Genome Research current issue 今日热榜

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最新

1.	Full-resolution HLA and KIR gene annotations for human genome assemblies [METHODS]	Zhou, Y., Song, L., Li, H.	
2.	Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization [RESOURCES]	Gardner, C., Chen, J., Hadfield, C., Lu, Z., Debruin, D., Zhan, Y., Donlin, M. J., Ahn, T.-H., Lin, Z.	
3.	Generation and analysis of a mouse multitissue genome annotation atlas [RESOURCES]	Adams, M., Vollmers, C.	
4.	Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter [METHODS]	Tesi, N., Salazar, A., Zhang, Y., van der Lee, S., Hulsman, M., Knoop, L., Wijesekera, S., Krizova, J., Schneider, A.-F., Pennings, M., Sleegers, K., Kamsteeg, E.-J., Reinders, M., Holstege, H.	
5.	Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations [RESOURCES]	Zhang, W., Guenther, A., Gao, Y., Ullrich, K., Huettel, B., Ahmad, A., Duan, L., Wei, K., Tautz, D.	
6.	Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding [RESOURCES]	Li, K., Smith, M. L., Blazier, J. C., Kochan, K. J., Wood, J. M. D., Howe, K., Kwitek, A. E., Dwinell, M. R., Chen, H., Ciosek, J. L., Masterson, P., Murphy, T. D., Kalbfleisch, T. S., Doris, P. A.	
7.	Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe [RESOURCES]	Byerly, P. A., von Thaden, A., Leushkin, E., Hilgers, L., Liu, S., Winter, S., Schell, T., Gerheim, C., Ben Hamadou, A., Greve, C., Betz, C., Bolz, H. J., Büchner, S., Lang, J., Meinig, H., Famira-Parcsetich, E. M., Stubbe, S. P., Mouton, A., Bertolino, S., Verbeylen, G., Briner, T., Freixas, L., Vinciguerra, L., Mueller, S. A., Nowak, C., Hiller, M.	
8.	High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation [RESOURCES]	Gustafson, J. A., Gibson, S. B., Damaraju, N., Zalusky, M. P. G., Hoekzema, K., Twesigomwe, D., Yang, L., Snead, A. A., Richmond, P. A., De Coster, W., Olson, N. D., Guarracino, A., Li, Q., Miller, A. L., Goffena, J., Anderson, Z. B., Storz, S. H. R., Ward, S. A., Sinha, M., Gonzaga-Jauregui, C., Clarke, W. E., Basile, A. O., Corvelo, A., Reeves, C., Helland, A., Musunuri, R. L., Revsine, M., Patterson, K. E., Paschal, C. R., Zakarian, C., Goodwin, S., Jensen, T. D., Robb, E., The 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CRDR), Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, McCombie, W. R., Sedlazeck, F. J., Zook, J. M., Montgomery, S. B., Garrison, E., Kolmogorov, M., Schatz, M. C., McLaughlin, R. N., Dashnow, H., Zody, M. C., Loose, M., Jain, M., Eichler, E. E., Miller, D. E.	
9.	Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR [RESOURCES]	De Coster, W., Höijer, I., Bruggeman, I., D'Hert, S., Melin, M., Ameur, A., Rademakers, R.	
10.	Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors [METHODS]	Lohde, M., Wagner, G. E., Dabernig-Heinz, J., Viehweger, A., Braun, S. D., Monecke, S., Diezel, C., Stein, C., Marquet, M., Ehricht, R., Pletz, M. W., Brandt, C.	
11.	Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution [METHODS]	Jagannatha, P., Tankka, A. T., Lorenz, D. A., Yu, T., Yee, B. A., Brannan, K. W., Zhou, C. J., Underwood, J. G., Yeo, G. W.	
12.	Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework [METHODS]	Teng, H., Stoiber, M., Bar-Joseph, Z., Kingsford, C.	
13.	Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation [METHODS]	Ritter, A. J., Draper, J. M., Vollmers, C., Sanford, J. R.	
14.	An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing [METHODS]	Zeglinski, K., Montellese, C., Ritchie, M. E., Alhamdoosh, M., Vonarburg, C., Bowden, R., Jordi, M., Gouil, Q., Aeschimann, F., Hsu, A.	
