bioRxiv Channel: Human Pangenome Reference Consortium (HPRC)
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This feed contains articles for bioRxiv Channel "Human Pangenome Reference Consortium (HPRC)"
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A Draft Human Pangenome Reference
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https://biorxiv.org/cgi/content/short/2022.07.09.499321v1?rss=1"
Liao, W.-W.Asri, M.Ebler, J.Doerr, D.Haukness, M.Hickey, G.Lu, S.Lucas, J. K.Monlong, J.Abel, H. J.Buonaiuto, S.Chang, X. H.Cheng, H.Chu, J.Colonna, V.Eizenga, J. M.Feng, X.Fischer, C.Fulton, R. S.Garg, S.Groza, C.Guarracino, A.Harvey, W. T.Heumos, S.Howe, K.Jain, M.Lu, T.-Y.Markello, C.Martin, F. J.Mitchell, M. W.Munson, K. M.Mwaniki, M. N.Novak, A. M.Olsen, H. E.Pesout, T.Porubsky, D.Prins, P.Sibbesen, J. A.Tomlinson, C.Villani, F.Vollger, M. R.Human Pangenome Reference Consortium,Bourque, G.Chaisson, M.2022-07-09doi:10.1101/2022.07.09.499321Cold Spring Harbor Laboratory Press2022-07-09
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StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps
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https://biorxiv.org/cgi/content/short/2021.08.19.457003v1?rss=1"
Vollger, M. R.Kerpedjiev, P.Phillippy, A. M.Eichler, E. E.2021-08-21doi:10.1101/2021.08.19.457003Cold Spring Harbor Laboratory Press2021-08-21
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Complete genomic and epigenetic maps of human centromeres
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https://biorxiv.org/cgi/content/short/2021.07.12.452052v1?rss=1"
Altemose, N.Logsdon, G.Bzikadze, A. V.Sidhwani, P.Langley, S. A.Caldas, G. V.Hoyt, S. J.Uralsky, L.Ryabov, F. D.Shew, C.Sauria, M. E. G.Borchers, M.Gershman, A.Mikheenko, A.Shepelev, V. A.Dvorkina, T.Kunyavskaya, O.Vollger, M. R.Rhie, A.McCartney, A. M.Asri, M.Lorig-Roach, R.Shafin, K.Aganezov, S.Olson, D.Gomes de Lima, L.Potapova, T.Hartley, G. A.Haukness, M.Kerpedjiev, P.Gusev, F.Tigyi, K.Brooks, S. Y.Young, A.Nurk, S.Koren, S.Salama, S.Paten, B.Rogaev, E. I.Streets, A. M.Karpen, G. H.Dernburg, A.Sullivan, B.2021-07-13doi:10.1101/2021.07.12.452052Cold Spring Harbor Laboratory Press2021-07-13
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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
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https://biorxiv.org/cgi/content/short/2021.07.02.450803v1?rss=1"
Mc Cartney, A. M.Shafin, K.Alonge, M.Bzikadze, A. V.Formenti, G.Fungtammasan, A.Howe, K.Jain, C.Koren, S.Logsdon, G. A.Miga, K. H.Mikheenko, A.Paten, B.Shumate, A.Soto, D. C.Sovic, I.Wood, J. M.Zook, J. M.Phillippy, A. M.Rhie, A.2021-07-02doi:10.1101/2021.07.02.450803Cold Spring Harbor Laboratory Press2021-07-02
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GBZ File Format for Pangenome Graphs
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https://biorxiv.org/cgi/content/short/2022.07.12.499787v1?rss=1"
Siren, J.Paten, B.2022-07-14doi:10.1101/2022.07.12.499787Cold Spring Harbor Laboratory Press2022-07-14
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A complete reference genome improves analysis of human genetic variation
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https://biorxiv.org/cgi/content/short/2021.07.12.452063v1?rss=1"
Aganezov, S.Yan, S. M.Soto, D. C.Kirsche, M.Zarate, S.Avdeyev, P.Taylor, D. J.Shafin, K.Shumate, A.Xiao, C.Wagner, J.McDaniel, J.Olson, N. D.Sauria, M. E. G.Vollger, M. R.Rhie, A.Meredith, M.Martin, S.Lee, J.Koren, S.Rosenfeld, J.Paten, B.Layer, R.Chin, C.-S.Sedlazeck, F. J.Hansen, N. F.Miller, D. E.Phillippy, A. M.Miga, K. H.McCoy, R. C.Dennis, M. Y.Zook, J. M.Schatz, M. C.2021-07-13doi:10.1101/2021.07.12.452063Cold Spring Harbor Laboratory Press2021-07-13
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Increased mutation rate and interlocus gene conversion within human segmental duplications.
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https://biorxiv.org/cgi/content/short/2022.07.06.498021v1?rss=1"
7 Mbp of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of ~800 protein-coding genes. The latter includes 171 genes that have "relocated" on average 1.61 Mbp in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are evolutionarily older when compared to unique sequences with most of this signal originating from putative IGC loci. SNVs within SDs, however, also exhibit a distinct mutational spectrum where there is a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts. In addition, we observe a 7.6% reduction in the frequency of CpG associated mutations when compared to unique DNA. We hypothesize that these distinct mutational properties help to maintain an overall higher GC content of SD DNA when compared to unique DNA, and we show that these GC-favoring mutational events are likely driven by GC-biased conversion between paralogous sequences.
]]>Vollger, M. R.DeWitt, W. S.Dishuck, P. C.Harvey, W. T.Guitart, X.Goldberg, M. E.Rozanski, A.Lucas, J.Asri, M.The Human Pangenome Reference Consortium,Munson, K. M.Lewis, A. P.Hoekzema, K.Logsdon, G. A.Porubsky, D.Paten, B.Harris, K.Hsieh, P.Eichler, E. E.2022-07-07doi:10.1101/2022.07.06.498021Cold Spring Harbor Laboratory Press2022-07-07
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The complete sequence of a human genome
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https://biorxiv.org/cgi/content/short/2021.05.26.445798v1?rss=1"
Nurk, S.Koren, S.Rhie, A.Rautiainen, M.Bzikadze, A. V.Mikheenko, A.Vollger, M. R.Altemose, N.Uralsky, L.Gershman, A.Aganezov, S.Hoyt, S. J.Diekhans, M.Logsdon, G. A.Alonge, M.Antonarakis, S. E.Borchers, M.Bouffard, G. G.Brooks, S. Y.Caldas, G. V.Cheng, H.Chin, C.-S.Chow, W.de Lima, L. G.Dishuck, P. C.Durbin, R.Dvorkina, T.Fiddes, I. T.Formenti, G.Fulton, R. S.Fungtammasan, A.Garrison, E.Grady, P. G. S.Graves-Lindsay, T. A.Hall, I. M.Hansen, N. F.Hartley, G. A.Haukness, M.Howe, K.Hunkapiller, M. W.Jain, C.Jain, M.2021-05-27doi:10.1101/2021.05.26.445798Cold Spring Harbor Laboratory Press2021-05-27
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Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
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https://biorxiv.org/cgi/content/short/2022.01.11.475254v1?rss=1"
Tan, K.-T.Slevin, M.Meyerson, M.Li, H.2022-01-12doi:10.1101/2022.01.11.475254Cold Spring Harbor Laboratory Press2022-01-12
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Gaps and complex structurally variant loci in phased genome assemblies
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https://biorxiv.org/cgi/content/short/2022.07.06.498874v1?rss=1"
Porubsky, D.Vollger, M. R.Harvey, W. T.Rozanski, A. N.Ebert, P.Hickey, G.Hasenfeld, P.Sanders, A. D.Stober, C.Human Pangenome Reference Consortium (HPRC),Korbel, J. O.Paten, B.Marschall, T.Eichler, E. E.2022-07-06doi:10.1101/2022.07.06.498874Cold Spring Harbor Laboratory Press2022-07-06
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CoLoRd: Compressing long reads
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https://biorxiv.org/cgi/content/short/2021.07.17.452767v1?rss=1"
Kokot, M.Gudys, A.Li, H.Deorowicz, S.2021-07-19doi:10.1101/2021.07.17.452767Cold Spring Harbor Laboratory Press2021-07-19
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A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis
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https://biorxiv.org/cgi/content/short/2021.11.24.469912v1?rss=1"
Markello, C.Huang, C.Rodriguez, A.Carroll, A.Chang, P.-C.Eizenga, J.Markello, T.Haussler, D.Paten, B.2021-11-25doi:10.1101/2021.11.24.469912Cold Spring Harbor Laboratory Press2021-11-25
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Succinct dynamic variation graphs
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https://biorxiv.org/cgi/content/short/2020.04.23.056317v1?rss=1"
Eizenga, J. M.Novak, A. M.Kobayashi, E.Villani, F.Cisar, C.Heumos, S.Hickey, G.Colonna, V.Paten, B.Garrison, E.2020-04-25doi:10.1101/2020.04.23.056317Cold Spring Harbor Laboratory Press2020-04-25
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Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling
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https://biorxiv.org/cgi/content/short/2021.12.16.472988v1?rss=1"
Bailey, A. D.Talkish, J.Ding, H.Igel, H.Duran, A.Mantripragada, S.Paten, B.Ares, M.2021-12-17doi:10.1101/2021.12.16.472988Cold Spring Harbor Laboratory Press2021-12-17
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Merfin: improved variant filtering and polishing via k-mer validation
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https://biorxiv.org/cgi/content/short/2021.07.16.452324v1?rss=1"
Formenti, G.Rhie, A.Walenz, B. P.Thibaud-Nissen, F.Shafin, K.Koren, S.Myers, E. W.Jarvis, E. D.Phillippy, A. M.2021-07-18doi:10.1101/2021.07.16.452324Cold Spring Harbor Laboratory Press2021-07-18
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Higher rates of processed pseudogene acquisition in humans and three great apes revealed by long read assemblies
