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https://biorxiv.org/cgi/content/short/656587v1?rss=1"
Ijaz, H.Koptyra, M. P.Gaonkar, K. S.Rokita, J. L.Baubet, V. P.Tauhid, L.Zhu, Y.Brown, M. A.Lopez Garcia, G.Zhang, B.Diskin, S. J.Vaksman, Z.Mason, J. L.Appert, E. M.Lilly, J. V.Lulla, R. R.De Raedt, T.Heath, A. P.Felmeister, A.Raman, P.Nazarian, J.Santi-Vicini, M.Storm, P. B.Resnick, A. C.Waanders, A. J.Cole, K. A.2019-05-31doi:10.1101/656587Cold Spring Harbor Laboratory Press2019-05-31
https://biorxiv.org/cgi/content/short/704114v1?rss=1"
Rashid, R.Gaglia, G.Chen, Y.-A.Lin, J.-R.Du, Z.Maliga, Z.Schapiro, D.Yapp, C.Muhlich, J.Sokolov, A.Sorger, P.Santagata, S.2019-07-17doi:10.1101/704114Cold Spring Harbor Laboratory Press2019-07-17
https://biorxiv.org/cgi/content/short/684340v1?rss=1"
Heiser, C. N.Lau, K. S.2019-06-27doi:10.1101/684340Cold Spring Harbor Laboratory Press2019-06-27
https://biorxiv.org/cgi/content/short/671180v1?rss=1"
Zhou, Z.Wang, J.Ye, C.Zhang, N.2019-06-14doi:10.1101/671180Cold Spring Harbor Laboratory Press2019-06-14
https://biorxiv.org/cgi/content/short/457622v1?rss=1"
Zhou, Z.Zhang, N. R.2018-10-30doi:10.1101/457622Cold Spring Harbor Laboratory Press2018-10-30
https://biorxiv.org/cgi/content/short/824326v1?rss=1"
Yu, W.Uzun, Y.Zhu, Q.Chen, C.Tan, K.2019-10-30doi:10.1101/824326Cold Spring Harbor Laboratory Press2019-10-30
https://biorxiv.org/cgi/content/short/2020.06.05.137000v1?rss=1"
Uzun, Y.Wu, H.Tan, K.2020-06-06doi:10.1101/2020.06.05.137000Cold Spring Harbor Laboratory Press2020-06-06
https://biorxiv.org/cgi/content/short/2020.03.27.001834v1?rss=1"
Rashid, R.Chen, Y.-A.Hoffer, J.Muhlich, J. L.Lin, J.-R.Krueger, R.Pfister, H.Mitchell, R.Santagata, S.Sorger, P.2020-03-30doi:10.1101/2020.03.27.001834Cold Spring Harbor Laboratory Press2020-03-30
https://biorxiv.org/cgi/content/short/2020.02.25.963272v1?rss=1"
Landau, H. J.Yellapantula, V.Diamond, B. J.Rustad, E. H.Maclachlan, K.Gundem, G.Medina-Martinez, J.Arango Ossa, J. E.Levine, M.Zhou, Y.Rajya, K. L.Baez, P.Attiyeh, M.Makohon-Moore, A.Zhang, L.Boyle, E. E.Ashby, C.Blaney, P.Patel, M.Zhang, Y.Dogan, A.Chung, D.Giralt, S.Lahoud, O. B.Peled, J.Scordo, M.Shah, G.Hassoun, H.Korde, N. S.Lesokhin, A. M.Lu, S.Mailankody, S.Shah, U. A.Smith, E.Hultcrantz, M. L.Ulaner, G.van Rhee, F.Morgan, G.Landgren, O.Papaemmanuil, E.Iacobuzio-Donahue, C. A.Maura, F.2020-02-26doi:10.1101/2020.02.25.963272Cold Spring Harbor Laboratory Press2020-02-26
https://biorxiv.org/cgi/content/short/842203v1?rss=1"
Ryser, M. D.Mallo, D.Hall, A.Hardman, T.King, L. M.Sorribes, I. C.Maley, C. C.Marks, J. R.Hwang, E. S.Shibata, D.2019-11-14doi:10.1101/842203Cold Spring Harbor Laboratory Press2019-11-14
https://biorxiv.org/cgi/content/short/2020.03.05.978965v1?rss=1"
Tollis, M.Schneider-Utaka, A. K.Maley, C. C.2020-03-05doi:10.1101/2020.03.05.978965Cold Spring Harbor Laboratory Press2020-03-05
https://biorxiv.org/cgi/content/short/812735v1?rss=1"
Narayanan, P. L.Raza, S. E. A.Hall, A.Marks, J. R.King, L.West, R. B.Hernandez, L.Dowsett, M.Gusterson, B.Maley, C.Hwang, S. E.Yuan, Y.2019-10-28doi:10.1101/812735Cold Spring Harbor Laboratory Press2019-10-28
https://biorxiv.org/cgi/content/short/843102v1?rss=1"
He, B.Gao, P.Ding, Y.-y.Chen, C.-h.Chen, G.Chen, C.Kim, H.Tasian, S. K.Hunger, S. P.Tan, K.2019-11-15doi:10.1101/843102Cold Spring Harbor Laboratory Press2019-11-15
