BEDTools: a flexible suite of utilities for comparing genomic features

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Improved tools for biological sequence comparison.

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The Human Genome Browser at UCSC

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Galaxy: a platform for interactive large-scale genome analysis.Preprint

Giardine, B., Riemer, C., Hardison, R., Burhans, R. C., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005) · Genome Research · doi:10.1101/gr.4086505 · Cited by 2,217

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

White, N. M. A., Cabanski, C. R., Silva-Fisher, J., Dang, H. X., Govindan, R., & Maher, C. A. (2014) · Genome biology · doi:10.1186/preaccept-8565849481270705 · Cited by 225

deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

Zheng, L., Li, J., Wu, J., Sun, W., Liu, S., Wang, Z., Zhou, H., Yang, J., & Qu, L. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1273 · Cited by 226

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

Mall, M., Kareta, M. S., Chanda, S., Ahlenius, H., Perotti, N., Zhou, B., Grieder, S. D., Ge, X., Drake, S., Euong Ang, C., et al. (2017) · Nature · doi:10.1038/nature21722 · Cited by 225

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Lauria, F., Tebaldi, T., Bernabò, P., Groen, E. J. N., Gillingwater, T. H., & Viero, G. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006169 · Cited by 227

Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer

Zhang, H., Pandey, S., Travers, M. E., Sun, H., Morton, G. C., Madžo, J., Chung, W., Khowsathit, J., Pérez, Ó. C., Barrero, C. A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.051 · Cited by 223

Distinct mechanisms of microRNA sorting into cancer cell-derived extracellular vesicle subtypes

Temoche-Diaz, M. M., Shurtleff, M. J., Nottingham, R. M., Yao, J., Fadadu, R. P., Lambowitz, A. M., & Schekman, R. (2019) · eLife · doi:10.7554/elife.47544 · Cited by 227

Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration

Achuthan, V., Perreira, J. M., Sowd, G. A., Puray-Chavez, M., McDougall, W. M., Paulucci-Holthauzen, A., Wu, X., Fadel, H. J., Poeschla, E. M., Multani, A. S., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.08.002 · Cited by 205

Molecular and functional variation in iPSC-derived sensory neurons

HIPSCI Consortium, Schwartzentruber, J., Foskolou, S., Kilpinen, H., Rodrigues, J., Alasoo, K., Knights, A. J., Patel, M., Goncalves, A., Ferreira, R., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0005-8 · Cited by 223

Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

Lelieveld, S. H., Spielmann, M., Mundlos, S., Veltman, J. A., & Gilissen, C. (2015) · Human Mutation · doi:10.1002/humu.22813 · Cited by 217

LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells

Cho, J., Chang, H., Kwon, S. C., Kim, B., Kim, Y., Choe, J., Ha, M., Kim, Y. K., & Kim, V. N. (2012) · Cell · doi:10.1016/j.cell.2012.10.019 · Cited by 223

Global gene disruption in human cells to assign genes to phenotypes

Carette, J. E., Guimarães, C. P., Wüthrich, I., Blomen, V. A., Varadarajan, M., Sun, C., Bell, G. W., Yuan, B., Muellner, M. K., Nijman, S. M. B., et al. (2011) · PubMed Central · doi:10.1038/nbt.1857

Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition

Gormally, M. V., Dexheimer, T. S., Marsico, G., Sanders, D. A., Lowe, C. E., Matak‐Vinković, D., Michael, S., Jadhav, A., Rai, G., Maloney, D. J., et al. (2014) · Nature Communications · doi:10.1038/ncomms6165 · Cited by 223

A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians

Wurtzel, O., Cote, L. E., Poirier, A., Satija, R., Regev, A., & Reddien, P. W. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.11.004 · Cited by 221

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

Barakat, T. S., Halbritter, F., Zhang, M., Rendeiro, A. F., Perenthaler, E., Bock, C., & Chambers, I. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.06.014 · Cited by 227

Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

Legras, J., Galéote, V., Bigey, F., Camarasa, C., Marsit, S., Nidelet, T., Sanchez, I., Couloux, A., Guy, J., Franco‐Duarte, R., et al. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy066 · Cited by 216

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Yoshida, Y., Koutsovoulos, G., Laetsch, D. R., Stevens, L., Kumar, S., Horikawa, D. D., Ishino, K., Komine, S., Kunieda, T., Tomita, M., et al. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2002266 · Cited by 229

Mouse totipotent stem cells captured and maintained through spliceosomal repression