15.	DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools [METHODS]	Jha, A., Bohaczuk, S. C., Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Dubocanin, D., Finkbeiner, C., Li, T., Whittington, D., Noble, W. S., Stergachis, A. B., Vollger, M. R.	
16.	Gapless assembly of complete human and plant chromosomes using only nanopore sequencing [METHODS]	Koren, S., Bao, Z., Guarracino, A., Ou, S., Goodwin, S., Jenike, K. M., Lucas, J., McNulty, B., Park, J., Rautiainen, M., Rhie, A., Roelofs, D., Schneiders, H., Vrijenhoek, I., Nijbroek, K., Nordesjo, O., Nurk, S., Vella, M., Lawrence, K. R., Ware, D., Schatz, M. C., Garrison, E., Huang, S., McCombie, W. R., Miga, K. H., Wittenberg, A. H. J., Phillippy, A. M.	
17.	Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing [METHODS]	Gocuk, S. A., Lancaster, J., Su, S., Jolly, J. K., Edwards, T. L., Hickey, D. G., Ritchie, M. E., Blewitt, M. E., Ayton, L. N., Gouil, Q.	
18.	Factors impacting target-enriched long-read sequencing of resistomes and mobilomes [METHODS]	Slizovskiy, I. B., Bonin, N., Bravo, J. E., Ferm, P. M., Singer, J., Boucher, C., Noyes, N. R.	
19.	Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications [METHODS]	Liu, X., Ni, Y., Ye, L., Guo, Z., Tan, L., Li, J., Yang, M., Chen, S., Li, R.	
20.	Telomere-to-telomere assembly by preserving contained reads [METHODS]	Kamath, S. S., Bindra, M., Pal, D., Jain, C.	
21.	Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations [RESEARCH]	Pacholewska, A., Lienhard, M., Brüggemann, M., Hänel, H., Bilalli, L., Königs, A., Hess, F., Becker, K., Köhrer, K., Kaiser, J., Gohlke, H., Gattermann, N., Hallek, M., Herling, C. D., König, J., Grimm, C., Herwig, R., Zarnack, K., Schweiger, M. R.	
22.	Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC [RESEARCH]	Gomez-Simmonds, A., Annavajhala, M. K., Seeram, D., Hokunson, T. W., Park, H., Uhlemann, A.-C.	
23.	Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events [RESEARCH]	Volaric, M., Despot-Slade, E., Veseljak, D., Mravinac, B., Mestrovic, N.	
24.	Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models [RESEARCH]	Diensthuber, G., Pryszcz, L. P., Llovera, L., Lucas, M. C., Delgado-Tejedor, A., Cruciani, S., Roignant, J.-Y., Begik, O., Novoa, E. M.	
25.	Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion [RESEARCH]	Lee, J., Snell, E. A., Brown, J., Booth, C. E., Banks, R. E., Turner, D. J., Vasudev, N. S., Lagos, D.	
26.	Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques [RESEARCH]	de Groot, N., van der Wiel, M., Le, N. G., de Groot, N. G., Bruijnesteijn, J., Bontrop, R. E.	
27.	Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps [RESEARCH]	Bilgrav Saether, K., Eisfeldt, J., Bengtsson, J. D., Lun, M. Y., Grochowski, C. M., Mahmoud, M., Chao, H.-T., Rosenfeld, J. A., Liu, P., Ek, M., Schuy, J., Ameur, A., Dai, H., Undiagnosed Diseases Network, Hwang, J. P., Sedlazeck, F. J., Bi, W., Marom, R., Wincent, J., Nordgren, A., Carvalho, C. M. B., Lindstrand, A.	
28.	Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes [RESEARCH]	Gulsuner, S., AbuRayyan, A., Mandell, J. B., Lee, M. K., Bernier, G. V., Norquist, B. M., Pierce, S. B., King, M.-C., Walsh, T.	
29.	Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing [RESEARCH]	Eisfeldt, J., Higginbotham, E. J., Lenner, F., Howe, J., Fernandez, B. A., Lindstrand, A., Scherer, S. W., Feuk, L.	
30.	Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans [RESEARCH]	Guitart, X., Porubsky, D., Yoo, D., Dougherty, M. L., Dishuck, P. C., Munson, K. M., Lewis, A. P., Hoekzema, K., Knuth, J., Chang, S., Pastinen, T., Eichler, E. E.	