https://biorxiv.org/cgi/content/short/2019.12.19.882050v1?rss=1"
Qiu, Q.Hu, P.Govek, K. W.Camara, P. G.Wu, H.2019-12-20doi:10.1101/2019.12.19.882050Cold Spring Harbor Laboratory Press2019-12-20
https://biorxiv.org/cgi/content/short/761429v1?rss=1"
Slyper, M.Porter, C. B. M.Ashenberg, O.Waldman, J.Drokhlyansky, E.Wakiro, I.Smillie, C.Smith-Rosario, G.Wu, J.Dionne, D.Vigneau, S.Jane-Valbuena, J.Napolitano, S.Su, M.-J.Patel, A. G.Karlstrom, A.Gritsch, S.Nomura, M.Waghray, A.Gohil, S. H.Tsankov, A. M.Jerby-Arnon, L.Cohen, O.Klughammer, J.Rosen, Y.Gould, J.Li, B.Nguyen, L.Wu, C. J.Izar, B.Haq, R.Hodi, F. S.Yoon, C. H.Hata, A. N.Baker, S. J.Suva, M. L.Bueno, R.Stover, E. H.Matulonis, U. A.Clay, M. R.Dyer, M. A.Collins, N. B.Wagle, N.Rotem, A.Johnson, B. E.2019-09-12doi:10.1101/761429Cold Spring Harbor Laboratory Press2019-09-12
https://biorxiv.org/cgi/content/short/2020.05.13.094268v1?rss=1"
Alon, S.Goodwin, D.Sinha, A.Wassie, A.Chen, F.Daugharthy, E.Bando, Y.Kajita, A.Xue, A.Marrett, K.Prior, R.Cui, Y.Payne, A.Yao, C.-C.Suk, H.-J.Wang, R.Yu, C.-C.Tillberg, P.Reginato, P.Pak, N.Liu, S.Punthambaker, S.Iyer, E.Kohman, R.Miller, J.Lein, E.Lako, A.Cullen, N.Rodig, S.Helvie, K.Abravanel, D.Wagle, N.Johnson, B.Klughammer, J.Slyper, M.Waldman, J.Jane-Valbuena, J.Rozenblatt-Rosen, O.Regev, A.Church, G.Marblestone, A.Boyden, E. S.2020-05-15doi:10.1101/2020.05.13.094268Cold Spring Harbor Laboratory Press2020-05-15
https://biorxiv.org/cgi/content/short/2020.04.01.020842v1?rss=1"
Ternes, L.Huang, G.Lanciault, C.Thibault, G.Riggers, R.Gray, J. W.Muschler, J.Chang, Y. H.2020-04-02doi:10.1101/2020.04.01.020842Cold Spring Harbor Laboratory Press2020-04-02
https://biorxiv.org/cgi/content/short/792770v1?rss=1"
Chang, Y. H.Chin, K.Thibault, G.Eng, J.Grace, L.Gray, J. W.2019-10-03doi:10.1101/792770Cold Spring Harbor Laboratory Press2019-10-03
https://biorxiv.org/cgi/content/short/689828v1?rss=1"
Schau, G. F.Burlingame, E. A.Thibault, G.Anekpuritanang, T.Wang, Y.Gray, J. W.Corless, C.Chang, Y. H.2019-07-02doi:10.1101/689828Cold Spring Harbor Laboratory Press2019-07-02
https://biorxiv.org/cgi/content/short/730309v1?rss=1"
Burlingame, E. A.McDonnell, M.Schau, G. F.Thibault, G.Lanciault, C.Morgan, T.Johnson, B. E.Corless, C.Gray, J. W.Chang, Y. H.2019-08-15doi:10.1101/730309Cold Spring Harbor Laboratory Press2019-08-15
https://biorxiv.org/cgi/content/short/675371v1?rss=1"
Riesterer, J. L.Lopez, C. S.Stempinski, E. S.Williams, M.Loftis, K.Stoltz, K.Thibault, G.Lanicault, C.Williams, T.Gray, J. W.2019-06-19doi:10.1101/675371Cold Spring Harbor Laboratory Press2019-06-19
https://biorxiv.org/cgi/content/short/2020.04.16.045617v1?rss=1"
Han, G.Sinjab, A.Treekitkarnmongkol, W.Brennan, P.Hara, K.Chang, K.Bogatenkova, E.Sanchez-Espiridion, B.Behrens, C.Gao, B.Girard, L.Zhang, J.Sepesi, B.Cascone, T.Byers, L.Gibbons, D. L.Chen, J.Moghaddam, S. J.Ostrin, E. J.Fujimoto, J.Shay, J.Heymach, J. V.Minna, J. D.Dubinett, S.Scheet, P. A.Wistuba, I. I.Hill, E.Telesco, S.Stevenson, C.Spira, A. E.Wang, L.Kadara, H.2020-04-17doi:10.1101/2020.04.16.045617Cold Spring Harbor Laboratory Press2020-04-17
https://biorxiv.org/cgi/content/short/743989v1?rss=1"
Schürch, C. M.Bhate, S. S.Barlow, G. L.Phillips, D. J.Noti, L.Zlobec, I.Chu, P.Black, S.Demeter, J.McIlwain, D. R.Samusik, N.Goltsev, Y.Nolan, G. P.2019-08-24doi:10.1101/743989Cold Spring Harbor Laboratory Press2019-08-24
https://biorxiv.org/cgi/content/short/790162v1?rss=1"