Shen, H., Yang, M., Li, S., Zhang, J., Peng, B., Wang, C., Chang, Z., Ong, J., & Du, P. (2021) · Cell · doi:10.1016/j.cell.2021.04.020 · Cited by 221

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Long, H. K., Sims, D., Heger, A., Blackledge, N. P., Kutter, C., Wright, M. L., Grützner, F., Odom, D. T., Patient, R. K., Ponting, C. P., et al. (2013) · eLife · doi:10.7554/elife.00348 · Cited by 232

Designing a transcriptome next‐generation sequencing project for a nonmodel plant species1

Strickler, S. R., Bombarely, A., & Mueller, L. A. (2012) · American Journal of Botany · doi:10.3732/ajb.1100292 · Cited by 232

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA ‐seq experiments

Vijay, N., Poelstra, J. W., Künstner, A., & Wolf, J. B. W. (2012) · Molecular Ecology · doi:10.1111/mec.12014 · Cited by 230

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

Cao, Q., Anyansi, C., Hu, X. S., Xu, L., Xiong, L., Tang, W., Mok, M. T. S., Cheng, C., Fan, X., Gerstein, M., et al. (2017) · Nature Genetics · doi:10.1038/ng.3950 · Cited by 220

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

Depledge, D. P., Srinivas, K. P., Sadaoka, T., Bready, D., Mori, Y., Placantonakis, D. G., Mohr, I., & Wilson, A. C. (2019) · Nature Communications · doi:10.1038/s41467-019-08734-9 · Cited by 217

Dynamics and genomic landscape of CD8+ T cells undergoing hepatic priming

Bénéchet, A. P., De Simone, G., Di Lucia, P., Cilenti, F., Barbiera, G., Le Bert, N., Fumagalli, V., Lusito, E., Moalli, F., Bianchessi, V., et al. (2019) · Nature · doi:10.1038/s41586-019-1620-6 · Cited by 222

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms

Kleppe, M., Koche, R., Zou, L., van Galen, P., Hill, C. E., Dong, L., De Groote, S., Papalexi, E., Hanasoge Somasundara, A. V., Cordner, K., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2017.11.009 · Cited by 279

Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

Günther, C., Kind, B., Reijns, M. A. M., Berndt, N., Martínez‐Bueno, M., Wolf, C., Tüngler, V., Chara, O., Lee, Y. A., Hübner, N., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci78001 · Cited by 226

Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2

Højfeldt, J. W., Laugesen, A., Willumsen, B. M., Damhofer, H., Hedehus, L., Tvardovskiy, A., Mohammad, F., Jensen, O. N., & Helin, K. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0036-6 · Cited by 235

Increasing tolerance of hospital Enterococcus faecium to handwash alcohols

Pidot, S. J., Gao, W., Buultjens, A. H., Monk, I. R., Guérillot, R., Carter, G. P., Lee, J. Y. H., Lam, M. M. C., Grayson, M. L., Ballard, S. A., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aar6115 · Cited by 222

DeepC: predicting 3D genome folding using megabase-scale transfer learning

Schweßinger, R., Gosden, M. E., Downes, D. J., Brown, R. C., Oudelaar, A. M., Telenius, J. M., Teh, Y. W., Lunter, G. A., & Hughes, J. R. (2020) · Nature Methods · doi:10.1038/s41592-020-0960-3 · Cited by 223

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancerPreprint

Leung, M. L., Davis, A., Gao, R., Casasent, T. D., Wang, Y., Sei, E., Vilar, E., Maru, D. M., Kopetz, S., & Navin, N. E. (2017) · Genome Research · doi:10.1101/gr.209973.116 · Cited by 220

Suppression of Arabidopsis protophloem differentiation and root meristem growth by CLE45 requires the receptor-like kinase BAM3

Depuydt, S., Rodríguez‐Villalón, A., Santuari, L., Wyser-Rmili, C., Ragni, L., & Hardtke, C. S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222314110 · Cited by 221

Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

Zenk, F. L., Loeser, E., Schiavo, R., Kilpert, F., Bogdanović, O., & Iovino, N. (2017) · Science · doi:10.1126/science.aam5339 · Cited by 218

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

Zhu, Y., Wang, X., Forouzmand, E., Jeong, J., Qiao, F., Sowd, G. A., Engelman, A., Xie, X. S., Hertel, K. J., & Shi, Y. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.031 · Cited by 221

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

Jia, G., Preussner, J., Chen, X. X., Günther, S., Yuan, X., Yekelchyk, M., Kuenne, C. T., Looso, M., Zhou, Y., Teichmann, S. A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07307-6 · Cited by 219