31.	Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics [REVIEWS]	Belchikov, N., Hsu, J., Li, X. J., Jarroux, J., Hu, W., Joglekar, A., Tilgner, H. U.	
32.	A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities [RESEARCH]	Eisfeldt, J., Ameur, A., Lenner, F., Ten Berk de Boer, E., Ek, M., Wincent, J., Vaz, R., Ottosson, J., Jonson, T., Ivarsson, S., Thunström, S., Topa, A., Stenberg, S., Rohlin, A., Sandestig, A., Nordling, M., Palmebäck, P., Burstedt, M., Nordin, F., Stattin, E.-L., Sobol, M., Baliakas, P., Bondeson, M.-L., Höijer, I., Saether, K. B., Lovmar, L., Ehrencrona, H., Melin, M., Feuk, L., Lindstrand, A.	
33.	Leveraging the power of long reads for targeted sequencing [REVIEWS]	Iyer, S. V., Goodwin, S., McCombie, W. R.	
34.	Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders [RESEARCH]	Hiatt, S. M., Lawlor, J. M. J., Handley, L. H., Latner, D. R., Bonnstetter, Z. T., Finnila, C. R., Thompson, M. L., Boston, L. B., Williams, M., Rodriguez Nunez, I., Jenkins, J., Kelley, W. V., Bebin, E. M., Lopez, M. A., Hurst, A. C. E., Korf, B. R., Schmutz, J., Grimwood, J., Cooper, G. M.	
35.	Revolutionizing genomics and medicine--one long molecule at a time [EDITORIAL]	Conesa, A., Hoischen, A., Sedlazeck, F. J.	
36.	Challenges in identifying mRNA transcript starts and ends from long-read sequencing data [PERSPECTIVE]	Calvo-Roitberg, E., Daniels, R. F., Pai, A. A.	

更新于 13 分钟前

近期历史最近 100 条记录

2024-11-21	Full-resolution HLA and KIR gene annotations for human genome assemblies [METHODS]	Zhou, Y., Song, L., Li, H.	
2024-11-21	Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization [RESOURCES]	Gardner, C., Chen, J., Hadfield, C., Lu, Z., Debruin, D., Zhan, Y., Donlin, M. J., Ahn, T.-H., Lin, Z.	
2024-11-21	Generation and analysis of a mouse multitissue genome annotation atlas [RESOURCES]	Adams, M., Vollmers, C.	
2024-11-21	Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter [METHODS]	Tesi, N., Salazar, A., Zhang, Y., van der Lee, S., Hulsman, M., Knoop, L., Wijesekera, S., Krizova, J., Schneider, A.-F., Pennings, M., Sleegers, K., Kamsteeg, E.-J., Reinders, M., Holstege, H.	
2024-11-21	Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations [RESOURCES]	Zhang, W., Guenther, A., Gao, Y., Ullrich, K., Huettel, B., Ahmad, A., Duan, L., Wei, K., Tautz, D.	
2024-11-21	Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding [RESOURCES]	Li, K., Smith, M. L., Blazier, J. C., Kochan, K. J., Wood, J. M. D., Howe, K., Kwitek, A. E., Dwinell, M. R., Chen, H., Ciosek, J. L., Masterson, P., Murphy, T. D., Kalbfleisch, T. S., Doris, P. A.	
2024-11-21	Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe [RESOURCES]	Byerly, P. A., von Thaden, A., Leushkin, E., Hilgers, L., Liu, S., Winter, S., Schell, T., Gerheim, C., Ben Hamadou, A., Greve, C., Betz, C., Bolz, H. J., Büchner, S., Lang, J., Meinig, H., Famira-Parcsetich, E. M., Stubbe, S. P., Mouton, A.,	
2024-11-21	High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation [RESOURCES]	Gustafson, J. A., Gibson, S. B., Damaraju, N., Zalusky, M. P. G., Hoekzema, K., Twesigomwe, D., Yang, L., Snead, A. A., Richmond, P. A., De Coster, W., Olson, N. D., Guarracino, A., Li, Q., Miller, A. L., Goffena, J., Anderson, Z. B., Storz, S. H. R., War	
2024-11-21	Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR [RESOURCES]	De Coster, W., Höijer, I., Bruggeman, I., D'Hert, S., Melin, M., Ameur, A., Rademakers, R.	