McKinley, E. T.Roland, J. T.Franklin, J. L.Macedonia, M. C.Vega, P. N.Shin, S.Coffey, R. J.Lau, K.2019-10-02doi:10.1101/790162Cold Spring Harbor Laboratory Press2019-10-02
https://biorxiv.org/cgi/content/short/2020.04.15.030874v1?rss=1"
Macedonia, M. C.Drewes, J. L.Markham, N. O.Simmons, A. J.Roland, J. T.Vega, P. N.Scurrah, C. R.Coffey, R. J.Shrubsole, M. J.Sears, C. L.Lau, K. S.2020-04-17doi:10.1101/2020.04.15.030874Cold Spring Harbor Laboratory Press2020-04-17
https://biorxiv.org/cgi/content/short/835488v1?rss=1"
Southard-Smith, A. N.Simmons, A. J.Chen, B.Jones, A. L.Ramirez-Solano, M. A.Vega, P. N.Scurrah, C. R.Zhao, Y.Brenan, M. J.Xuan, J.Porter, E. B.Chen, X.Brenan, C. J. H.Liu, Q.Quigley, L. N. M.Lau, K. N.2019-11-08doi:10.1101/835488Cold Spring Harbor Laboratory Press2019-11-08
https://biorxiv.org/cgi/content/short/776724v1?rss=1"
Banerjee, A.Herring, C. A.Kim, H.Chen, B.Simmons, A. J.Southard-Smith, A. N.White, J. R.Ramirez Solano, M. A.Scoville, E. A.Liu, Q.Washington, M. K.Lau, K. S.2019-09-20doi:10.1101/776724Cold Spring Harbor Laboratory Press2019-09-20
https://biorxiv.org/cgi/content/short/2020.12.01.406363v1?rss=1"
Chan, J. M.Quintanal-Villalonga, A.Gao, V.Xie, Y.Allaj, V.Chaudhary, O.Masilionis, I.Egger, J.Chow, A.Walle, T.Mattar, M.Yarlagadda, D. V.Wang, J. L.Offin, M.Ciampricotti, M.Bhanot, U. K.Lai, W. V.Bott, M. J.Jones, D. R.Ruiz, A.Hollmann, T.Poirier, J. T.Nawy, T.Mazutis, L.Sen, T.Pe'er, D.Rudin, C. M.2020-12-01doi:10.1101/2020.12.01.406363Cold Spring Harbor Laboratory Press2020-12-01
https://biorxiv.org/cgi/content/short/2020.12.06.413930v1?rss=1"
Chen, C.Yu, W.Alikarami, F.Qiu, Q.Chen, C.-h.Flournoy, J.Gao, P.Uzun, Y.Fang, L.Yu, Y.Zhu, Q.Wang, K.Libbrecht, C.Felmeister, A.Rozich, I.Ding, Y.-y.Hunger, S. P.Wu, H.Brown, P. A.Guest, E. M.Barrett, D. M.Bernt, K. M.Tan, K.2020-12-07doi:10.1101/2020.12.06.413930Cold Spring Harbor Laboratory Press2020-12-07
https://biorxiv.org/cgi/content/short/2020.12.03.408500v1?rss=1"
Johnson, B. E.Creason, A. L.Stommel, J. M.Keck, J.Parmar, S.Betts, C. B.Blucher, A.Boniface, C.Bucher, E.Burlingame, E. A.Chin, K.Eng, J.Feiler, H. S.Kolodzie, A.Kong, B.Labrie, M.Leyshock, P.Mitri, S.Patterson, J.Riesterer, J. L.Sivagnanam, S.Sudar, D.Thibault, G.Zheng, C.Nan, X.Heiser, L. M.Spellman, P. T.Thomas, G. V.Demir, E.Chang, Y. H.Coussens, L. M.Guimaraes, A. R.Corless, C.Goecks, J.Bergan, R.Mitri, Z.Mills, G. B.Gray, J. W.2020-12-03doi:10.1101/2020.12.03.408500Cold Spring Harbor Laboratory Press2020-12-03
https://biorxiv.org/cgi/content/short/2020.12.25.424416v1?rss=1"
Yanagawa, J.Tran, L. M.Fung, E.Wallace, W. D.Prosper, A. E.Fishbein, G. A.Shea, C.Hong, R.Liu, B.Salehi-Rad, R.Deng, J. Z.Gower, A.Campbell, J. D.Mazzilli, S. A.Beane, J.Kadara, H.Lenburg, M. E.Spira, A.Aberle, D. R.Krysan, K.Dubinett, S. M.2020-12-26doi:10.1101/2020.12.25.424416Cold Spring Harbor Laboratory Press2020-12-26
https://biorxiv.org/cgi/content/short/2021.01.11.426044v1?rss=1"
Chen, B.McKinley, E. T.Simmons, A. J.Ramirez, M. A.Zhu, X.Southard-Smith, A. N.Markham, N. O.Sheng, Q.Drewes, J.Xu, Y.Heiser, C. N.Zhou, Y.Revetta, F.Berry, L. D.Zheng, W.Washington, M. K.Cai, Q.Sears, C. L.Goldenring, J. R.Franklin, J. L.Vandekar, S.Roland, J. T.Su, T.Huh, W. J.Liu, Q.Coffey, R. J.Shrubsole, M. J.Lau, K.2021-01-13doi:10.1101/2021.01.11.426044Cold Spring Harbor Laboratory Press2021-01-13