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https://biorxiv.org/cgi/content/short/2020.06.07.139212v1?rss=1"
Feng, X.Li, H.2020-06-08doi:10.1101/2020.06.07.139212Cold Spring Harbor Laboratory Press2020-06-08
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Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures
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https://biorxiv.org/cgi/content/short/2020.11.30.404947v1?rss=1"
DING, H.Anastopoulos, I.Bailey, A. D.Paten, B.Stuart, J.2020-12-02doi:10.1101/2020.11.30.404947Cold Spring Harbor Laboratory Press2020-12-02
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Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes
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https://biorxiv.org/cgi/content/short/2021.06.07.444885v1?rss=1"
Wagner, J.Olson, N. D.Harris, L.McDaniel, J.Cheng, H.Fungtammasan, A.Hwang, Y.-C.Gupta, R.Wenger, A. M.Rowell, W. J.Khan, Z. M.Farek, J.Zhu, Y.Pisupati, A.Mahmoud, M.Xiao, C.Yoo, B.Sahraeian, S. M. E.Miller, D. E.Jaspez, D.Lorenzo-Salazar, J. M.Munoz-Barrera, A.Rubio-Rodriguez, L. A.Flores, C.Narzisi, G.Evani, U. S.Clarke, W. E.Lee, J.Mason, C. E.Lincoln, S. E.Miga, K. H.Ebbert, M. T.Shumate, A.Li, H.Chin, C.-S.Zook, J. M.Sedlazeck, F. J.2021-06-07doi:10.1101/2021.06.07.444885Cold Spring Harbor Laboratory Press2021-06-07
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Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
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https://biorxiv.org/cgi/content/short/2021.03.26.437240v1?rss=1"
Sibbesen, J. A.Eizenga, J. M.Novak, A. M.Siren, J.Chang, X.Garrison, E.Paten, B.2021-03-28doi:10.1101/2021.03.26.437240Cold Spring Harbor Laboratory Press2021-03-28
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Segmental duplications and their variation in a complete human genome
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https://biorxiv.org/cgi/content/short/2021.05.26.445678v1?rss=1"
Vollger, M. R.Guitart, X.Dishuck, P. C.Mercuri, L.Harvey, W. T.Gershman, A.Diekhans, M.Sulovari, A.Munson, K. M.Lewis, A. M.Hoekzema, K.Porubsky, D.Li, R.Nurk, S.Koren, S.Miga, K. H.Phillippy, A. M.Timp, W.Ventura, M.Eichler, E. E.2021-05-26doi:10.1101/2021.05.26.445678Cold Spring Harbor Laboratory Press2021-05-26
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The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution
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https://biorxiv.org/cgi/content/short/2022.05.26.493621v1?rss=1"
Nair, S.Barrett, A.Li, D.Raney, B. J.Lee, B. T.Kerpedjiev, P.Ramalingam, V.Pampari, A.Lekschas, F.Wang, T.Haeussler, M.Kundaje, A.2022-05-28doi:10.1101/2022.05.26.493621Cold Spring Harbor Laboratory Press2022-05-28
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Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks
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https://biorxiv.org/cgi/content/short/2021.03.04.433952v1?rss=1"
Shafin, K.Pesout, T.Chang, P.-C.Nattestad, M.Kolesnikov, A.Goel, S.Baid, G.Eizenga, J. M.Miga, K. H.Carnevali, P.Jain, M.Carroll, A.Paten, B.2021-03-05doi:10.1101/2021.03.04.433952Cold Spring Harbor Laboratory Press2021-03-05
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Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis
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https://biorxiv.org/cgi/content/short/2023.01.09.523347v1?rss=1"
He, S.Shao, W.Chen, S.Wang, T.Gibson, M.2023-01-10doi:10.1101/2023.01.09.523347Cold Spring Harbor Laboratory Press2023-01-10
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T1K: efficient and accurate KIR and HLA genotyping with next-generation sequencing data
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https://biorxiv.org/cgi/content/short/2022.10.26.513955v1?rss=1"
Song, L.Bai, G.Liu, X. S.Li, B.Li, H.2022-10-27doi:10.1101/2022.10.26.513955Cold Spring Harbor Laboratory Press2022-10-27
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AGC: Compact representation of assembled genomes
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https://biorxiv.org/cgi/content/short/2022.04.07.487441v1?rss=1"
Deorowicz, S.Danek, A.Li, H.2022-04-07doi:10.1101/2022.04.07.487441Cold Spring Harbor Laboratory Press2022-04-07
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Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit
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https://biorxiv.org/cgi/content/short/2020.12.04.412486v1?rss=1"
Siren, J.Monlong, J.Chang, X.Novak, A. M.Eizenga, J. M.Markello, C.Sibbesen, J. A.Hickey, G.Chang, P.-C.Carroll, A.Haussler, D.Garrison, E.Paten, B.2020-12-06doi:10.1101/2020.12.04.412486Cold Spring Harbor Laboratory Press2020-12-06
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Constructing founder sets under allelic and non-allelic homologous recombination
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https://biorxiv.org/cgi/content/short/2022.05.27.493721v1?rss=1"
Bonnet, K.Marschall, T.Doerr, D.2022-05-29doi:10.1101/2022.05.27.493721Cold Spring Harbor Laboratory Press2022-05-29
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Inversion polymorphism in a complete human genome assembly
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https://biorxiv.org/cgi/content/short/2022.10.06.511148v1?rss=1"
Porubsky, D.Harvey, W. T.Rozanski, A. N.Ebler, J.Hoeps, W.Ashraf, H.Hasenfeld, P.Paten, B.Sanders, A. D.Marschall, T.Korbel, J. O.Eichler, E. E.2022-10-06doi:10.1101/2022.10.06.511148Cold Spring Harbor Laboratory Press2022-10-06
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
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https://biorxiv.org/cgi/content/short/2023.01.12.523790v1?rss=1"
Kolmogorov, M.Billingsley, K. J.Mastoras, M.Meredith, M.Monlong, J.Lorig-Roach, R.Asri, M.Alvarez Jerez, P.Malik, L.Dewan, R.Reed, X.Genner, R. M.Daida, K.Behera, S.Shafin, K.Pesout, T.Prabakaran, J.Carnevali, P.North American Brain Expression Consortium (NABEC),Yang, J.Rhie, A.Scholz, S. W.Traynor, B. J.Miga, K. H.Jain, M.Timp, W.Phillippy, A. M.Chaisson, M.Sedlazeck, F. J.Blauwendraat, C.Paten, B.2023-01-15doi:10.1101/2023.01.12.523790Cold Spring Harbor Laboratory Press2023-01-15
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Optimal gap-affine alignment in O(s) space
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https://biorxiv.org/cgi/content/short/2022.04.14.488380v1?rss=1"
Marco-Sola, S.Eizenga, J. M.Guarracino, A.Paten, B.Garrison, E.Moreto, M.2022-04-15doi:10.1101/2022.04.14.488380Cold Spring Harbor Laboratory Press2022-04-15
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UCSC Cell Browser: Visualize Your Single-Cell Data
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https://biorxiv.org/cgi/content/short/2020.10.30.361162v1?rss=1"
Speir, M. L.Bhaduri, A.Markov, N. S.Moreno, P.Nowakowski, T. J.Papatheodorou, I.Pollen, A. A.Seninge, L.Kent, W. J.Haeussler, M.2020-10-31doi:10.1101/2020.10.30.361162Cold Spring Harbor Laboratory Press2020-10-31
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Improving the time and space complexity of the WFA algorithm and generalizing its scoring
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https://biorxiv.org/cgi/content/short/2022.01.12.476087v1?rss=1"
Eizenga, J. M.Paten, B.2022-01-15doi:10.1101/2022.01.12.476087Cold Spring Harbor Laboratory Press2022-01-15
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Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser
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https://biorxiv.org/cgi/content/short/2022.01.18.476849v1?rss=1"
Li, D.Purushotham, D.Harrison, J. K.Wang, T.2022-01-21doi:10.1101/2022.01.18.476849Cold Spring Harbor Laboratory Press2022-01-21
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Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation
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https://biorxiv.org/cgi/content/short/2022.12.01.518658v1?rss=1"
2-fold higher recurrence rate compared to inversions in the rest of the human genome. Ampliconic sequences associated with these inversions further show differing mutation rates that are sequence context-dependent and some ampliconic genes show evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, the Yq12, is composed of alternating arrays of DYZ1 and DYZ2 repeat units that show extensive variation in the number, size and distribution of these arrays, but retain a 1:1 copy number ratio of the monomer repeats, consistent with the notion that functional or evolutionary forces are acting on this chromosomal region. Finally, our data suggests that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kbp distal to the currently established boundary. The availability of sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of specific traits with Y-chromosomal variants and garnering novel insights into the evolution and function of complex regions of the human genome.