2024-11-21	Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors [METHODS]	Lohde, M., Wagner, G. E., Dabernig-Heinz, J., Viehweger, A., Braun, S. D., Monecke, S., Diezel, C., Stein, C., Marquet, M., Ehricht, R., Pletz, M. W., Brandt, C.	
2024-11-21	Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution [METHODS]	Jagannatha, P., Tankka, A. T., Lorenz, D. A., Yu, T., Yee, B. A., Brannan, K. W., Zhou, C. J., Underwood, J. G., Yeo, G. W.	
2024-11-21	Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework [METHODS]	Teng, H., Stoiber, M., Bar-Joseph, Z., Kingsford, C.	
2024-11-21	Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation [METHODS]	Ritter, A. J., Draper, J. M., Vollmers, C., Sanford, J. R.	
2024-11-21	An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing [METHODS]	Zeglinski, K., Montellese, C., Ritchie, M. E., Alhamdoosh, M., Vonarburg, C., Bowden, R., Jordi, M., Gouil, Q., Aeschimann, F., Hsu, A.	
2024-11-21	DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools [METHODS]	Jha, A., Bohaczuk, S. C., Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Dubocanin, D., Finkbeiner, C., Li, T., Whittington, D., Noble, W. S., Stergachis, A. B., Vollger, M. R.	
2024-11-21	Gapless assembly of complete human and plant chromosomes using only nanopore sequencing [METHODS]	Koren, S., Bao, Z., Guarracino, A., Ou, S., Goodwin, S., Jenike, K. M., Lucas, J., McNulty, B., Park, J., Rautiainen, M., Rhie, A., Roelofs, D., Schneiders, H., Vrijenhoek, I., Nijbroek, K., Nordesjo, O., Nurk, S., Vella, M., Lawrence, K. R., Ware, D., Sc	
2024-11-21	Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing [METHODS]	Gocuk, S. A., Lancaster, J., Su, S., Jolly, J. K., Edwards, T. L., Hickey, D. G., Ritchie, M. E., Blewitt, M. E., Ayton, L. N., Gouil, Q.	
2024-11-21	Factors impacting target-enriched long-read sequencing of resistomes and mobilomes [METHODS]	Slizovskiy, I. B., Bonin, N., Bravo, J. E., Ferm, P. M., Singer, J., Boucher, C., Noyes, N. R.	
2024-11-21	Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications [METHODS]	Liu, X., Ni, Y., Ye, L., Guo, Z., Tan, L., Li, J., Yang, M., Chen, S., Li, R.	
2024-11-21	Telomere-to-telomere assembly by preserving contained reads [METHODS]	Kamath, S. S., Bindra, M., Pal, D., Jain, C.	
2024-11-21	Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations [RESEARCH]	Pacholewska, A., Lienhard, M., Brüggemann, M., Hänel, H., Bilalli, L., Königs, A., Hess, F., Becker, K., Köhrer, K., Kaiser, J., Gohlke, H., Gattermann, N., Hallek, M., Herling, C. D., König, J.,	
2024-11-21	Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC [RESEARCH]	Gomez-Simmonds, A., Annavajhala, M. K., Seeram, D., Hokunson, T. W., Park, H., Uhlemann, A.-C.	
2024-11-21	Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events [RESEARCH]	Volaric, M., Despot-Slade, E., Veseljak, D., Mravinac, B., Mestrovic, N.	
2024-11-21	Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models [RESEARCH]	Diensthuber, G., Pryszcz, L. P., Llovera, L., Lucas, M. C., Delgado-Tejedor, A., Cruciani, S., Roignant, J.-Y., Begik, O., Novoa, E. M.	
2024-11-21	Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion [RESEARCH]	Lee, J., Snell, E. A., Brown, J., Booth, C. E., Banks, R. E., Turner, D. J., Vasudev, N. S., Lagos, D.	
2024-11-21	Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques [RESEARCH]	de Groot, N., van der Wiel, M., Le, N. G., de Groot, N. G., Bruijnesteijn, J., Bontrop, R. E.	
2024-11-21	Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps [RESEARCH]	Bilgrav Saether, K., Eisfeldt, J., Bengtsson, J. D., Lun, M. Y., Grochowski, C. M., Mahmoud, M., Chao, H.-T., Rosenfeld, J. A., Liu, P., Ek, M., Schuy, J., Ameur, A., Dai, H., Undiagnosed Diseases Network, Hwang, J. P., Sedlazeck, F. J., Bi, W., Marom, R.	