https://biorxiv.org/cgi/content/short/2021.01.25.427845v1?rss=1"
Peng, T.Chen, G.Tan, K.2021-01-26doi:10.1101/2021.01.25.427845Cold Spring Harbor Laboratory Press2021-01-26
https://biorxiv.org/cgi/content/short/2021.03.15.435473v1?rss=1"
Schapiro, D.Sokolov, A.Yapp, C.Muhlich, J. L.Hess, J.Lin, J.-R.Chen, Y.-A.Nariya, M. K.Baker, G. J.Ruokonen, J.Maliga, Z.Jacobson, C. A.Farhi, S. L.Abbondanza, D.McKinley, E. T.Betts, C.Regev, A.Coffey, R. J.Coussens, L. M.Santagata, S.Sorger, P. K.2021-03-16doi:10.1101/2021.03.15.435473Cold Spring Harbor Laboratory Press2021-03-16
https://biorxiv.org/cgi/content/short/2020.11.16.385328v1?rss=1"
Hong, R.Koga, Y.Bandyadka, S.Leshchyk, A.Wang, Z.Alabdullatif, S.Wang, Y.Akavoor, V.Cao, X.Sarfraz, I.Jansen, F.Johnson, W. E.Yajima, M.Campbell, J. D.2020-11-17doi:10.1101/2020.11.16.385328Cold Spring Harbor Laboratory Press2020-11-17
https://biorxiv.org/cgi/content/short/2021.01.13.426413v1?rss=1"
Cui Zhou, D.Jayasinghe, R. G.Herndon, J. M.Storrs, E.Mo, C.-K.Wu, Y.Fulton, R. S.Wyczalkowski, M. A.Fronick, C. C.Fulton, L. A.Thammavong, L.Sato, K.Zhu, H.Sun, H.Wang, L.-B.Li, Y.Zuo, C.McMichael, J. F.Davies, S. R.Appelbaum, E. L.Robbins, K. J.Chasnoff, S. E.Yang, X.Liu, R.Reeb, A. N.Wendl, M. C.Oh, C.Serasanambati, M.Lal, P.Varghese, R.Mashl, J. R.Ponce, J.Terekhanova, N. V.Naser Al Deen, N.Yao, L.Wang, F.Chen, L.Schnaubelt, M.Puram, S. V.Kim, A. H.Song, S.-K.Shoghi, K. I.Ju, T.Hawkins, W. G.Chen, K.Ch2021-01-14doi:10.1101/2021.01.13.426413Cold Spring Harbor Laboratory Press2021-01-14
https://biorxiv.org/cgi/content/short/2021.01.05.425362v1?rss=1"
Risom, T.Glass, D. R.Liu, C. C.Rivero-Gutierrez, B.Baranski, A.McCaffrey, E. F.Greenwald, N. F.Kagel, A. C.Strand, S. H.Varma, S.Kong, A.Keren, L.Srivastava, S.Zhu, C.Khair, Z.Veis, D. J.Deschryver, K.Vennam, S.Maley, C.Hwang, E. S.Marks, J. R.Bendall, S. C.Colditz, G. A.West, R. B.Angelo, M.2021-01-06doi:10.1101/2021.01.05.425362Cold Spring Harbor Laboratory Press2021-01-06
https://biorxiv.org/cgi/content/short/2021.01.30.426796v1?rss=1"
Pelka, K.Hofree, M.Chen, J.Sarkizova, S.Pirl, J. D.Jorgji, V.Bejnood, A.Dionne, D.Ge, W. H.Xu, K. H.Chao, S. X.Zollinger, D. R.Lieb, D. J.Reeves, J. W.Fuhrman, C. A.Hoang, M. L.Delorey, T.Nguyen, L. T.Waldmann, J. A.Klapholz, M.Wakiro, I.Cohen, O.Smillie, C. S.Cuoco, M. S.Wu, J.Su, M.-j.Yeung, J.Vijaykumar, B.Magnuson, A. M.Asinovski, N.Moll, T.Goder-Reiser, M. N.Applebaum, A. S.Brais, L. K.DelloStritto, L. K.Denning, S. L.Phillips, S. T.Hill, E. K.Meehan, J. K.Frederick, D. T.Sharova, T.Kanodia, A.Todres, E. Z2021-02-01doi:10.1101/2021.01.30.426796Cold Spring Harbor Laboratory Press2021-02-01
https://biorxiv.org/cgi/content/short/2021.03.31.437984v1?rss=1"
Lin, J.-R.Wang, S.Coy, S.Tyler, M. A.Yapp, C.Chen, Y.-A.Heiser, C. N.Lau, K.Santagata, S.Sorger, P. K.2021-04-02doi:10.1101/2021.03.31.437984Cold Spring Harbor Laboratory Press2021-04-02
https://biorxiv.org/cgi/content/short/2020.10.08.332288v1?rss=1"
Heiser, C. N.Wang, V. M.Chen, B.Hughey, J. J.Lau, K. S.2020-10-09doi:10.1101/2020.10.08.332288Cold Spring Harbor Laboratory Press2020-10-09
https://biorxiv.org/cgi/content/short/2021.03.24.436532v1?rss=1"
Becker, W. R.Nevins, S. A.Chen, D. C.Chiu, R.Horning, A.Laquindanum, R.Mills, M.Chaib, H.Ladabaum, U.Longacre, T.Shen, J.Esplin, E. D.Kundaje, A.Ford, J. M.Curtis, C.Snyder, M. P.Greenleaf, W. J.2021-03-25doi:10.1101/2021.03.24.436532Cold Spring Harbor Laboratory Press2021-03-25