]]>Hallast, P.Ebert, P.Loftus, M.Yilmaz, F.Audano, P. A.Logsdon, G. A.Bonder, M. J.Zhou, W.Hoeps, W.Kim, K.Li, C.Dishuck, P. C.Porubsky, D.Tsetsos, F.Kwon, J. Y.Zhu, Q.Munson, K. M.Hasenfeld, P.Harvey, W. T.Lewis, A. P.Kordosky, J.Hoekzema, K.(HGSVC), T. H. G. S. V. C.Korbel, J. O.Tyler-Smith, C.Eichler, E. E.Shi, X.Beck, C. R.Marschall, T.Konkel, M. K.Lee, C.2022-12-01doi:10.1101/2022.12.01.518658Cold Spring Harbor Laboratory Press2022-12-01
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Evolution of transposable element-derived enhancer activity
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https://biorxiv.org/cgi/content/short/2022.03.16.483999v1?rss=1"
Du, A. Y.Zhuo, X.Sundaram, V.Jensen, N. O.Chaudhari, H. G.Saccone, N. L.Cohen, B. A.Wang, T.2022-03-17doi:10.1101/2022.03.16.483999Cold Spring Harbor Laboratory Press2022-03-17
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Efficient chromosome-scale haplotype-resolved assembly of human genomes
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https://biorxiv.org/cgi/content/short/810341v1?rss=1"
Garg, S.Arkarachai Fungtammasan, A.Carroll, A.Chou, M.Schmitt, A.Zhou, X.Mac, S.Peluso, P.Hatas, E.Ghurye, J.Maguire, J.Mahmoud, M.Cheng, H.Heller, D.Zook, J. M.Moemke, T.Marschall, T.Sedlazeck, F. J.Aach, J.Chin, C.-S.Church, G. M.Li, H. M.2019-10-18doi:10.1101/810341Cold Spring Harbor Laboratory Press2019-10-18
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From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
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https://biorxiv.org/cgi/content/short/2021.07.12.451456v1?rss=1"
Hoyt, S. J.Storer, J. M.Hartley, G. A.Grady, P. G. S.Gershman, A.de Lima, L. G.Limouse, C.Halabian, R.Wojenski, L.Rodriguez, M.Altemose, N.Core, L.Gerton, J. L.Makalowski, W.Olson, D.Rosen, J.Smit, A. F. A.Straight, A. F.Vollger, M. R.Wheeler, T.Schatz, M.Eichler, E.Phillippy, A. M.Timp, W.Miga, K. H.O'Neill, R. J.2021-07-12doi:10.1101/2021.07.12.451456Cold Spring Harbor Laboratory Press2021-07-12
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Automated assembly of high-quality diploid human reference genomes
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https://biorxiv.org/cgi/content/short/2022.03.06.483034v1?rss=1"
Jarvis, E. D.Formenti, G.Rhie, A.Guarracino, A.Yang, C.Wood, J.Tracey, A.Thibaud-Nissen, F.Vollger, M. R.Porubsky, D.Cheng, H.Asri, M.Logsdon, G. A.Carnevali, P.Chaisson, M.Chin, C.-S.Cody, S.Collins, J.Ebert, P.Escalona, M.Fedrigo, O.Fulton, R. S.Fulton, L. L.Garg, S.Ghurye, J.Green, E.Hall, I. M.Harvey, W. H.Hasenfeld, P.Hastie, A.Haukness, M.Jain, M.Kirsche, M.Kolmogorov, M.Korbel, J. O.Koren, S.Korlach, J.Lee, J.Li, D.Lindsay, T.Lucas, J.Luo, F.Marschall, T.McDaniel, J.Nie, F.Olsen, H. E.Olson, N.2022-03-06doi:10.1101/2022.03.06.483034Cold Spring Harbor Laboratory Press2022-03-06
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SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing
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https://biorxiv.org/cgi/content/short/2020.02.25.964445v1?rss=1"
Heller, D.Vingron, M.Church, G.Li, H.Garg, S.2020-02-26doi:10.1101/2020.02.25.964445Cold Spring Harbor Laboratory Press2020-02-26
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Exploring the coronavirus epidemic using the new WashU Virus Genome Browser
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https://biorxiv.org/cgi/content/short/2020.02.07.939124v1?rss=1"
Flynn, J.Purushotham, D.Choudhary, M. N.Zhuo, X.Fan, C.Matt, G.Li, D.Wang, T.2020-02-11doi:10.1101/2020.02.07.939124Cold Spring Harbor Laboratory Press2020-02-11
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Epigenetic Patterns in a Complete Human Genome
]]>
https://biorxiv.org/cgi/content/short/2021.05.26.443420v1?rss=1"
Gershman, A.Sauria, M. E. G.Hook, P. W.Hoyt, S.Razaghi, R.Koren, S.Altemose, N.Caldas, G. V.Vollger, M. R.Logsdon, G.Rhie, A.Eichler, E.Schatz, M.O'Neill, R. J.Phillippy, A. M.Miga, K. H.Timp, W.2021-05-27doi:10.1101/2021.05.26.443420Cold Spring Harbor Laboratory Press2021-05-27
<![CDATA[
Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders
]]>
https://biorxiv.org/cgi/content/short/2021.12.20.472354v1?rss=1"
Porubsky, D.Höps, W.Ashraf, H.Hsieh, P.Rodriguez-Martin, B.Yilmaz, F.Ebler, J.Hallast, P.Maggiolini, F. A. M.Harvey, W. T.Henning, B.Audano, P. A.Gordon, D. S.Ebert, P.Hasenfeld, P.Benito, E.Zhu, Q.Human Genome Structural Variation Consortium,Lee, C.Antonacci, F.Steinrücken, M.Beck, C. R.Sanders, A. D.Marschall, T.Eichler, E. E.Korbel, J. O.2021-12-20doi:10.1101/2021.12.20.472354Cold Spring Harbor Laboratory Press2021-12-20
<![CDATA[
Transcript assembly improves expression quantification of transposable elements in single cell RNA-seq data
]]>
https://biorxiv.org/cgi/content/short/2020.07.31.231027v1?rss=1"
Shao, W.Wang, T.2020-07-31doi:10.1101/2020.07.31.231027Cold Spring Harbor Laboratory Press2020-07-31
<![CDATA[
A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development
]]>
https://biorxiv.org/cgi/content/short/2021.03.24.436683v1?rss=1"
Modzelewski, A. J.Shao, W.Chen, J.Lee, A.Qi, X.Noon, M.Tjokro, K.Sales, G.Biton, A.Speed, T.Xuan, Z.Wang, T.Risso, D.He, L.2021-03-25doi:10.1101/2021.03.24.436683Cold Spring Harbor Laboratory Press2021-03-25
<![CDATA[
De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation
]]>
https://biorxiv.org/cgi/content/short/2020.12.16.423102v1?rss=1"
Ebert, P.Audano, P. A.Zhu, Q.Rodriguez-Martin, B.Porubsky, D.Bonder, M. J.Sulovari, A.Ebler, J.Zhou, W.Serra Mari, R.Yilmaz, F.Zhao, X.Hsieh, P.Lee, J.Kumar, S.Lin, J.Rausch, T.Chen, Y.Ren, J.Santamarina, M.Hoeps, W.Ashraf, H.Chuang, N. T.Yang, X.Munson, K. M.Lewis, A. P.Fairley, S.Tallon, L. J.Clarke, W. E.Basile, A. O.Byrska-Bishop, M.Corvelo, A.Chaisson, M. J. P.Chen, J.Li, C.Brand, H.Wenger, A. M.Ghareghani, M.Harvey, W.Raeder, B.Hasenfeld, P.Regier, A.Abel, H.Hall, I.Flicek, P.Stegle, O.Gerstein, M2020-12-16doi:10.1101/2020.12.16.423102Cold Spring Harbor Laboratory Press2020-12-16
<![CDATA[
The structure, function, and evolution of a complete human chromosome 8
]]>
https://biorxiv.org/cgi/content/short/2020.09.08.285395v1?rss=1"
Logsdon, G. A.Vollger, M. R.Hsieh, P.Mao, Y.Liskovykh, M. A.Koren, S.Nurk, S.Mercuri, L.Dishuck, P. C.Rhie, A.de Lima, L. G.Porubsky, D.Bzikadze, A. V.Kremitzki, M.Graves-Lindsay, T. A.Jain, C.Hoekzema, K.Murali, S. C.Munson, K. M.Baker, C.Sorenson, M.Lewis, A. M.Surti, U.Gerton, J. L.Larionov, V.Ventura, M.Miga, K. H.Phillippy, A. M.Eichler, E. E.2020-09-08doi:10.1101/2020.09.08.285395Cold Spring Harbor Laboratory Press2020-09-08
<![CDATA[
Co-opted transposons help perpetuate conserved higher-order chromosomal structures
]]>
https://biorxiv.org/cgi/content/short/485342v1?rss=1"
Choudhary, M. N.Friedman, R. Z.Wang, J. T.Jang, H. S.Zhuo, X.Wang, T.2018-12-05doi:10.1101/485342Cold Spring Harbor Laboratory Press2018-12-05
<![CDATA[
The complete sequence of a human Y chromosome
]]>
https://biorxiv.org/cgi/content/short/2022.12.01.518724v1?rss=1"
Rhie, A.Nurk, S.Cechova, M.Hoyt, S. J.Taylor, D. J.Altemose, N.Hook, P. W.Koren, S.Rautiainen, M.Alexandrov, I. A.Allen, J.Asri, M.Bzikadze, A. V.Chen, N.-C.Chin, C.-S.Diekhans, M.Flicek, P.Formenti, G.Fungtammasan, A.Garcia Giron, C.Garrison, E.Gershman, A.Gerton, J.Grady, P. G.Guarracino, A.Haggerty, L.Halabian, R.Hansen, N. F.Harris, R.Hartley, G. A.Harvey, W. T.Haukness, M.Heinz, J.Hourlier, T.Hubley, R. M.Hunt, S. E.Hwang, S.Jain, M.Kesharwani, R. K.Lewis, A. P.Li, H.Logsdon, G. A.Lucas, J. K.Makalowski,2022-12-01doi:10.1101/2022.12.01.518724Cold Spring Harbor Laboratory Press2022-12-01
<![CDATA[
Comparing Genomic and Epigenomic Features across Species Using the WashU Comparative Epigenome Browser
]]>
https://biorxiv.org/cgi/content/short/2022.11.29.518374v1?rss=1"
Zhuo, X.Hsu, S.Purushotham, D.Chen, S.Li, D.Wang, T.2022-12-02doi:10.1101/2022.11.29.518374Cold Spring Harbor Laboratory Press2022-12-02
<![CDATA[
Highly accurate assembly polishing with DeepPolisher
]]>
https://biorxiv.org/cgi/content/short/2024.09.17.613505v1?rss=1"
Mastoras, M.Asri, M.Brambrink, L.Hebbar, P.Kolesnikov, A.Cook, D. E.Nattestad, M.Lucas, J.Won, T. S.Chang, P.-C.Carroll, A.Paten, B.Shafin, K.2024-09-19doi:10.1101/2024.09.17.613505Cold Spring Harbor Laboratory Press2024-09-19
<![CDATA[
SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings
]]>
https://biorxiv.org/cgi/content/short/2024.08.12.607489v1?rss=1"
Rubin, J. D.van Waaij, J.Kraft, L. M.Siren, J.Sackett, P. W.Renaud, G.2024-08-12doi:10.1101/2024.08.12.607489Cold Spring Harbor Laboratory Press2024-08-12
<![CDATA[
High-resolution global diversity copy number variation maps and association with ctyper
]]>
https://biorxiv.org/cgi/content/short/2024.08.11.607269v1?rss=1"
Chaisson, M.Ma, W.2024-08-11doi:10.1101/2024.08.11.607269Cold Spring Harbor Laboratory Press2024-08-11
<![CDATA[
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies
]]>
https://biorxiv.org/cgi/content/short/2024.08.16.608331v1?rss=1"
Park, J.Cook, D. E.Chang, P.-C.Kolesnikov, A.Brambrink, L.Mier, J. C.Gardner, J.McNulty, B.Sacco, S.Keskus, A.Bryant, A.Ahmad, T.Shetty, J.Zhao, Y.Tran, B.Narzisi, G.Helland, A.Yoo, B.Pushel, I.Lansdon, L. A.Bi, C.Walter, A.Gibson, M.Pastinen, T.Farooqi, M. S.Robine, N.Miga, K. H.Carroll, A.Kolmogorov, M.Paten, B.Shafin, K.2024-08-19doi:10.1101/2024.08.16.608331Cold Spring Harbor Laboratory Press2024-08-19
<![CDATA[
Panacus: fast and exact pangenome growth and core size estimation
]]>
https://biorxiv.org/cgi/content/short/2024.06.11.598418v1?rss=1"
Parmigiani, L.Garrison, E.Stoye, J.Marschall, T.Doerr, D.2024-06-12doi:10.1101/2024.06.11.598418Cold Spring Harbor Laboratory Press2024-06-12
<![CDATA[
Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads
]]>
https://biorxiv.org/cgi/content/short/2024.05.18.594796v1?rss=1"
Stanojevic, D.Lin, D.Florez De Sessions, P.Sikic, M.2024-05-21doi:10.1101/2024.05.18.594796Cold Spring Harbor Laboratory Press2024-05-21
<![CDATA[
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
]]>
https://biorxiv.org/cgi/content/short/2024.03.15.585294v1?rss=1"
Koren, S.Bao, Z.Guarracino, A.Ou, S.Goodwin, S.Jenike, K. M.Lucas, J.McNulty, B.Park, J.Rautianinen, M.Rhie, A.Roelofs, D.Schneiders, H.Vrijenhoek, I.Nijbroek, K.Ware, D.Schatz, M. C.Garrison, E.Huang, S.McCombie, W. R.Miga, K. H.Wittenberg, A. H. J.Phillippy, A. M.2024-03-17doi:10.1101/2024.03.15.585294Cold Spring Harbor Laboratory Press2024-03-17
<![CDATA[
Full resolution HLA and KIR genes annotation for human genome assemblies
]]>
https://biorxiv.org/cgi/content/short/2024.01.20.576452v1?rss=1"
Zhou, Y.Song, L.Li, H.2024-01-23doi:10.1101/2024.01.20.576452Cold Spring Harbor Laboratory Press2024-01-23
<![CDATA[
The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data
]]>
https://biorxiv.org/cgi/content/short/2023.11.01.565049v1?rss=1"
QV60). We mapped the haplotype-specific genomic variation specific to this cell line including t(Xq;10q), a stable 73.18 Mb duplication of chromosome 10 translocated onto the microdeleted chromosome X telomere t(Xq;10q). Polymorphisms between haplotypes of the same genome reveals genetic and epigenetic variation for all chromosomes, especially at centromeres. The RPE-1 assembly as matched reference genome improves mapping quality of multi-omics reads originating from RPE-1 cells with drastic reduction in alignments mismatches compared to using the most complete human reference to date (CHM13). Leveraging the accuracy achieved using a matched reference, we were able to identify the kinetochore sites at base pair resolution and show unprecedented variation between haplotypes. This work showcases the use of matched reference genomes for multi-omics analyses and serves as the foundation for a call to comprehensively assemble experimentally relevant cell lines for widespread application.
