org/cgi/content/short/2020.05.25.115287v1?rss=1"
Belote, R. L.Le, D.Maynard, A.Lang, U. E.Sinclair, A.Planells-Palop, V.Baskin, L. S.Tward, A. D.Darmanis, S.Judson-Torres, R. L.2020-05-28doi:10.1101/2020.05.25.115287Cold Spring Harbor Laboratory Press2020-05-28
https://biorxiv.org/cgi/content/short/2020.05.25.115675v1?rss=1"
Chan, D.Chien, J.-C.Axpe, E.Blankemeier, L.Baker, S. W.Swaminathan, S.Piunova, V. A.Zubarev, D. Y.Soh, H. T.Appel, E. A.2020-05-28doi:10.1101/2020.05.25.115675Cold Spring Harbor Laboratory Press2020-05-28
https://biorxiv.org/cgi/content/short/2020.05.28.121541v1?rss=1"
Bassler, K.Fujii, W.Kapellos, T. S.Horne, A.Reiz, B.Dudkin, E.Luecken, M.Reusch, N.Osei-Sarpong, C.Warnat-Herresthal, S.Wagner, A.Bonaguro, L.Guenther, P.Pizarro, C.Schreiber, T.Becker, M.Haendler, K.Wohnhaas, C. T.Baumgartner, F.Koehler, M.Theis, H.Kraut, M.Wadsworth, M. H.Hughes, T. K.Ferreira, H. J. G.Schulte-Schrepping, J.Hinkley, E.Kaltheuner, I. H.Geyer, M.Thiele, C.Shalek, A. K.Feisst, A.Thomas, D.Dickten, H.Beyer, M.Baum, P.Yosef, N.Aschenbrenner, A. C.Ulas, T.Hasenauer, J.Theis, F. J.Skowasch, D.Schult2020-05-30doi:10.1101/2020.05.28.121541Cold Spring Harbor Laboratory Press2020-05-30
https://biorxiv.org/cgi/content/short/2020.05.28.122242v1?rss=1"
Pederick, D. T.Lui, J. H.Gingrich, E. C.Xu, C.Liu, Y.He, Z.Quake, S. R.Luo, L.2020-05-29doi:10.1101/2020.05.28.122242Cold Spring Harbor Laboratory Press2020-05-29
https://biorxiv.org/cgi/content/short/2020.05.29.117960v1?rss=1"
Townshend, B.Xiang, J.Manzanarez, G.Hayden, E. J.Smolke, C. D.2020-05-31doi:10.1101/2020.05.29.117960Cold Spring Harbor Laboratory Press2020-05-31
https://biorxiv.org/cgi/content/short/2020.05.29.123158v1?rss=1"
Knapp, B. D.Zhu, L.Huang, K. C.2020-06-01doi:10.1101/2020.05.29.123158Cold Spring Harbor Laboratory Press2020-06-01
https://biorxiv.org/cgi/content/short/2020.05.29.123166v1?rss=1"
Knapp, B. D.Zhu, L.Huang, K. C.2020-06-01doi:10.1101/2020.05.29.123166Cold Spring Harbor Laboratory Press2020-06-01
https://biorxiv.org/cgi/content/short/2020.05.29.124008v1?rss=1"
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