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

Stuart, T., Eichten, S. R., Cahn, J., Karpievitch, Y. V., Borevitz, J., & Lister, R. (2016) · eLife · doi:10.7554/elife.20777 · Cited by 216

Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss

Guo, C., Cai, P., Jin, L., Sha, Q., Yu, Q., Zhang, W., Jiang, C., Liu, Q., Zong, D., Li, K., et al. (2021) · Cell Discovery · doi:10.1038/s41421-020-00236-z · Cited by 226

Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Hajdinjak, M., Mafessoni, F., Skov, L., Vernot, B., Hübner, A., Fu, Q., Essel, E., Nagel, S., Nickel, B., Richter, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03335-3 · Cited by 232

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Tian, L., Jabbari, J. S., Thijssen, R., Gouil, Q. A., Amarasinghe, S. L., Voogd, O., Kariyawasam, H., Du, M. R. M., Schuster, J., Wang, C., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02525-6 · Cited by 215

Gene regulation by gonadal hormone receptors underlies brain sex differences

Gegenhuber, B., Wu, M. V., Bronstein, R., & Tollkuhn, J. (2022) · Nature · doi:10.1038/s41586-022-04686-1 · Cited by 221

Principles of transcriptome analysis and gene expression quantification: an RNA ‐seq tutorial

Wolf, J. B. W. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12109 · Cited by 235

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Li, Q., Gent, J. I., Zynda, G. J., Song, J., Makarevitch, I., Hirsch, C. D., Hirsch, C. N., Dawe, R. K., Madzima, T. F., McGinnis, K. M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514680112 · Cited by 223

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs

Garzia, A., Jafarnejad, S. M., Meyer, C., Chapat, C., Gogakos, T., Morozov, P. S., Amiri, M., Shapiro, M., Molina, H., Tuschl, T., et al. (2017) · Nature Communications · doi:10.1038/ncomms16056 · Cited by 216

Evaluation of TagSeq, a reliable low‐cost alternative for RNA seq

Lohman, B. K., Weber, J. N., & Bolnick, D. I. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12529 · Cited by 224

The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer

Vervoort, S. J., Welsh, S. A., Devlin, J. R., Barbieri, E., Knight, D. A., Offley, S. R., Bjelosevic, S., Costacurta, M., Todorovski, I., Kearney, C. J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.022 · Cited by 211

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cellsPreprint

Pezić, D., Manakov, S. A., Sachidanandam, R., & Aravin, A. A. (2014) · Genes & Development · doi:10.1101/gad.240895.114 · Cited by 239

Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions

Ishigaki, S., Masuda, A., Fujioka, Y., Iguchi, Y., Katsuno, M., Shibata, A., Urano, F., Sobue, G., & Ohno, K. (2012) · Scientific Reports · doi:10.1038/srep00529 · Cited by 219

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

Lind, A., Wisecaver, J. H., Lameiras, C., Wiemann, P., Palmer, J. M., Keller, N. P., Rodrigues, F. J. S., Goldman, G. H., & Rokas, A. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2003583 · Cited by 212

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylationPreprint

Gruber, A. J., Schmidt, R., Gruber, A. J., Martin, G., Ghosh, S., Belmadani, M., Keller, W., & Zavolan, M. (2016) · Genome Research · doi:10.1101/gr.202432.115 · Cited by 213

Ultra-fast deep-learned CNS tumour classification during surgery

Vermeulen, C., Pagès-Gallego, M., Kester, L., Kranendonk, M. E. G., Wesseling, P., Verburg, N., de Witt Hamer, P., Kooi, E. J., Dankmeijer, L., van der Lugt, J., et al. (2023) · Nature · doi:10.1038/s41586-023-06615-2 · Cited by 216

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

Cotney, J. L., Leng, J., Yin, J., Reilly, S. K., DeMare, L. E., Emera, D., Ayoub, A. E., RAKIC, P. T., & Noonan, J. P. (2013) · Cell · doi:10.1016/j.cell.2013.05.056 · Cited by 215

Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair–deficient Prostate Cancer

Annala, M., Struss, W. J., Warner, E. W., Beja, K., Vandekerkhove, G. R., Wong, A., Khalaf, D. J., Seppälä, I.-L., So, A., Lo, G. K., et al. (2017) · European Urology · doi:10.1016/j.eururo.2017.02.023 · Cited by 218

Migratory DCs activate TGF-β to precondition naïve CD8 + T cells for tissue-resident memory fate

Mani, V., Bromley, S. K., Äijö, T., Mora‐Buch, R., Carrizosa, E., Warner, R. D., Hamze, M., Sen, D. R., Chasse, A. Y., Lorant, A. K., et al. (2019) · Science · doi:10.1126/science.aav5728 · Cited by 226