HighlightsO_LIWe generated the complete phased genome assembly of one of the most widely used non-cancer cell lines (RPE-1) with a stable diploid karyotype
C_LIO_LIWe used this genome as a matched reference to analyze sequencing data from RPE-1
C_LIO_LIMapping to the RPE1v1.0 genome improves alignment quality, faithful assignment of reads to each haplotype, and epigenome peak calling accuracy uncovering inter-haplotype variation
C_LIO_LIUse of the matched reference genome enables epigenetic precision in identifying for the first time the kinetochore site at base pair resolution for each haplotype
C_LIO_LIThe RPE-1 genome represents a new telomere-to-telomere (T2T) human diploid reference for the scientific community that will advance genetic and epigenetic research across fields using this cell line
C_LI
]]>Volpe, E.Corda, L.Di Tommaso, E.Pelliccia, F.Ottalevi, R.Licastro, D.Formenti, G.Capulli, M.Guarracino, A.Tassone, E.Giunta, S.2023-11-03doi:10.1101/2023.11.01.565049Cold Spring Harbor Laboratory Press2023-11-03
<![CDATA[
Personalized Pangenome References
]]>
https://biorxiv.org/cgi/content/short/2023.12.13.571553v1?rss=1"
Siren, J.Eskandar, P.Ungaro, M. T.Hickey, G.Eizenga, J. M.Novak, A. M.Chang, X.Chang, P.-C.Kolmogorov, M.Carroll, A.Monlong, J.Paten, B.2023-12-14doi:10.1101/2023.12.13.571553Cold Spring Harbor Laboratory Press2023-12-14
<![CDATA[
Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing
]]>
https://biorxiv.org/cgi/content/short/2023.11.30.569101v1?rss=1"
Tan, K.-T.Slevin, M. K.Leibowitz, M. L.Garrity-Janger, M.Li, H.Meyerson, M.2023-12-01doi:10.1101/2023.11.30.569101Cold Spring Harbor Laboratory Press2023-12-01
<![CDATA[
Local read haplotagging enables accurate long-read small variant calling
]]>
https://biorxiv.org/cgi/content/short/2023.09.07.556731v1?rss=1"
Kolesnikov, A.Cook, D. E.Nattestad, M.Ashley, E. A.Gorzynski, J.Goenka, S. D.Jain, M.McNulty, B.Miga, K. H.Paten, B.Chang, P.-C.Carroll, A.Shafin, K.2023-09-12doi:10.1101/2023.09.07.556731Cold Spring Harbor Laboratory Press2023-09-12
<![CDATA[
Evaluation of haplotype-aware long-read error correction with hifieval
]]>
https://biorxiv.org/cgi/content/short/2023.06.05.543788v1?rss=1"
99% in accuracy. It has enabled the development of a new generation of de novo sequence assemblers, which all have sequencing error correction as the first step. As HiFi is a new data type, this critical step has not been evaluated before. Here, we introduced hifieval, a new command-line tool for measuring over- and under-corrections produced by error correction algorithms. We assessed the accuracy of the error correction components of existing HiFi assemblers on the CHM13 and the HG002 datasets and further investigated the performance of error correction methods in challenging regions such as homopolymer regions, centromeric regions, and segmental duplications. Hifieval will help HiFi assemblers to improve error correction and assembly quality in the long run.
Availability and implementationThe source code is available at https://github.com/magspho/hifieval
Contacthli@ds.dfci.harvard.edu
Supplementary informationSupplementary data are available at Bioinformatics online.
]]>Guo, Y.Feng, X.Li, H.2023-06-07doi:10.1101/2023.06.05.543788Cold Spring Harbor Laboratory Press2023-06-07
<![CDATA[
A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure
]]>
https://biorxiv.org/cgi/content/short/2023.05.15.540856v1?rss=1"
Li, C.Bonder, M. J.Syed, S.Human Genome Structural Variation Consortium (HGSVC),HGSVC Functional Analysis Working Group,Zody, M. C.Chaisson, M. J. P.Talkowski, M. E.Marschall, T.Korbel, J. O.Eichler, E. E.Lee, C.Shi, X.2023-05-15doi:10.1101/2023.05.15.540856Cold Spring Harbor Laboratory Press2023-05-15
<![CDATA[
Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall
]]>
https://biorxiv.org/cgi/content/short/2023.05.04.539448v1?rss=1"
Harvey, W. T.Ebert, P.Ebler, J.Audano, P. A.Munson, K. M.Hoekzema, K.Porubsky, D. E.Beck, C. R.Marschall, T. R.Garimella, K. V.Eichler, E. E.2023-05-04doi:10.1101/2023.05.04.539448Cold Spring Harbor Laboratory Press2023-05-04
<![CDATA[
A haplotype-aware de novo assembly of related individuals using pedigree graph
]]>
https://biorxiv.org/cgi/content/short/580159v1?rss=1"
Garg, S.Aach, J.Li, H.Durbin, R.Church, G.2019-03-17doi:10.1101/580159Cold Spring Harbor Laboratory Press2019-03-17
<![CDATA[
A refined characterization of large-scale genomic differences in the first complete human genome
]]>
https://biorxiv.org/cgi/content/short/2022.12.17.520860v1?rss=1"
Yang, X.Wang, X.Zou, Y.Zhang, S.Xia, M.Vollger, M. R.Chen, N.-C.Taylor, D. J.Harvey, W. T.Logsdon, G. A.Meng, D.Shi, J.McCoy, R. C.Schatz, M. C.Li, W.Eichler, E. E.Lu, Q.Mao, Y.2022-12-19doi:10.1101/2022.12.17.520860Cold Spring Harbor Laboratory Press2022-12-19
<![CDATA[
BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data
]]>
https://biorxiv.org/cgi/content/short/2023.09.22.559047v1?rss=1"
Tian, W.Ding, W.Ecker, J. R.2023-09-25doi:10.1101/2023.09.22.559047Cold Spring Harbor Laboratory Press2023-09-25
<![CDATA[
Building pangenome graphs
]]>
https://biorxiv.org/cgi/content/short/2023.04.05.535718v1?rss=1"
Garrison, E.Guarracino, A.Heumos, S.Villani, F.Bao, Z.Tattini, L.Hagmann, J.Vorbrugg, S.Marco-Sola, S.Kubica, C.Ashbrook, D. G.Thorell, K.Rusholme-Pilcher, R. L.Liti, G.Rudbeck, E.Nahnsen, S.Yang, Z.Moses, M. N.Nobrega, F. L.Wu, Y.Chen, H.de Ligt, J.Sudmant, P. H.Soranzo, N.Colonna, V.Williams, R. W.Prins, P.2023-04-06doi:10.1101/2023.04.05.535718Cold Spring Harbor Laboratory Press2023-04-06
<![CDATA[
Characterizing cytosine methylation of polymorphic human transposable element insertions using human pangenome resources
]]>
https://biorxiv.org/cgi/content/short/2024.11.22.623804v1?rss=1"
Zhuo, X.Tomlinson, C.Belter, E. A.Kuntala, P. K.Saintilnord, W. N.Lindsay, T.Macias, J.Fulton, R. S.Wang, T.2024-11-23doi:10.1101/2024.11.22.623804Cold Spring Harbor Laboratory Press2024-11-23
<![CDATA[
Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using targeted CRISPR-targeted ultra-long read sequencing (CTLR-Seq)
]]>
https://biorxiv.org/cgi/content/short/2020.10.23.349621v1?rss=1"
Zhou, B.Shin, G.Greer, S. U.Vervoort, L.Huang, Y.Pattni, R.Ho, M.Wong, W. H.Vermeesch, J. R.Ji, H.Urban, A. E.2020-10-23doi:10.1101/2020.10.23.349621Cold Spring Harbor Laboratory Press2020-10-23
<![CDATA[
Evolutionary constraint and innovation across hundreds of placental mammals
]]>
https://biorxiv.org/cgi/content/short/2023.03.09.531574v1?rss=1"
Christmas, M. J.Kaplow, I. M.Genereux, D. P.Dong, M. X.Hughes, G. M.Li, X.Sullivan, P. F.Hindle, A. G.Andrews, G.Armstrong, J. C.Bianchi, M.Breit, A. M.Diekhans, M.Fanter, C.Foley, N. M.Goodman, D. B.Goodman, L.Keough, K. C.Kirilenko, B.Kowalczyk, A.Lawless, C.Lind, A. L.Meadows, J. R. S.Moreira, L. R.Redlich, R. W.Ryan, L.Swofford, R.Valenzuela, A.Wagner, F.Wallerman, O.Brown, A. R.Damas, J.Fan, K.Gatesy, J.Grimshaw, J.Johnson, J.Kozyrev, S. V.Lawler, A. J.Marinescu, V. D.Morrill, K. M.Osmanski, A.Paulat, N. S.2023-03-09doi:10.1101/2023.03.09.531574Cold Spring Harbor Laboratory Press2023-03-09
<![CDATA[
Gene expansions contributing to human brain evolution
]]>
https://biorxiv.org/cgi/content/short/2024.09.26.615256v1?rss=1"
Soto, D. C.Uribe-Salazar, J. M.Kaya, G.Valdarrago, R.Sekar, A.Haghani, N. K.Hino, K.La, G. N.Mariano, N. A. F.Ingamells, C.Baraban, A. E.Turner, T. N.Green, E. D.Simo, S.Quon, G.Andres, A.Dennis, M. Y.2024-09-26doi:10.1101/2024.09.26.615256Cold Spring Harbor Laboratory Press2024-09-26
<![CDATA[
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
]]>
https://biorxiv.org/cgi/content/short/2020.03.14.992248v1?rss=1"
10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30x HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultra-long Oxford Nanopore reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of 9 complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance towards the complete assembly of human genomes.