2024-11-21	Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes [RESEARCH]	Gulsuner, S., AbuRayyan, A., Mandell, J. B., Lee, M. K., Bernier, G. V., Norquist, B. M., Pierce, S. B., King, M.-C., Walsh, T.	
2024-11-21	Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing [RESEARCH]	Eisfeldt, J., Higginbotham, E. J., Lenner, F., Howe, J., Fernandez, B. A., Lindstrand, A., Scherer, S. W., Feuk, L.	
2024-11-21	Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans [RESEARCH]	Guitart, X., Porubsky, D., Yoo, D., Dougherty, M. L., Dishuck, P. C., Munson, K. M., Lewis, A. P., Hoekzema, K., Knuth, J., Chang, S., Pastinen, T., Eichler, E. E.	
2024-11-21	Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics [REVIEWS]	Belchikov, N., Hsu, J., Li, X. J., Jarroux, J., Hu, W., Joglekar, A., Tilgner, H. U.	
2024-11-21	A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities [RESEARCH]	Eisfeldt, J., Ameur, A., Lenner, F., Ten Berk de Boer, E., Ek, M., Wincent, J., Vaz, R., Ottosson, J., Jonson, T., Ivarsson, S., Thunström, S., Topa, A., Stenberg, S., Rohlin, A., Sandestig, A., Nordling, M., Palmebäck, P., Bursted	
2024-11-21	Leveraging the power of long reads for targeted sequencing [REVIEWS]	Iyer, S. V., Goodwin, S., McCombie, W. R.	
2024-11-21	Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders [RESEARCH]	Hiatt, S. M., Lawlor, J. M. J., Handley, L. H., Latner, D. R., Bonnstetter, Z. T., Finnila, C. R., Thompson, M. L., Boston, L. B., Williams, M., Rodriguez Nunez, I., Jenkins, J., Kelley, W. V., Bebin, E. M., Lopez, M. A., Hurst, A. C. E., Korf, B. R., Sch	
2024-11-21	Revolutionizing genomics and medicine--one long molecule at a time [EDITORIAL]	Conesa, A., Hoischen, A., Sedlazeck, F. J.	
2024-11-21	Challenges in identifying mRNA transcript starts and ends from long-read sequencing data [PERSPECTIVE]	Calvo-Roitberg, E., Daniels, R. F., Pai, A. A.	
2024-10-29	Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change [METHODS]	Narechania, A., Bobo, D., Deitz, K., DeSalle, R., Planet, P. J., Mathema, B.	
2024-10-29	Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis [METHODS]	Derelle, R., von Wachsmann, J., Mäklin, T., Hellewell, J., Russell, T., Lalvani, A., Chindelevitch, L., Croucher, N. J., Harris, S. R., Lees, J. A.	
2024-10-29	Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads [METHODS]	Han, S. W., Jewell, S., Thomas-Tikhonenko, A., Barash, Y.	
2024-10-29	Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data [METHODS]	Petrany, A., Chen, R., Zhang, S., Chen, Y.	
2024-10-29	Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements [RESEARCH]	Valentin-Alvarado, L. E., Shi, L.-D., Appler, K. E., Crits-Christoph, A., De Anda, V., Adler, B. A., Cui, M. L., Ly, L., Leao, P., Roberts, R. J., Sachdeva, R., Baker, B. J., Savage, D. F., Banfield, J. F.	
2024-10-29	Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories [METHODS]	Hristov, B. H., Noble, W. S., Bertero, A.	
2024-10-29	PWAS Hub for exploring gene-based associations of common complex diseases [RESOURCES]	Kelman, G., Zucker, R., Brandes, N., Linial, M.	
2024-10-29	Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level [RESOURCES]	Deng, W., Citu, C., Liu, A., Zhao, Z.	
2024-10-29	AGAP duplicons associate with structural diversity at Chromosome 10q11.22 [RESEARCH]	Fornezza, S., Delvecchio, V. S., Harvey, W. T., Dishuck, P. C., Eichler, E. E., Giannuzzi, G.	