https://biorxiv.org/cgi/content/short/2021.05.11.443641v1?rss=1"
Nachmanson, D.Officer, A.Mori, H.Gordon, J.Evans, M. F.Steward, J.Yao, H.O'Keefe, T.Hasteh, F.Stein, G. S.Jepsen, K.Weaver, D. L.Hirst, G.Sprague, B. L.Esserman, L. J.Borowsky, A. D.Stein, J. L.Harismendy, O.2021-05-12doi:10.1101/2021.05.11.443641Cold Spring Harbor Laboratory Press2021-05-12
https://biorxiv.org/cgi/content/short/2021.05.23.445310v1?rss=1"
Nirmal, A. J.Maliga, Z.Vallius, T.Quattrochi, B.Chen, A. A.Jacobson, C. A.Pelletier, R. J.Yapp, C.Arias-Camison, R.Chen, Y.-A.Lian, C. G.Murphy, G. F.Santagata, S.Sorger, P. K.2021-05-23doi:10.1101/2021.05.23.445310Cold Spring Harbor Laboratory Press2021-05-23
https://biorxiv.org/cgi/content/short/2021.04.20.440625v1?rss=1"
Muhlich, J. L.Chen, Y.-A.Russell, D. P. W.Sorger, P. K.2021-04-21doi:10.1101/2021.04.20.440625Cold Spring Harbor Laboratory Press2021-04-21
https://biorxiv.org/cgi/content/short/2021.04.02.438285v1?rss=1"
Yapp, C.Novikov, E.Jang, W.-D.Chen, Y.-A.Cicconet, M.Maliga, Z.Jacobson, C. A.Wei, D.Santagata, S.Pfister, H.Sorger, P. K.2021-04-04doi:10.1101/2021.04.02.438285Cold Spring Harbor Laboratory Press2021-04-04
https://biorxiv.org/cgi/content/short/2021.06.16.448585v1?rss=1"
Strand, S. H.Rivero-Gutierrez, B.Houlahan, K. E.Seoane, J. A.King, L.Risom, T.Simpson, L. A.Vennam, S.Khan, A.Cisneros, L.Hardman, T.Harmon, B.Couch, F.Gallagher, K.Kilgore, M.Rocque, G. B.DeMichele, A.King, T.McAuliffe, P.Nangia, J.Lee, J.Tseng, J.Storniolo, A. M.Thompson, A.Gupta, G.Burns, R.Veis, D. J.DeSchryver, K.Zhu, C.Matusiak, M.Wang, J.Zhu, S. X.Tappenden, J.Ding, D. Y.Zhang, D.Luo, J.Jiang, S.Varma, S.Anderson, L.Straub, C.Srivastava, S.Curtis, C.Tibshirani, R.Angelo, R. M.Hall, A.Owzar, K.Pol2021-06-16doi:10.1101/2021.06.16.448585Cold Spring Harbor Laboratory Press2021-06-16
https://biorxiv.org/cgi/content/short/2022.08.25.505257v1?rss=1"
Chung, H.Melnikov, A.McCabe, C.Drokhlyansky, E.Van Wittenberghe, N.Magee, E. M.Waldman, J.Spira, A.Chen, F.Mazzilli, S.Rozenblatt-Rosen, O.Regev, A.2022-08-25doi:10.1101/2022.08.25.505257Cold Spring Harbor Laboratory Press2022-08-25
https://biorxiv.org/cgi/content/short/2022.10.14.512148v1?rss=1"
Semaan, A.Bernard, V.Wong, J.Makino, Y.Swartzlander, D.Rajapakshe, K. I.Lee, J.Officer, A.Schmidt, C. M.Wu, H. H.Scaife, C. L.Affolter, K. E.Nachmanson, D.Firpo, M. A.Yip-Schneider, M.Lowy, A. M.Harismendy, O.Sen, S.Maitra, A. A.Jakubek, Y. A.Guerrero, P. A.2022-10-18doi:10.1101/2022.10.14.512148Cold Spring Harbor Laboratory Press2022-10-18
https://biorxiv.org/cgi/content/short/2022.11.25.517982v1?rss=1"
Zhang, D. K.Segerstolpe, A.Slyper, M.Waldman, J.Murray, E.Cohen, O.Ashenberg, O.Abravanel, D.Jane-Valbuena, J.Mages, S.Lako, A.Helvie, K.Rozenblatt-Rosen, O.Rodig, S.Chen, F.Wagle, N.Regev, A.Klughammer, J.2022-11-27doi:10.1101/2022.11.25.517982Cold Spring Harbor Laboratory Press2022-11-27
https://biorxiv.org/cgi/content/short/2023.02.23.529809v1?rss=1"
Sims, Z.Strgar, L.Thirumalaisamy, D.Heussner, R.Thibault, G.Chang, Y. H.2023-02-24doi:10.1101/2023.02.23.529809Cold Spring Harbor Laboratory Press2023-02-24
https://biorxiv.org/cgi/content/short/2023.03.09.530832v1?rss=1"
Heiser, C. N.Simmons, A. J.Revetta, F.McKinley, E. T.Ramirez-Solano, M. A.Wang, J.Shao, J.Ayers, G. D.Wang, Y.Glass, S. E.Kaur, H.Rolong, A.Chen, B.Vega, P. N.Drewes, J. L.Saleh, N.Vandekar, S.Jones, A. L.Washington, M. K.Roland, J. T.Sears, C. L.Liu, Q.Shrubsole, M. J.Coffey, R. J.Lau, K. S.2023-03-12doi:10.1101/2023.03.09.530832Cold Spring Harbor Laboratory Press2023-03-12