AvailabilityHiCanu is implemented within the Canu assembly framework and is available from https://github.com/marbl/canu.
]]>Nurk, S.Walenz, B. P.Rhie, A.Vollger, M. R.Logsdon, G. A.Grothe, R.Miga, K. H.Eichler, E. E.Phillippy, A. M.Koren, S.2020-03-17doi:10.1101/2020.03.14.992248Cold Spring Harbor Laboratory Press2020-03-17
<![CDATA[
KmerKeys: a web resource for searching indexed genome assemblies and variants
]]>
https://biorxiv.org/cgi/content/short/2021.05.17.444256v1?rss=1"
Pavlichin, D. S.Lee, H.Greer, S. U.Grimes, S. M.Weissman, T.Ji, H. P.2021-05-18doi:10.1101/2021.05.17.444256Cold Spring Harbor Laboratory Press2021-05-18
<![CDATA[
KmerSV: a visualization and annotation tool for structural variants using Human Pangenome derived k-mers
]]>
https://biorxiv.org/cgi/content/short/2023.10.11.561941v1?rss=1"
Meng, Q.Ji, H. P.Lee, H.2023-10-15doi:10.1101/2023.10.11.561941Cold Spring Harbor Laboratory Press2023-10-15
<![CDATA[
lra: the Long Read Aligner for Sequences and Contigs
]]>
https://biorxiv.org/cgi/content/short/2020.11.15.383273v1?rss=1"
Ren, J.Chaisson, M.2020-11-17doi:10.1101/2020.11.15.383273Cold Spring Harbor Laboratory Press2020-11-17
<![CDATA[
LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung
]]>
https://biorxiv.org/cgi/content/short/2021.12.05.471312v1?rss=1"
Gaddis, N.Fortriede, J.Guo, M.Bardes, E. E.Kouril, M.Tabar, S.Burns, K.Ardini-Poleske, M. E.Loos, S.Schnell, D.Jin, K.Iyer, B.Du, Y.Korte, J.Munshi, R.Smith, V.Herbst, A.Kitzmiller, J. A.Clair, G. C.Carson, J.Adkins, J.Morrisey, E. E.Pryhuber, G. S.Misra, R.Whitsett, J. A.Sun, X.Heathorn, T.Paten, B.Prasath, V. B. S.Xu, Y.Tickle, T.Aronow, B. J.Salomonis, N.2021-12-06doi:10.1101/2021.12.05.471312Cold Spring Harbor Laboratory Press2021-12-06
<![CDATA[
ntsm: an alignment-free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection
]]>
https://biorxiv.org/cgi/content/short/2023.11.01.565041v1?rss=1"
Chu, J.Rong, J.Feng, X.Li, H.2023-11-03doi:10.1101/2023.11.01.565041Cold Spring Harbor Laboratory Press2023-11-03
<![CDATA[
Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus
]]>
https://biorxiv.org/cgi/content/short/2022.10.06.511217v1?rss=1"
Hickey, G.Monlong, J.Novak, A.Eizenga, J. M.Human Pangenome Reference Consortium,Li, H.Paten, B.2022-10-07doi:10.1101/2022.10.06.511217Cold Spring Harbor Laboratory Press2022-10-07
<![CDATA[
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
]]>
https://biorxiv.org/cgi/content/short/2023.02.21.529152v1?rss=1"
Lorig-Roach, R.Meredith, M.Monlong, J.Jain, M.Olsen, H.McNulty, B.Porubsky, D.Montague, T. G.Lucas, J.Condon, C.Eizenga, J.Juul, S.McKenzie, S.Simmonds, S.Park, J.Asri, M.Koren, S.Eichler, E.Axel, R.Martin, B.Carnevali, P.Miga, K.Paten, B.2023-02-22doi:10.1101/2023.02.21.529152Cold Spring Harbor Laboratory Press2023-02-22
<![CDATA[
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
]]>
https://biorxiv.org/cgi/content/short/2020.08.13.249839v1?rss=1"
Lu, T.-Y. T.The Human Genome Structural Variation Consortium,Chaisson, M. J.2020-08-14doi:10.1101/2020.08.13.249839Cold Spring Harbor Laboratory Press2020-08-14
<![CDATA[
Recombination between heterologous human acrocentric chromosomes
]]>
https://biorxiv.org/cgi/content/short/2022.08.15.504037v1?rss=1"
Guarracino, A.Buonaiuto, S.Potapova, T.Rhie, A.Koren, S.Rubinstein, B.Fischer, C.Human Pangenome Reference Consortium,Gerton, J. L.Phillippy, A. M.Colonna, V.Garrison, E.2022-08-15doi:10.1101/2022.08.15.504037Cold Spring Harbor Laboratory Press2022-08-15
<![CDATA[
Regulatory Transposable Elements in the Encyclopedia of DNA Elements
]]>
https://biorxiv.org/cgi/content/short/2023.09.05.556380v1?rss=1"
Du, A. Y.Chobirko, J. D.Zhuo, X.Feschotte, C.Wang, T.2023-09-06doi:10.1101/2023.09.05.556380Cold Spring Harbor Laboratory Press2023-09-06
<![CDATA[
Single cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing
]]>
https://biorxiv.org/cgi/content/short/2021.07.01.450805v1?rss=1"
Kim, H. S.Grimes, S. M.Hooker, A. C.Lau, B. T.Ji, H. P.2021-07-02doi:10.1101/2021.07.01.450805Cold Spring Harbor Laboratory Press2021-07-02
<![CDATA[
Structural polymorphism and diversity of human segmental duplications
]]>
https://biorxiv.org/cgi/content/short/2024.06.04.597452v1?rss=1"
Jeong, H.Dishuck, P. C.Yoo, D.Harvey, W. T.Munson, K. M.Lewis, A. P.Kordosky, J.Garcia, G. H.Human Genome Structural Variation Consortium (HGSVC),Yilmaz, F.Hallast, P.Lee, C.Pastinen, T.Eichler, E. E.2024-06-06doi:10.1101/2024.06.04.597452Cold Spring Harbor Laboratory Press2024-06-06
<![CDATA[
Structurally divergent and recurrently mutated regions of primate genomes
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531415v1?rss=1"
Mao, Y.Harvey, W. T.Porubsky, D.Munson, K. M.Hoekzema, K.Lewis, A. P.Audano, P. A.Rozanski, A.Yang, X.Zhang, S.Gordon, D. S.Wei, X.Logsdon, G. A.Haukness, M.Dishuck, P. C.Jeong, H.del Rosario, R.Bauer, V. L.Fattor, W. T.Wilkerson, G. K.Lu, Q.Paten, B.Feng, G.Sawyer, S. L.Warren, W. C.Carbone, L.Eichler, E. E.2023-03-07doi:10.1101/2023.03.07.531415Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
Telomere-to-telomere assembly of a complete human X chromosome
]]>
https://biorxiv.org/cgi/content/short/735928v1?rss=1"
Miga, K. H.Koren, S.Rhie, A.Vollger, M. R.Gershman, A.Bzikadze, A.Brooks, S.Howe, E.Porubsky, D.Logsdon, G. A.Schneider, V. A.Potapova, T.Wood, J.Chow, W.Armstrong, J.Fredrickson, J.Pak, E.Tigyi, K.Kremitzki, M.Markovic, C.Maduro, V.Dutra, A.Bouffard, G. G.Chang, A. M.Hansen, N. F.Thibaud-Nissen, F.Schmitt, A. D.Belton, J.-M.Selvaraj, S.Dennis, M. Y.Soto, D. C.Sahasrabudhe, R.Kaya, G.Quick, J.Loman, N. J.Holmes, N.Loose, M.Surti, U.Risques, R. a.Lindsay, T. A. G.Fulton, R.Hall, I.Paten, B.Howe, K.Timp, W.2019-08-16doi:10.1101/735928Cold Spring Harbor Laboratory Press2019-08-16
<![CDATA[
The motif composition of variable-number tandem repeats impacts gene expression
]]>
https://biorxiv.org/cgi/content/short/2022.03.17.484784v1?rss=1"
Lu, T.-Y. T.Chaisson, M.2022-03-19doi:10.1101/2022.03.17.484784Cold Spring Harbor Laboratory Press2022-03-19
<![CDATA[
The qBED track: a novel genome browser visualization for point processes
]]>
https://biorxiv.org/cgi/content/short/2020.04.27.060061v1?rss=1"
Moudgil, A.Li, D.Hsu, S.Purushotham, D.Wang, T.Mitra, R. D.2020-04-29doi:10.1101/2020.04.27.060061Cold Spring Harbor Laboratory Press2020-04-29
<![CDATA[
The Transcription Factor Bach2 Negatively Regulates Natural Killer Cell Maturation and Function
]]>
https://biorxiv.org/cgi/content/short/2022.02.14.480364v1?rss=1"
Li, S.Bern, M.Miao, B.Inoue, T.Piersma, S. J.Colonna, M.Kurosaki, T.Yokoyama, W. M.2022-02-14doi:10.1101/2022.02.14.480364Cold Spring Harbor Laboratory Press2022-02-14
<![CDATA[
Unbiased pangenome graphs
]]>
https://biorxiv.org/cgi/content/short/2022.02.14.480413v1?rss=1"
Garrison, E.Guarracino, A.2022-02-16doi:10.1101/2022.02.14.480413Cold Spring Harbor Laboratory Press2022-02-16
<![CDATA[
Unique K-mer sequences for validating cancer-related substitution, insertion and deletion mutations
]]>
https://biorxiv.org/cgi/content/short/2020.06.20.163113v1?rss=1"
Lee, H.Shuaibi, A. A.Bell, J.Pavlichin, D. S.Ji, H.2020-06-20doi:10.1101/2020.06.20.163113Cold Spring Harbor Laboratory Press2020-06-20
<![CDATA[
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation
]]>
https://biorxiv.org/cgi/content/short/2024.12.16.628723v1?rss=1"
Billingsley, K. J.Meredith, M.Daida, K.Alvarez Jerez, P.Negi, S.Malik, L.Genner, R. M.Moller, A.Zheng, X.Gibson, S. B.Mastoras, M.Baker, B.Kouam, C.Paquette, K.Jarreau, P.Makarious, M. B.Moore, A.Hong, S.Vitale, D.Shah, S.Monlong, J.Pantazis, C. B.Asri, M.Shafin, K.Carnevali, P.Marenco, S.Auluck, P.Mandal, A.Miga, K. H.Rhie, A.Reed, X.Ding, J.Cookson, M. R.Nalls, M.Singleton, A.Miller, D. E.Chaisson, M.Timp, W.Gibbs, J. R.Phillippy, A. M.Kolmogorov, M.Jain, M.Sedlazeck, F. J.Paten, B.Blauwendraat, C.2024-12-18doi:10.1101/2024.12.16.628723Cold Spring Harbor Laboratory Press2024-12-18
<![CDATA[
Population differences of chromosome 22q11.2 duplication structure predisposes differentially to microdeletion and inversion.