2024-10-29	Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists [RESEARCH]	Sajek, M. P., Bilodeau, D. Y., Beer, M. A., Horton, E., Miyamoto, Y., Velle, K. B., Eckmann, L., Fritz-Laylin, L., Rissland, O. S., Mukherjee, N.	
2024-10-29	De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes [RESEARCH]	Bista, B., Gonzalez-Rodelas, L., Alvarez-Gonzalez, L., Wu, Z.-q., Montiel, E. E., Lee, L. S., Badenhorst, D. B., Radhakrishnan, S., Literman, R., Navarro-Dominguez, B., Iverson, J. B., Orozco-Arias, S., Gonzalez, J., Ruiz-Herrera, A., Valenzuela, N.	
2024-10-29	Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain [RESEARCH]	Shepherdson, J. L., Granas, D. M., Li, J., Shariff, Z., Plassmeyer, S. P., Holehouse, A. S., White, M. A., Cohen, B. A.	
2024-10-29	Evidence for compensatory evolution within pleiotropic regulatory elements [RESEARCH]	Kliesmete, Z., Orchard, P., Lee, V. Y. K., Geuder, J., Krauss, S. M., Ohnuki, M., Jocher, J., Vieth, B., Enard, W., Hellmann, I.	
2024-10-29	Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer [RESEARCH]	Song, Y., Li, F., Wang, S., Wang, Y., Lai, C., Chen, L., Jiang, N., Li, J., Chen, X., Bailey, S. D., Zhang, X.	
2024-10-29	Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples [RESEARCH]	Hu, T., Mosbruger, T. L., Tairis, N. G., Dinou, A., Jayaraman, P., Sarmady, M., Brewster, K., Li, Y., Hayeck, T. J., Duke, J. L., Monos, D. S.	
2024-10-29	Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries [RESEARCH]	Hu, S., Zeng, X., Liu, Y., Li, Y., Qu, M., Jiao, W.-B., Han, Y., Kang, C.	
2024-10-29	The chromatin tapestry as a framework for neurodevelopment [MINI-REVIEW]	Nolan, B., Reznicek, T. E., Cummings, C. T., Rowley, M. J.	
2024-10-11	A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data [METHOD]	Park, C., Mani, S., Beltran-Velez, N., Maurer, K., Huang, T., Li, S., Gohil, S., Livak, K. J., Knowles, D. A., Wu, C. J., Azizi, E.	
2024-10-11	Bayesian inference of sample-specific coexpression networks [METHOD]	Saha, E., Fanfani, V., Mandros, P., Ben Guebila, M., Fischer, J., Shutta, K. H., DeMeo, D. L., Lopes-Ramos, C. M., Quackenbush, J.	
2024-10-11	Accurate assembly of circular RNAs with TERRACE [METHOD]	Zahin, T., Shi, Q., Zang, X. C., Shao, M.	
2024-10-11	Spatial Cellular Networks from omics data with SpaCeNet [METHOD]	Schrod, S., Lück, N., Lohmayer, R., Solbrig, S., Völkl, D., Wipfler, T., Shutta, K. H., Ben Guebila, M., Schäfer, A., Beissbarth, T., Zacharias, H. U., Oefner, P. J., Quackenbush, J., Altenbuchinger, M.	
2024-10-11	Memory-bound k-mer selection for large and evolutionarily diverse reference libraries [METHOD]	Sapcı, A. O. B., Mirarab, S.	
2024-10-11	Haplotype-aware sequence alignment to pangenome graphs [METHOD]	Chandra, G., Gibney, D., Jain, C.	
2024-10-11	Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption [METHOD]	Goldenberg, M., Mualem, L., Shahar, A., Snir, S., Akavia, A.	
2024-10-11	Protein domain embeddings for fast and accurate similarity search [METHOD]	Iovino, B. G., Tang, H., Ye, Y.	
2024-10-11	Matrix sketching framework for linear mixed models in association studies [METHOD]	Burch, M., Bose, A., Dexter, G., Parida, L., Drineas, P.	
2024-10-11	Secure discovery of genetic relatives across large-scale and distributed genomic data sets [METHOD]	Hong, M. M., Froelicher, D., Magner, R., Popic, V., Berger, B., Cho, H.	
2024-10-11	A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits [METHOD]	Fu, B., Anand, P., Anand, A., Mefford, J., Sankararaman, S.	