https://biorxiv.org/cgi/content/short/2023.03.15.532870v1?rss=1"
Houlahan, K. E.Khan, A.Greenwald, N. F.West, R. B.Angelo, M.Curtis, C.2023-03-16doi:10.1101/2023.03.15.532870Cold Spring Harbor Laboratory Press2023-03-16
https://biorxiv.org/cgi/content/short/2023.03.17.533041v1?rss=1"
Remsik, J.Tong, X.Kunes, R. Z.Li, M. J.Osman, A.Chabot, K.Sener, U.Wilcox, J. A.Isakov, D.Snyder, J.Bale, T.Chaligne, R.Pe'er, D. D.Boire, A.2023-03-20doi:10.1101/2023.03.17.533041Cold Spring Harbor Laboratory Press2023-03-20
https://biorxiv.org/cgi/content/short/2023.03.21.533680v1?rss=1"
Comiter, C.Vaishnav, E. D.Ciapmricotti, M.Li, B.Yang, Y.Rodig, S. J.Turner, M.Pfaff, K. L.Jane-Valbuena, J.Slyper, M.Waldman, J.Vigneau, S.Wu, J.Blosser, T. R.Segerstolpe, A.Abravanel, D.Wagle, N.Zhuang, X.Rudin, C. M.Klughammer, J.Rozenblatt-Rosen, O.Kobayash-Kirschvink, K. J.Shu, J.Regev, A.2023-03-23doi:10.1101/2023.03.21.533680Cold Spring Harbor Laboratory Press2023-03-23
https://biorxiv.org/cgi/content/short/2023.02.15.528365v1?rss=1"
Zhang, S.Kim, K.-B.Huang, Y.Kim, D.-W.Kim, B.Ko, K.-P.Zou, G.Zhang, J.Jun, S.Kirk, N. A.Hwang, Y. E.Ban, Y. H.Chan, J. M.Rudin, C. M.PARK, K.-S.Park, J.-I.2023-02-15doi:10.1101/2023.02.15.528365Cold Spring Harbor Laboratory Press2023-02-15
https://biorxiv.org/cgi/content/short/2023.07.21.548450v1?rss=1"
Prabhakaran, S.Yapp, C.Baker, G. J.Beyer, J.Chang, Y. H.Creason, A. L.Krueger, R.Muhlich, J.Patterson, N. H.Sidak, K.Sudar, D.Taylor, A. J.Ternes, L.Troidl, J.Yubin, X.Sokolov, A.Tyson, D. R.Participants of the Cell Imaging Hackathon 2022,2023-07-24doi:10.1101/2023.07.21.548450Cold Spring Harbor Laboratory Press2023-07-24
https://biorxiv.org/cgi/content/short/2023.07.31.551378v1?rss=1"
Kapsetaki, S. E.Basile, A. J.Compton, Z. T.Rupp, S. M.Duke, E. G.Boddy, A. M.Harrison, T. M.Sweazea, K. L.Maley, C. C.2023-08-02doi:10.1101/2023.07.31.551378Cold Spring Harbor Laboratory Press2023-08-02
https://biorxiv.org/cgi/content/short/2023.05.10.540265v1?rss=1"
Sims, Z.Chang, Y. H.2023-05-13doi:10.1101/2023.05.10.540265Cold Spring Harbor Laboratory Press2023-05-13
https://biorxiv.org/cgi/content/short/2023.05.05.539614v1?rss=1"
Zhang, Z.Mathew, D.Lim, T.Huang, S.Wherry, E. J.Minn, A. J.Ma, Z.Zhang, N. R.2023-05-08doi:10.1101/2023.05.05.539614Cold Spring Harbor Laboratory Press2023-05-08
https://biorxiv.org/cgi/content/short/2023.08.18.553854v1?rss=1"
Eksi, S. E.Ak, C.Sayar, Z.Thibault, G.Burlingame, E.Eng, J.Chitsazan, A.Adey, A.Boniface, C.Spellman, P. T.Thomas, G. V.Kopp, R.Demir, E.Chang, Y. H.Stavrinides, V.2023-08-21doi:10.1101/2023.08.18.553854Cold Spring Harbor Laboratory Press2023-08-21
https://biorxiv.org/cgi/content/short/2023.08.24.554733v1?rss=1"
50,000) when using conventional enumeration methods. On the other hand, our proposed approach is unbiased to ROI size. The SVM classifier trained on the {beta}-VAE encodings achieved an F1 score of 0.80, matching the average performance of annotators. Our pipeline enables researchers to explore the role of CHCs in cancer progression and assess their potential as a clinical biomarker for metastasis. Further, we demonstrate that the pipeline can identify discrete cellular phenotypes among PBMCs, highlighting its utility beyond CHCs.