]]>
https://biorxiv.org/cgi/content/short/2025.07.04.662981v1?rss=1"
Porubsky, D.Yoo, D.Dishuck, P. C.Koundinya, N.Souche, E.Harvey, W. T.Munson, K. M.Hoekzema, K.Chan, D. D.Leung, T. Y.Santos, M. S.Meynants, S.Swillen, A.Breckpot, J.Tsapalou, V.Hasenfeld, P.Korbel, J. O.Lansdorp, P. M.Vermeesch, J. R.Eichler, E. E.2025-07-05doi:10.1101/2025.07.04.662981Cold Spring Harbor Laboratory Press2025-07-05
<![CDATA[
Pangenome-aware DeepVariant
]]>
https://biorxiv.org/cgi/content/short/2025.06.05.657102v1?rss=1"
Asri, M.Chang, P.-C.Mier, J. C.Siren, J.Eskandar, P.Kolesnikov, A.Cook, D. E.Brambrink, L.Hickey, G.Novak, A. M.Dorfman, L.Webster, D. R.Carroll, A.Paten, B.Shafin, K.2025-06-06doi:10.1101/2025.06.05.657102Cold Spring Harbor Laboratory Press2025-06-06
<![CDATA[
Lossless Pangenome Indexing Using Tag Arrays
]]>
https://biorxiv.org/cgi/content/short/2025.05.12.653561v1?rss=1"
Eskandar, P.Paten, B.Siren, J.2025-05-15doi:10.1101/2025.05.12.653561Cold Spring Harbor Laboratory Press2025-05-15
<![CDATA[
A haplotype-resolved view of human gene regulation
]]>
https://biorxiv.org/cgi/content/short/2024.06.14.599122v1?rss=1"
Vollger, M. R.Swanson, E. G.Neph, S. J.Ranchalis, J.Munson, K. M.Ho, C.-H.Sedeno-Cortes, A. E.Fondrie, W. E.Bohaczuk, S. C.Mao, Y.Parmalee, N. L.Mallory, B. J.Harvey, W. T.Kwon, Y.Garcia, G. H.Hoekzema, K.Meyer, J. G.Cicek, M.Eichler, E. E.Noble, W. S.Witten, D. M.Bennett, J. T.Ray, J. P.Stergachis, A. B.2024-06-16doi:10.1101/2024.06.14.599122Cold Spring Harbor Laboratory Press2024-06-16
<![CDATA[
Assembling unmapped reads reveals hidden variation in South Asian genomes
]]>
https://biorxiv.org/cgi/content/short/2025.05.14.653340v1?rss=1"
15,000 placements within 1 kbp of a known GWAS hit. We used long read data from a subset of samples to validate the majority of their assembled sequences, aligned RNA-seq data to identify hundreds of unplaced contigs with transcriptional potential, and queried existing nucleotide databases to infer the origins of the remaining unplaced sequences. Our results highlight the limitations of even the most complete reference genomes and provide a model for understanding the distribution of hidden variation in any human population.
]]>Das, A.Biddanda, A.McCoy, R. C.Schatz, M.2025-05-14doi:10.1101/2025.05.14.653340Cold Spring Harbor Laboratory Press2025-05-14
<![CDATA[
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
]]>
https://biorxiv.org/cgi/content/short/2025.04.14.648685v1?rss=1"
Cheng, H.Qu, H.McKenzie, S.Lawrence, K. R.Windsor, R.Vella, M.Park, P. J.Li, H.2025-04-17doi:10.1101/2025.04.14.648685Cold Spring Harbor Laboratory Press2025-04-17
<![CDATA[
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
]]>
https://biorxiv.org/cgi/content/short/2025.05.26.656191v1?rss=1"
Huang, N.Human Pangenome Reference Consortium,Li, H.2025-05-29doi:10.1101/2025.05.26.656191Cold Spring Harbor Laboratory Press2025-05-29
<![CDATA[
Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702431v1?rss=1"
Qiu, Q.Zhang, H.Xia, Z.Gao, W.Leu, J.Liang, D.Li, Y.Su, Y.Feierman, E.Horn, E. V.Ming, G.-l.Korb, E.Song, H.Zhou, Z.Wu, H.2026-01-29doi:10.64898/2026.01.29.702431Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
Highly sensitive and scalable time-resolved RNA sequencing in single cells with scNT-seq2
]]>
https://biorxiv.org/cgi/content/short/2025.06.03.657745v1?rss=1"
Qiu, Q.Zhang, H.Gao, W.Li, F.Liang, D.Wu, H.2025-06-03doi:10.1101/2025.06.03.657745Cold Spring Harbor Laboratory Press2025-06-03
<![CDATA[
Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts
]]>
https://biorxiv.org/cgi/content/short/2025.04.01.646460v1?rss=1"
Gao, W.Hu, P.Qiu, Q.Kang, X.Bedi, K.Sasaki, K.Margulies, K.Wu, H.2025-04-07doi:10.1101/2025.04.01.646460Cold Spring Harbor Laboratory Press2025-04-07
<![CDATA[
5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells
]]>
https://biorxiv.org/cgi/content/short/2023.09.26.559662v1?rss=1"
Wei, A.Zhang, H.Qiu, Q.Fabyanic, E. B.Hu, P.Wu, H.2023-09-27doi:10.1101/2023.09.26.559662Cold Spring Harbor Laboratory Press2023-09-27
<![CDATA[
A transient dermal niche and dual epidermal programs underlie sweat gland development
]]>
https://biorxiv.org/cgi/content/short/2023.04.15.537037v1?rss=1"
Dingwall, H. L.Tomizawa, R. R.Aharoni, A.Hu, P.Qiu, Q.Kokalari, B.Martinez, S. M.Donahue, J. C.Aldea, D.Mendoza, M.Glass, I. A.Birth Defects Research Laboratory,Wu, H.Kamberov, Y. G.2023-04-17doi:10.1101/2023.04.15.537037Cold Spring Harbor Laboratory Press2023-04-17
<![CDATA[
pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction
]]>
https://biorxiv.org/cgi/content/short/2026.03.12.711379v1?rss=1"
Su, Y.Liu, D.Menon, V.Song, B.Boccara, S.Zhang, N.Zhao, H.Zhao, J. H.Wang, L.Hu, N.Nzima, M.Katz, A.Swargam, B. K.Ament, S. A.Diao, Y.Zhang, H.Chao, L.Hon, G.Huangfu, D.Li, W.2026-03-16doi:10.64898/2026.03.12.711379Cold Spring Harbor Laboratory Press2026-03-16
<![CDATA[
FourC: identifying significant and differential contacts in 1D chromatin conformation data
]]>
https://biorxiv.org/cgi/content/short/2026.03.05.709811v1?rss=1"
Wong, W.Kaplan, S. J.Luo, R.Pulecio Rojas, J. A.Yan, J.Huangfu, D.Leslie, C. S.2026-03-07doi:10.64898/2026.03.05.709811Cold Spring Harbor Laboratory Press2026-03-07
<![CDATA[
Reprogramming of neuronal genome function and phenotype by astrocytes
]]>
https://biorxiv.org/cgi/content/short/2026.03.07.710282v1?rss=1"
200 astrocyte-responsive TF genes uncovered discrete functional clusters that promote neuronal maturity or stemness
C_LIO_LIAstrocyte-responsive TF genes reprogram neuronal electrophysiology and neurite morphology
C_LI
]]>Li, B.Hagy, K.Safi, A.Beer, M. A.Barrera, A.Geraghty, S.Rai, R.Pederson, A. N.Reisman, S. J.Love, M. I.Sullivan, P. F.Eroglu, C.Crawford, G. E.Gersbach, C. A.2026-03-07doi:10.64898/2026.03.07.710282Cold Spring Harbor Laboratory Press2026-03-07
<![CDATA[
Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation
]]>
https://biorxiv.org/cgi/content/short/2025.08.07.669196v1?rss=1"
Yan, J.Cho, H. S.Luo, R.Beer, M. A.Li, W.Huangfu, D.2025-08-08doi:10.1101/2025.08.07.669196Cold Spring Harbor Laboratory Press2025-08-08
<![CDATA[
Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells
]]>
https://biorxiv.org/cgi/content/short/2024.12.21.628413v1?rss=1"
Yan, J.Luo, R.Rosen, B. P.Liu, D.Wong, W.Leslie, C. S.Huangfu, D.2024-12-21doi:10.1101/2024.12.21.628413Cold Spring Harbor Laboratory Press2024-12-21
<![CDATA[
Parallel genome-scale CRISPR screens distinguish pluripotency and self-renewal
]]>
https://biorxiv.org/cgi/content/short/2023.05.03.539283v1?rss=1"
Rosen, B. P.Li, Q. V.Cho, H.Liu, D.Yang, D.Graff, S.Yan, J.Luo, R.Verma, N.Damodaran, J. R.Beer, M. A.Sidoli, S.Huangfu, D.2023-05-03doi:10.1101/2023.05.03.539283Cold Spring Harbor Laboratory Press2023-05-03
<![CDATA[
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant
]]>
https://biorxiv.org/cgi/content/short/2024.04.26.591412v1?rss=1"
Kaplan, S. J.Wong, W.Yan, J.Pulecio, J.Cho, H.Leslie-Iyer, J.Kazakov, J.Zhao, J.Li, Q.Murphy, D.Luo, R.Dey, K. K.Apostolou, E.Lesie, C. S.Huangfu, D.2024-04-29doi:10.1101/2024.04.26.591412Cold Spring Harbor Laboratory Press2024-04-29
<![CDATA[
Decoding Heterogenous Single-cell Perturbation Responses
]]>
https://biorxiv.org/cgi/content/short/2023.10.30.564796v1?rss=1"
Song, B.Liu, D.Dai, W.McMyn, N.Wang, Q.Yang, D.Krejci, A.Vasilyev, A.Untermoser, N.Loregger, A.Song, D.Williams, B.Rosen, B.Cheng, X.Chao, L.Kale, H.Zhang, H.Diao, Y.Bürckstümmer, T.Siliciano, J. M.Li, J. J.Siliciano, R.Huangfu, D.Li, W.2023-11-02doi:10.1101/2023.10.30.564796Cold Spring Harbor Laboratory Press2023-11-02
<![CDATA[
Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells
]]>
https://biorxiv.org/cgi/content/short/2023.06.14.544990v1?rss=1"
Pulecio, J.Tayyebi, Z.Liu, D.Wong, W.Luo, R.Damodaran, J. R.Kaplan, S.Cho, H.Yan, J.Murphy, D. J.Rickert, R.Shukla, A.Zhong, A.Gonzalez, F.Yang, D.Li, W.Zhou, T.Apostolou, E.Leslie, C.Huangfu, D.2023-06-14doi:10.1101/2023.06.14.544990Cold Spring Harbor Laboratory Press2023-06-14
<![CDATA[
Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions
]]>
https://biorxiv.org/cgi/content/short/2023.03.07.531569v1?rss=1"
Luo, R.Yan, J.Oh, J. W.Xi, W.Shigaki, D.Wong, W.Cho, H.Murphy, D.Cutler, R.Rosen, B. P.Pulecio, J.Yang, D.Glenn, R.Chen, T.Li, Q. V.Vierbuchen, T.Sidoli, S.Apostolou, E.Huangfu, D.Beer, M. A.2023-03-09doi:10.1101/2023.03.07.531569Cold Spring Harbor Laboratory Press2023-03-09
<![CDATA[
Functional genomics reveals mediators of beta cell survival in ER stress and type 2 diabetes risk
]]>
https://biorxiv.org/cgi/content/short/2026.03.30.715154v1?rss=1"
Okino, M.-L.Zhu, H.Corban, S.Benaglio, P.Djulamsah, J.OMahony, B.Vanderstel, K.Elgamal, R.Miller, M.Wang, A.Sander, M.Gaulton, K. J.2026-04-02doi:10.64898/2026.03.30.715154Cold Spring Harbor Laboratory Press2026-04-02
<![CDATA[
Comprehensive molecular impact mapping of common and rare variants at GWAS loci
]]>
https://biorxiv.org/cgi/content/short/2025.06.05.658079v1?rss=1"
7 times as many contexts as Enformer, which allows for better detection of variant effects at expression quantitative trait loci (eQTLs). We also introduce DNACipher Deep Variant Impact Mapping (DVIM), a method to identify variants with molecular effects at genome-wide association study (GWAS) loci. Application of DVIM to type 1 diabetes (T1D) reduced the mean fine-mapping credible set size from 24 to 1.4 variants per signal. DVIM variants had significantly higher fine-mapping posterior probabilities, and their predicted effects were supported by single-nucleus ATAC-seq and luciferase assays. DVIM also detected 6547 rare variants with molecular effects at 96% of GWAS T1D loci, and these were enriched for associations with immune traits. In summary, DNACipher DVIM prioritises common and rare variants at GWAS loci by predicting molecular effects across a broad range of contexts.