2024-10-11	Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy [METHOD]	Jeong, M., Pazokitoroudi, A., Liu, Z., Sankararaman, S.	
2024-10-11	Genetics-driven risk predictions leveraging the Mendelian randomization framework [METHOD]	Sens, D., Shilova, L., Gräf, L., Grebenshchikova, M., Eskofier, B. M., Casale, F. P.	
2024-10-11	Designing realistic regulatory DNA with autoregressive language models [METHOD]	Lal, A., Garfield, D., Biancalani, T., Eraslan, G.	
2024-10-11	Size-based expectation maximization for characterizing nucleosome positions and subtypes [METHOD]	Yang, J., Yen, K., Mahony, S.	
2024-10-11	A best-match approach for gene set analyses in embedding spaces [METHOD]	Li, L., Dannenfelser, R., Cruz, C., Yao, V.	
2024-10-11	CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing [METHOD]	Zhu, K., Jones, M. G., Luebeck, J., Bu, X., Yi, H., Hung, K. L., Wong, I. T.-L., Zhang, S., Mischel, P. S., Chang, H. Y., Bafna, V.	
2024-10-11	Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction [METHOD]	Zeng, S., Wang, D., Jiang, L., Xu, D.	
2024-10-11	Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil [METHOD]	Giurgiu, M., Wittstruck, N., Rodriguez-Fos, E., Chamorro Gonzalez, R., Brückner, L., Krienelke-Szymansky, A., Helmsauer, K., Hartebrodt, A., Euskirchen, P., Koche, R. P., Haase, K., Reinert, K., Henssen, A. G.	
2024-10-11	Graph-based self-supervised learning for repeat detection in metagenomic assembly [METHOD]	Azizpour, A., Balaji, A., Treangen, T. J., Segarra, S.	
2024-10-11	Innovations in computational biology: RECOMB 2024 Special Issue [EDITORIAL]	Ma, J., Berger, B.	
2024-09-26	Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize [RESOURCES]	Tibbs-Cortes, L. E., Guo, T., Andorf, C. M., Li, X., Yu, J.	
2024-09-26	Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs [RESOURCES]	Anderson, A. G., Moyers, B. A., Loupe, J. M., Rodriguez-Nunez, I., Felker, S. A., Lawlor, J. M. J., Bunney, W. E., Bunney, B. G., Cartagena, P. M., Sequeira, A., Watson, S. J., Akil, H., Mendenhall, E. M., Cooper, G. M., Myers, R. M.	
2024-09-26	A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types [RESOURCES]	Peng, F., Nordgren, C. E., Murray, J. I.	
2024-09-26	Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries [METHODS]	Wiens, M., Farahani, H., Scott, R. W., Underhill, T. M., Bashashati, A.	
2024-09-26	Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies [METHODS]	Hung, T.-K., Liu, W.-C., Lai, S.-K., Chuang, H.-W., Lee, Y.-C., Lin, H.-Y., Hsu, C.-L., Chen, C.-Y., Yang, Y.-C., Hsu, J. S., Chen, P.-L.	
2024-09-26	A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data [METHODS]	Chen, S., Wang, J., Jung, I., Qiu, Z., Gao, X., Li, Y.	
2024-09-26	A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma [METHODS]	Müller, J., Hartwig, C., Sonntag, M., Bitzer, L., Adelmann, C., Vainshtein, Y., Glanz, K., Decker, S. O., Brenner, T., Weber, G. F., von Haeseler, A., Sohn, K.	
2024-09-26	A simple method for finding related sequences by adding probabilities of alternative alignments [METHODS]	Frith, M. C.	
2024-09-26	Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage [RESEARCH]	Lowry, E., Wang, Y., Dagan, T., Mitchell, A.	
2024-09-26	Differences in activity and stability drive transposable element variation in tropical and temperate maize [RESEARCH]	Ou, S., Scheben, A., Collins, T., Qiu, Y., Seetharam, A. S., Menard, C. C., Manchanda, N., Gent, J. I., Schatz, M. C., Anderson, S. N., Hufford, M. B., Hirsch, C. N.	
2024-09-26	Genome-wide patterns of selection-drift variation strongly associate with organismal traits across the green plant lineage [RESEARCH]	Uthanumallian, K., Del Cortona, A., Coelho, S. M., De Clerck, O., Duchene, S., Verbruggen, H.	