]]>Anderson, A.Theison, H.Baik, J.Gibbs, S.Wong, M. H.Chang, Y. H.2023-08-26doi:10.1101/2023.08.24.554733Cold Spring Harbor Laboratory Press2023-08-26
https://biorxiv.org/cgi/content/short/2023.09.27.557464v1?rss=1"
Creason, A. L.Egger, J.Watson, C.Sivagnanam, S.Chin, K.MacPherson, K.Lin, J.-R.Chen, Y.-A.Johnson, B. E.Feiler, H. S.Galipeau, D.Navin, N. E.Demir, E.Chang, Y. H.Corless, C. L.Mitri, Z. I.Thomas, G.Sorger, P. K.Adey, A. C.Coussens, L. M.Gray, J. W.Mills, G. B.Goecks, J.2023-09-29doi:10.1101/2023.09.27.557464Cold Spring Harbor Laboratory Press2023-09-29
https://biorxiv.org/cgi/content/short/2023.09.28.560000v1?rss=1"
Strand, S. H.Houlahan, K. E.Branch, V.Lynch, T.Harmon, B.Couch, F.Gallagher, K.Kilgore, M.Wei, S.DeMichele, A.King, T.McAuliffe, P.Curtis, C.Owzar, K.Marks, J. R.Colditz, G. A.Hwang, E. S.West, R. B.2023-10-02doi:10.1101/2023.09.28.560000Cold Spring Harbor Laboratory Press2023-10-02
https://biorxiv.org/cgi/content/short/2023.03.06.531314v1?rss=1"
Wang, Y.Sarfraz, I.Teh, W. K.Sokolov, A.Herb, B. R.Creasy, H. H.Virshup, I.Dries, R.Degatano, K.Mahurkar, A.Schnell, D. J.Madrigal, P.Hilton, J.Gehlenborg, N.Tickle, T.Campbell, J. D.2023-03-07doi:10.1101/2023.03.06.531314Cold Spring Harbor Laboratory Press2023-03-07
https://biorxiv.org/cgi/content/short/2023.12.18.572260v1?rss=1"
Islam, M.Yang, Y.Simmons, A. J.Shah, V. M.Pavan, M. K.Xu, Y.Tasneem, N.Chen, Z.Trinh, L. T.Molina, P.Ramirez-Solano, M. A.Sadien, I.Dou, J.Chen, K.Magnuson, M. A.Rathmell, J.Macara, I. G.Winton, D. J.Liu, Q.Zafar, H.Kalhor, R.Church, G. M.Shrubsole, M. J.Coffey, R. J.Lau, K.2023-12-19doi:10.1101/2023.12.18.572260Cold Spring Harbor Laboratory Press2023-12-19
https://biorxiv.org/cgi/content/short/2023.11.10.566670v1?rss=1"
Yapp, C.Nirmal, A. J.Zhou, F. Y.Maliga, Z.Montero Llopis, P.Murphy, G. F.Lian, C.Danuser, G.Santagata, S.Sorger, P. K.2023-11-15doi:10.1101/2023.11.10.566670Cold Spring Harbor Laboratory Press2023-11-15
https://biorxiv.org/cgi/content/short/2023.11.07.566063v1?rss=1"
Coy, S.Cheng, B.Lee, J. S.Rashid, R.Browning, L.Xu, Y.Chakrabarty, S. S.Yapp, C.Chan, S.Tefft, J. B.Spektor, A.Ligon, K. L.Baker, G. J.Pellman, D.Sorger, P. K.Santagata, S.2023-11-11doi:10.1101/2023.11.07.566063Cold Spring Harbor Laboratory Press2023-11-11
https://biorxiv.org/cgi/content/short/2023.10.31.565031v1?rss=1"
Iglesia, M. D.Jayasinghe, R. G.Chen, S.Terekhanova, N. V.Herndon, J. M.Storrs, E.Karpova, A.Zhou, D. C.Naser Al Deen, N.Shinkle, A. T.Lu, R. J.-H.Caravan, W.Houston, A.Zhao, Y.Sato, K.Lal, P.Street, C.Rodrigues, F. M.Southard-Smith, A. N.Targino da Costa, A. L. N.Zhu, H.Mo, C.-K.Crowson, L.Fulton, R. S.Wyczalkowski, M. A.Fronick, C. C.Fulton, L. A.Sun, H.Davies, S. R.Appelbaum, E. L.Chasnoff, S. E.Carmody, M.Brooks, C.Liu, R.Wendl, M. C.Oh, C.Bender, D.Cruchaga, C.Harari, O.Bredemeyer, A.Lavine, K.Bose, R.Marge2023-11-02doi:10.1101/2023.10.31.565031Cold Spring Harbor Laboratory Press2023-11-02
https://biorxiv.org/cgi/content/short/2023.12.01.569676v1?rss=1"
5cm in size with at least one additional high-risk feature: young age (<45 years), high nuclear grade, hormone receptor negativity, HER2 positivity, the presence of comedonecrosis, or a palpable mass. The tumor immune microenvironment was characterized using multiplex immunofluorescence to identify immune cells and their spatial relationships within the ducts and stroma. Gene copy number analysis and whole exome DNA sequencing identified the mutational burden and driver mutations, and quantitative whole-transcriptome/gene expression analyses were performed. There was no association between the percent