]]>Balderson, B.Tule, S.Okino, M.-L.Rieger, W. J.Corban, S.Jaureguy, J.Palpant, N.Gaulton, K. J.Boden, M.McVicker, G.2025-06-06doi:10.1101/2025.06.05.658079Cold Spring Harbor Laboratory Press2025-06-06
<![CDATA[
Linking molecular pathways and islet cell dysfunction in human type 1 diabetes
]]>
https://biorxiv.org/cgi/content/short/2025.02.20.639325v1?rss=1"
dos Santos, T.Dai, X. Q.Jones, R. C.Spigelman, A. F.Mummey, H. M.Ewald, J. D.Ellis, C. E.Lyon, J. G.Smith, N.Bautista, A.Manning Fox, J. E.Neff, N. F.Detweiler, A.Tan, M.Arrojo e Drigo, R.Xia, J.Camunas-Soler, J.Gaulton, K. J.Quake, S. R.MacDonald, P. E.2025-02-21doi:10.1101/2025.02.20.639325Cold Spring Harbor Laboratory Press2025-02-21
<![CDATA[
GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics
]]>
https://biorxiv.org/cgi/content/short/2025.01.15.633240v1?rss=1"
Laub, D.Ho, A.Jaureguy, J.Klie, A.Salem, R. M.McVicker, G.Carter, H.2025-01-17doi:10.1101/2025.01.15.633240Cold Spring Harbor Laboratory Press2025-01-17
<![CDATA[
Single cell multiome profiling of pancreatic islets reveals physiological changes in cell type-specific regulation associated with diabetes risk
]]>
https://biorxiv.org/cgi/content/short/2024.08.03.606460v1?rss=1"
Mummey, H.Elison, W.Korgaonkar, K.Elgamel, R.Kudtarkar, P.Griffin, E.Benaglio, P.Miller, M.Jha, A.Manning Fox, J. E.Mccarthy, M.Preissl, S.Gloyn, A. L.Macdonald, P. E.Gaulton, K. J.2024-08-06doi:10.1101/2024.08.03.606460Cold Spring Harbor Laboratory Press2024-08-06
<![CDATA[
Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes.
]]>
https://biorxiv.org/cgi/content/short/2024.04.11.589096v1?rss=1"
Qadir, M. M. F.Elgamal, R. M.Song, K.Kudtarkar, P.Sakamuri, S. S. V. P.Katakam, P. V.El-Dahr, S.Kolls, J. K.Gaulton, K. J.Mauvais-Jarvis, F.2024-04-14doi:10.1101/2024.04.11.589096Cold Spring Harbor Laboratory Press2024-04-14
<![CDATA[
Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS
]]>
https://biorxiv.org/cgi/content/short/2023.08.03.551876v1?rss=1"
Ozturk, K.Panwala, R.Sheen, J.Ford, K.Payne, N.Zhang, D.-E.Hutter, S.Haferlach, T.Ideker, T.Mali, P.Carter, H.2023-08-04doi:10.1101/2023.08.03.551876Cold Spring Harbor Laboratory Press2023-08-04
<![CDATA[
EUGENe: A Python toolkit for predictive analyses of regulatory sequences
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513593v1?rss=1"
Klie, A.Stites, H.Jores, T.Carter, H.2022-10-26doi:10.1101/2022.10.24.513593Cold Spring Harbor Laboratory Press2022-10-26
<![CDATA[
MissenseHMM: state-based annotations for missense variants through joint modeling of pathogenicity scores
]]>
https://biorxiv.org/cgi/content/short/2026.01.31.703062v1?rss=1"
Li, R.Ernst, J.2026-02-03doi:10.64898/2026.01.31.703062Cold Spring Harbor Laboratory Press2026-02-03
<![CDATA[
Fast and powerful statistical method for context-specific QTL mapping in multi-context genomic studies
]]>
https://biorxiv.org/cgi/content/short/2021.06.17.448889v1?rss=1"
Lu, A.Thompson, M.Gordon, M. G.Dahl, A.Ye, C. J.Zaitlen, N.Balliu, B.2021-06-18doi:10.1101/2021.06.17.448889Cold Spring Harbor Laboratory Press2021-06-18
<![CDATA[
map3C: a computational tool for processing multiomic single-cell Hi-C data
]]>
https://biorxiv.org/cgi/content/short/2025.10.10.681728v1?rss=1"
Galasso, J.Wang, Y.Alber, F.Ernst, J.Luo, C.2025-10-15doi:10.1101/2025.10.10.681728Cold Spring Harbor Laboratory Press2025-10-15
<![CDATA[
GECSI: Large-scale chromatin state imputation from gene expression
]]>
https://biorxiv.org/cgi/content/short/2025.10.02.679828v1?rss=1"
Fu, J.Ernst, J.2025-10-04doi:10.1101/2025.10.02.679828Cold Spring Harbor Laboratory Press2025-10-04
<![CDATA[
Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux
]]>
https://biorxiv.org/cgi/content/short/2025.08.21.671671v1?rss=1"
95%) and was able to correctly assign singlets at considerably high ambient fractions (up to 60%) for both RNA and ATAC modalities. In comparison with models that do not consider ambient contamination, these only maintained similar sensitivity levels at considerably lower ambient fractions (up to 25%). We then generated a real data set of seven visceral adipose tissue biopsies run on a single 10x Multiome channel. We ran ambimux and detected 4,986 singlets, capturing similar numbers as other methods.
Then, we sought to evaluate the fidelity of the ambient fraction estimates from ambimux. We split singlets into ambient-enriched (>5% contamination in both modalities) or nuclear-enriched (<5% in both) droplets and performed gene-peak linkage analysis. Low ambient droplets resulted in more significant hits with gene-peak links enriched at the transcription start site relative to high ambient droplets, suggesting that the ambient droplets identified by ambimux hamper the identification of biologically meaningful signals. In summary, we developed a joint single-cell multiome demultiplexing method, ambimux, that accurately models and estimates ambient molecule contamination in each modality.
]]>Alvarez, M.Li, T.Lee, S. H. T.Arasu, U. T.Selvarajan, I.Örd, T.Rahmani, E.Chen, Z. J.Avram, O.Kar, A.Kaminska, D.Männistö, V.Halperin, E.Pihlajamäki, J.Luo, C.Kaikkonen, M. U.Zaitlen, N.Pajukanta, P.2025-08-26doi:10.1101/2025.08.21.671671Cold Spring Harbor Laboratory Press2025-08-26
<![CDATA[
The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments
]]>
https://biorxiv.org/cgi/content/short/2025.02.06.636969v1?rss=1"
Li, T.Alvarez, M.Liu, C.Abuhanna, K.Sun, Y.Ernst, J.Plath, K.Balliu, B.Luo, C.Zaitlen, N.2025-02-08doi:10.1101/2025.02.06.636969Cold Spring Harbor Laboratory Press2025-02-08
<![CDATA[
Learning a Pairwise Epigenomic and Transcription Factor Binding Association Score Across the Human Genome
]]>
https://biorxiv.org/cgi/content/short/2024.12.19.629547v1?rss=1"
Kwon, S. B.Ernst, J.2024-12-22doi:10.1101/2024.12.19.629547Cold Spring Harbor Laboratory Press2024-12-22
<![CDATA[
Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence and sex information
]]>
https://biorxiv.org/cgi/content/short/2024.03.20.585624v1?rss=1"
Li, R.Ernst, J.2024-03-21doi:10.1101/2024.03.20.585624Cold Spring Harbor Laboratory Press2024-03-21
<![CDATA[
Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types
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https://biorxiv.org/cgi/content/short/2023.07.14.549056v1?rss=1"
Dincer, T. U.Ernst, J.2023-07-15doi:10.1101/2023.07.14.549056Cold Spring Harbor Laboratory Press2023-07-15
<![CDATA[
Universal chromatin state annotation of the mouse genome
]]>
https://biorxiv.org/cgi/content/short/2022.12.19.521116v1?rss=1"
Vu, H. T.Ernst, J.2022-12-20doi:10.1101/2022.12.19.521116Cold Spring Harbor Laboratory Press2022-12-20
<![CDATA[
Chromatin state modeling across individuals reveals global patterns of histone modifications
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https://biorxiv.org/cgi/content/short/2022.08.02.502571v1?rss=1"
Zou, J.Ernst, J.2022-08-03doi:10.1101/2022.08.02.502571Cold Spring Harbor Laboratory Press2022-08-03
<![CDATA[
ChromGene: Gene-Based Modeling of Epigenomic Data
]]>
https://biorxiv.org/cgi/content/short/2022.05.24.493345v1?rss=1"
Jaroszewicz, A.Ernst, J.2022-05-25doi:10.1101/2022.05.24.493345Cold Spring Harbor Laboratory Press2022-05-25
<![CDATA[
A framework for summarizing chromatin state annotations within and identifying differential annotations across groups of samples
]]>
https://biorxiv.org/cgi/content/short/2022.05.08.491094v1?rss=1"
Vu, H. T.Koch, Z.Fiziev, P.Ernst, J.2022-05-08doi:10.1101/2022.05.08.491094Cold Spring Harbor Laboratory Press2022-05-08
<![CDATA[
Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells
]]>
https://biorxiv.org/cgi/content/short/2025.04.24.650458v1?rss=1"
Karbalayghareh, A.Barisic, D.Chin, C. R.Melnick, A.Leslie, C. S.2025-04-26doi:10.1101/2025.04.24.650458Cold Spring Harbor Laboratory Press2025-04-26
<![CDATA[
Deep topic modeling of spatial transcriptomics in the rheumatoid arthritis synovium identifies distinct classes of ectopic lymphoid structures
]]>
https://biorxiv.org/cgi/content/short/2025.01.08.631928v1?rss=1"
Periyakoil, P. K.Smith, M. H.Kshirsagar, M.Ramirez, D.DiCarlo, E. F.Goodman, S. M.Rudensky, A.Donlin, L.Leslie, C. S.2025-01-10doi:10.1101/2025.01.08.631928Cold Spring Harbor Laboratory Press2025-01-10
<![CDATA[
Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states
]]>
https://biorxiv.org/cgi/content/short/2024.07.31.606073v1?rss=1"
Southard, K. M.Ardy, R. C.Tang, A.O'Sullivan, D. D.Metzner, E.Guruvayurappan, K.Norman, T. M.2024-08-03doi:10.1101/2024.07.31.606073Cold Spring Harbor Laboratory Press2024-08-03
<![CDATA[
An encyclopedia of enhancer-gene regulatory interactions in the human genome
]]>
https://biorxiv.org/cgi/content/short/2023.11.09.563812v1?rss=1"
13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 element-gene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancer-promoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.