2024-09-26	Widespread natural selection on metabolite levels in humans [RESEARCH]	Timasheva, Y., Lepik, K., Liska, O., Papp, B., Kutalik, Z.	
2024-08-21	Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana [RESOURCES]	Denyer, T., Wu, P.-J., Colt, K., Abramson, B. W., Pang, Z., Solansky, P., Mamerto, A., Nobori, T., Ecker, J. R., Lam, E., Michael, T. P., Timmermans, M. C. P.	
2024-08-21	Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs [METHODS]	Kuronen, J., Horsfield, S. T., Pöntinen, A. K., Mallawaarachchi, S., Arredondo-Alonso, S., Thorpe, H., Gladstone, R. A., Willems, R. J. L., Bentley, S. D., Croucher, N. J., Pensar, J., Lees, J. A., Tonkin-Hill, G., Corander, J.	
2024-08-21	Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [RESOURCES]	Xiang, G., He, X., Giardine, B. M., Isaac, K. J., Taylor, D. J., McCoy, R. C., Jansen, C., Keller, C. A., Wixom, A. Q., Cockburn, A., Miller, A., Qi, Q., He, Y., Li, Y., Lichtenberg, J., Heuston, E. F., Anderson, S. M., Luan, J., Vermunt, M. W., Yue, F.,	
2024-08-21	Delineating yeast cleavage and polyadenylation signals using deep learning [METHODS]	Stroup, E. K., Ji, Z.	
2024-08-21	Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences [METHODS]	Xu, C., Bao, S., Wang, Y., Li, W., Chen, H., Shen, Y., Jiang, T., Zhang, C.	
2024-08-21	A gene regulatory network-aware graph learning method for cell identity annotation in single-cell RNA-seq data [METHODS]	Zhao, M., Li, J., Liu, X., Ma, K., Tang, J., Guo, F.	
2024-08-21	CodonBERT large language model for mRNA vaccines [METHODS]	Li, S., Moayedpour, S., Li, R., Bailey, M., Riahi, S., Kogler-Anele, L., Miladi, M., Miner, J., Pertuy, F., Zheng, D., Wang, J., Balsubramani, A., Tran, K., Zacharia, M., Wu, M., Gu, X., Clinton, R., Asquith, C., Skaleski, J., Boeglin, L., Chivukula, S.,	
2024-08-21	High-fidelity, large-scale targeted profiling of microsatellites [METHODS]	Loh, C. A., Shields, D. A., Schwing, A., Evrony, G. D.	
2024-08-21	The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution [RESEARCH]	Li, X., Mank, J. E., Ban, L.	
2024-08-21	The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores [RESEARCH]	Liu, Y., Zhai, G., Su, J., Gong, Y., Yang, B., Lu, Q., Xi, L., Zheng, Y., Cao, J., Liu, H., Jin, J., Zhang, Z., Yang, Y., Zhu, X., Wang, Z., Gong, G., Mei, J., Yin, Z., Gozlan, R. E., Xie, S., Han, D.	
2024-07-24	Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere [CORRIGENDUM]	Wong, L. H., Brettingham-Moore, K. H., Chan, L., Quach, J. M., Anderson, M. A., Northrop, E. L., Hannan, R., Saffery, R., Shaw, M. L., Williams, E., Choo, K. H. A.	
2024-07-24	DEAD box RNA helicases are pervasive protein kinase interactors and activators [RESOURCES]	Hirth, A., Fatti, E., Netz, E., Acebron, S. P., Papageorgiou, D., Svorinic, A., Cruciat, C.-M., Karaulanov, E., Gopanenko, A., Zhu, T., Sinning, I., Krijgsveld, J., Kohlbacher, O., Niehrs, C.	
2024-07-24	Global compositional and functional states of the human gut microbiome in health and disease [RESOURCES]	Lee, S., Portlock, T., Le Chatelier, E., Garcia-Guevara, F., Clasen, F., Onate, F. P., Pons, N., Begum, N., Harzandi, A., Proffitt, C., Rosario, D., Vaga, S., Park, J., von Feilitzen, K., Johansson, F., Zhang, C., Edwards, L. A., Lombard, V., Gauthier, F.	
2024-07-24	Accurate estimation of pathway activity in single cells for clustering and differential analysis [METHODS]	Davis, D., Wizel, A., Drier, Y.	

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