of the DCIS genome characterized by copy number variants (CNAs) and recurrence events (DCIS or invasive). Mutations, especially missense mutations, in the breast cancer driver genes PIK3CA and TP53 were common in this high-risk DCIS cohort (47% of evaluated lesions). Tumor infiltrating lymphocyte (TIL) density was higher in DCIS lesions with TP53 mutations (p=0.0079) compared to wildtype lesions, but not in lesions with PIK3CA mutations (p=0.44). Immune infiltrates were negatively associated with hormone receptor status and positively associated with HER2 expression. High levels of CD3+CD8-T cells were associated with good outcomes with respect to any subsequent recurrence (DCIS or invasive cancer), whereas high levels of CD3+Foxp3+ Treg cells were associated with poor outcomes. Spatial proximity analyses of immune cells and tumor cells demonstrated that close proximity of T cells with tumor cells was associated with good outcomes with respect to any recurrence as well as invasive recurrences. Interestingly, we found that myoepithelial continuity (distance between myoepithelial cells surrounding the involved ducts) was significantly lower in DCIS lesions compared to normal tissue (p=0.0002) or to atypical ductal hyperplasia (p=0.011). Gene set enrichment analysis identified several immune pathways associated with low myoepithelial continuity and a low myoepithelial continuity score was associated with better outcomes, suggesting that gaps in the myoepithelial layer may allow access/interactions between immune infiltrates and tumor cells. Our study demonstrates the immune microenvironment of DCIS, in particular the spatial proximity of tumor cells and T cells, and myoepithelial continuity are important determinants for progression of disease.
]]>Glencer, A.Ramalingam, K.Schindler, N.Mori, H.Ghule, P.Lee, K. C.Nachmanson, D.Officer, A.Harismendy, O.Stein, J. L.Stein, G.Weaver, D.Yau, C.Hirst, G. L.Campbell, M. J.Esserman, L. J.Borowsky, A. D.2023-12-04doi:10.1101/2023.12.01.569676Cold Spring Harbor Laboratory Press2023-12-04
https://biorxiv.org/cgi/content/short/2024.03.06.583588v1?rss=1"
Sussman, J. H.Oldridge, D. A.Yu, W.Chen, C.-H.Zellmer, A. M.Rong, J.Parvaresh-Rizi, A.Thadi, A.Xu, J.Bandyopadhyay, S.Sun, Y.Wu, D.Hunter, C. E.Brosius, S.Ahn, K. J.Baxter, A. E.Koptyra, M. P.Vanguri, R.McGrory, S.Resnick, A. C.Storm, P. B.Amankulor, N. M.Santi, M.Viaene, A. N.Zhang, N.De Raedt, T.Cole, K.Tan, K.2024-03-08doi:10.1101/2024.03.06.583588Cold Spring Harbor Laboratory Press2024-03-08
https://biorxiv.org/cgi/content/short/2023.06.28.546977v1?rss=1"
Zhao, W.Kepecs, B.Mahadevan, N. R.Segerstolpe, A.Weirather, J. L.Besson, N. R.Giotti, B.Soong, B. Y.Li, C.Vigneau, S.Slyper, M.Wakiro, I.Jane-Valbuena, J.Ashenberg, O.Rotem, A.Bueno, R.Rozenblatt-Rosen, O.Pfaff, K.Rodig, S.Hata, A. N.Regev, A.Johnson, B. E.Tsankov, A. M.2023-06-29doi:10.1101/2023.06.28.546977Cold Spring Harbor Laboratory Press2023-06-29
https://biorxiv.org/cgi/content/short/2024.01.07.574538v1?rss=1"
Patel, A. G.Ashenberg, O.Collins, N. B.Segerstolpe, A.Jiang, S.Slyper, M.Huang, X.Caraccio, C.Jin, H.Sheppard, H.Xu, K.Chang, T.-C.Orr, B. A.Shirinifard, A.Chapple, R. H.Shen, A.Clay, M. R.Tatevossian, R. G.Reilly, C.Patel, J.Lupo, M.Cline, C.Dionne, D.Porter, C. B. M.Waldman, J.Bai, Y.Zhu, B.Barrera, I.Murray, E.Vigneau, S.Napolitano, S.Wakiro, I.Wu, J.Grimaldi, G.Dellostritto, L.Helvie, K.Rotem, A.Lako, A.Cullen, N.Pfaff, K. L.Karlstrom, A.Jane-Valbuena, J.Todres, E.Thorner, A.Geeleher, P.Rodig, S. J.2024-01-07doi:10.1101/2024.01.07.574538Cold Spring Harbor Laboratory Press2024-01-07