]]>Gschwind, A. R.Mualim, K. S.Karbalayghareh, A.Sheth, M. U.Dey, K. K.Jagoda, E.Nurtdinov, R. N.Xi, W.Tan, A. S.Jones, H.Ma, X. R.Yao, D.Nasser, J.Avsec, Z.James, B. T.Shamim, M. S.Durand, N. C.Rao, S. S. P.Mahajan, R.Doughty, B. R.Andreeva, K.Ulirsch, J. C.Fan, K.Perez, E. M.Nguyen, T. C.Kelley, D. R.Finucane, H. K.Moore, J. E.Weng, Z.Kellis, M.Bassik, M. C.Price, A. L.Beer, M. A.Guigo, R.Stamatoyannopoulos, J. A.Aiden, E. L.Greenleaf, W. J.Leslie, C. S.Steinmetz, L. M.Kundaje, A.Engreitz, J. M.2023-11-13doi:10.1101/2023.11.09.563812Cold Spring Harbor Laboratory Press2023-11-13
<![CDATA[
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility
]]>
https://biorxiv.org/cgi/content/short/2023.07.27.550836v1?rss=1"
Gao, V. R.Yang, R.Das, A.Luo, R.Luo, H.McNally, D. R.Karagiannidis, I.Rivas, M. A.Wang, Z.-m.Barisic, D.Karbalayghareh, A.Wong, W.Zhan, Y.Chin, C. R.Noble, W. S.Bilmes, J. A.Apostolou, E.Kharas, M.Beguelin, W.Viny, A. D.Huangfu, D.Rudensky, A.Melnick, A.Leslie, C. S.2023-07-28doi:10.1101/2023.07.27.550836Cold Spring Harbor Laboratory Press2023-07-28
<![CDATA[
Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
]]>
https://biorxiv.org/cgi/content/short/2022.05.02.490368v1?rss=1"
Schmidt, H.Zhang, M.Mourelatos, H.Sanchez-Rivera, F. J.Lowe, S. W.Ventura, A.Leslie, C. S.Pritykin, Y.2022-05-03doi:10.1101/2022.05.02.490368Cold Spring Harbor Laboratory Press2022-05-03
<![CDATA[
Heterogeneity of Inflammation-associated Synovial Fibroblasts in Rheumatoid Arthritis and Its Drivers
]]>
https://biorxiv.org/cgi/content/short/2022.02.28.482131v1?rss=1"
Smith, M. H.Gao, V. R.Schizas, M.Kochen, A.DiCarlo, E.Goodman, S.Norman, T. M.Donlin, L.Leslie, C. S.Rudensky, A. Y.2022-03-02doi:10.1101/2022.02.28.482131Cold Spring Harbor Laboratory Press2022-03-02
<![CDATA[
A scalable approach to resolving variants of uncertain significance
]]>
https://biorxiv.org/cgi/content/short/2026.02.14.705848v1?rss=1"
90,000 unobserved variants; 62% had enough evidence to be "preclassified" as pathogenic or benign. We validated our data, evidence and classifications using All of Us and created interactive resources to enable clinical use of the calibrated data. Thus, for 40 genes, representing 1% of the clinical genome, we resolve most existing VUS and future variants, illustrating how systematic use of scalable evidence can empower genomic medicine.
]]>Tejura, M.Chen, Y.McEwen, A. E.Stewart, R.Sverchkov, Y.Laval, F.Woo, I.Zeiberg, D.Shen, R.Fayer, S.Stone, J.Smith, N.Casadei, S.Wang, Z. R.Snyder, M.Capodanno, B. J.Gupta, P.Benazouz, M.Jain, S.Heidl, S.Muffley, L.Dong, S.Lin, K.Hitz, B. C.Gabdank, I.Da, E. Y.Best, S.Grindstaff, S.Reinhart, D.Rodriguez-Salas, L.Seid, O.Vandi, A. J.Wenman, C.Wheelock, M. K.Pendyala, S.Holmes, D.Xu, A.Hosokai, A.Tixhon, M.Reno, C.Ewald, J. D.Spirohn-Fitzgerald, K.Teelucksingh, T.Hao, T.Chen, Z. S.Haghighi, M.Hamid, A. K.2026-02-15doi:10.64898/2026.02.14.705848Cold Spring Harbor Laboratory Press2026-02-15
<![CDATA[
Uncertainty-aware synthetic lethality prediction with pretrained foundation models
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https://biorxiv.org/cgi/content/short/2026.02.25.708096v1?rss=1"
Hua, K.Haber, E.Ma, J.2026-02-27doi:10.64898/2026.02.25.708096Cold Spring Harbor Laboratory Press2026-02-27
<![CDATA[
Fully T2T pedigree assemblies reveal genetic stability and epigenetic plasticity of human centromeres across inheritance and cell-fate transitions
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https://biorxiv.org/cgi/content/short/2026.02.14.705860v1?rss=1"
Dong, S.Xing, X.Cechova, M.Loucks, H.Vijayalingam, S.Neilson, A.Sentmanat, M.Macias-Velasco, J. F.Liu, T.Dong, Z.Miao, B.Zhang, W.Tomlinson, C.Schmidt, H.Belter, E. A.Hu, M.Cui, X.Stitziel, N. O.Miga, K. H.Wang, T.2026-02-17doi:10.64898/2026.02.14.705860Cold Spring Harbor Laboratory Press2026-02-17
<![CDATA[
ToxiTaRGET: a multi-omics resource for toxicant-responsive molecular targets
]]>
https://biorxiv.org/cgi/content/short/2025.07.28.667228v1?rss=1"
Kumar, R.Fu, T.Kuntala, P. K.Fu, S.Li, D.Bartolomei, M. S.Walker, C. L.Wang, T.Zhang, B. A.2025-08-02doi:10.1101/2025.07.28.667228Cold Spring Harbor Laboratory Press2025-08-02
<![CDATA[
EYKTHYR reveals transcriptional regulators of spatial gene programs
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https://biorxiv.org/cgi/content/short/2025.05.19.654884v1?rss=1"
Krieger, S.Haber, E.Ma, J.2025-05-23doi:10.1101/2025.05.19.654884Cold Spring Harbor Laboratory Press2025-05-23
<![CDATA[
POPARI: Modeling multisample variation in spatial transcriptomics
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https://biorxiv.org/cgi/content/short/2025.05.08.652741v1?rss=1"
Alam, S.Zhou, T.Haber, E.Chidester, B.Liu, S.Chen, F.Ma, J.2025-05-13doi:10.1101/2025.05.08.652741Cold Spring Harbor Laboratory Press2025-05-13
<![CDATA[
STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues
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https://biorxiv.org/cgi/content/short/2025.04.06.647437v1?rss=1"
Liang, S.Tang, J.Wang, G.Ma, J.2025-04-10doi:10.1101/2025.04.06.647437Cold Spring Harbor Laboratory Press2025-04-10
<![CDATA[
Unified integration of spatial transcriptomics across platforms
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https://biorxiv.org/cgi/content/short/2025.03.31.646238v1?rss=1"
Haber, E.Deshpande, A.Ma, J.Krieger, S.2025-04-05doi:10.1101/2025.03.31.646238Cold Spring Harbor Laboratory Press2025-04-05
<![CDATA[
Expression spectrum of TE-derived transcripts in human adult tissues
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https://biorxiv.org/cgi/content/short/2025.03.29.646092v1?rss=1"
Miao, B.Zhang, B.WU, T. P.Luo, X.Ademovic, A.Yang, Y.2025-04-03doi:10.1101/2025.03.29.646092Cold Spring Harbor Laboratory Press2025-04-03
<![CDATA[
Machine Learning-Based Identification of Survival-Associated CpG Biomarkers in Pancreatic Ductal Adenocarcinoma
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https://biorxiv.org/cgi/content/short/2025.03.29.646090v1?rss=1"
Zhang, B.Zhang, Y.Zhao, Y.2025-04-01doi:10.1101/2025.03.29.646090Cold Spring Harbor Laboratory Press2025-04-01
<![CDATA[
DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks
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https://biorxiv.org/cgi/content/short/2025.01.06.631595v1?rss=1"
Cheng, W.Song, Z.Zhang, Y.Wang, S.Wang, D.Yang, M.Li, L.Ma, J.2025-01-08doi:10.1101/2025.01.06.631595Cold Spring Harbor Laboratory Press2025-01-08
<![CDATA[
L2G: Repurposing Language Models for Genomics Tasks
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https://biorxiv.org/cgi/content/short/2024.12.09.627422v1?rss=1"
Cheng, W.Shen, J.Khodak, M.Ma, J.Talwalkar, A.2024-12-11doi:10.1101/2024.12.09.627422Cold Spring Harbor Laboratory Press2024-12-11