A metabolic labeling method detects m6A transcriptome-wide at single base resolution

Shu, X., Cao, J., Cheng, M., Xiang, S., Gao, M., Li, T., Ying, X., Wang, F., Yue, Y., Lu, Z., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0526-9 · Cited by 219

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Sun, H., Jiao, W., Krause, K., Campoy, J. A., Goel, M., Folz‐Donahue, K., Kukat, C., Hüettel, B., & Schneeberger, K. (2022) · Nature Genetics · doi:10.1038/s41588-022-01015-0 · Cited by 221

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelementsPreprint

Turelli, P., Castro-Díaz, N., Marzetta, F., Kapopoulou, A., Raclot, C., Duc, J., Tieng, V., Quenneville, S., & Trono, D. (2014) · Genome Research · doi:10.1101/gr.172833.114 · Cited by 226

Genome modeling and design across all domains of life with Evo 2Preprint

Brixi, G., Durrant, M. G., Ku, J., Poli, M., Brockman, G., Chang, D., Gonzalez, G. A., King, S. B., Li, D. B., Merchant, A. T., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.18.638918 · Cited by 218

Loss-of-function mutations in the IL-21 receptor gene cause a primary immunodeficiency syndrome

Kotlarz, D., Ziętara, N., Uzel, G., Weidemann, T., Braun, C. J., Diestelhorst, J., Krawitz, P. M., Robinson, P. N., Hecht, J., Puchałka, J., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20111229 · Cited by 223

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

Reid, A. J., Talman, A. M., Bennett, H. M., Gomes, A. R., Sanders, M. J., Illingworth, C. J. R., Billker, O., Berriman, M., & Lawniczak, M. (2018) · eLife · doi:10.7554/elife.33105 · Cited by 220

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Pilkington, S. M., Crowhurst, R. N., Hilario, E., Nardozza, S., Fraser, L. G., Peng, Y., Gunaseelan, K., Simpson, R. M., Tahir, J., Deroles, S. C., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4656-3 · Cited by 221

Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia

He, Y. H., Spyrou, M. A., Karapetian, M. K., Shnaider, S. V., Radzevičiūtė, R., Nägele, K., Neumann, G. U., Penske, S., Zech, J., Lucas, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.037 · Cited by 225

A hybrid approach for de novo human genome sequence assembly and phasing

Mostovoy, Y., Levy‐Sakin, M., Lam, J. C., Lam, E. T., Hastie, A. R., Marks, P., Lee, J., Chu, C., Lin, C. J., Džakula, Ž., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3865 · Cited by 216

Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells

Michelson, D. A., Hase, K., Kaisho, T., Benoist, C. O., & Mathis, D. J. (2022) · Cell · doi:10.1016/j.cell.2022.05.018 · Cited by 213

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing

Bonin, N., Doster, E., Worley, H., Pinnell, L. J., Bravo, J. E., Ferm, P., Marini, S., Prosperi, M., Noyes, N. R., Morley, P. S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1047 · Cited by 226

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

Roosan, M. R., Jackson, L. K., Johnson, W. E., Li, D. Y., Bild, A. H., & Piccolo, S. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv377 · Cited by 212

Genome sequence of the olive tree, Olea europaea

Cruz, F., Julca, I., Gómez‐Garrido, J., Loska, D., Marcet‐Houben, M., Cano, E., Galán, B., Frías, L., Ribeca, P., Derdak, S. V., et al. (2016) · GigaScience · doi:10.1186/s13742-016-0134-5 · Cited by 225

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton

Wang, M., Wang, P., Lin, M., Ye, Z., Li, G., Tu, L., Shen, C., Li, J., Yang, Q., & Zhang, X. (2018) · Nature Plants · doi:10.1038/s41477-017-0096-3 · Cited by 217

Gut-Liver Physiomimetics Reveal Paradoxical Modulation of IBD-Related Inflammation by Short-Chain Fatty Acids

Trapecar, M., Communal, C., Velazquez, J., Maass, C. A., Huang, Y.-J., Schneider, K., Wright, C. W., Butty, V., Eng, G., Yilmaz, O., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2020.02.008 · Cited by 218

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe, A., Bélicard, T., Pen, J. L., Sarkies, P., Frézal, L., Lehrbach, N. J., Félix, M., & Miska, E. A. (2013) · eLife · doi:10.7554/elife.00994 · Cited by 215

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells

Park, N. I., Guilhamon, P., Desai, K., McAdam, R. F., Langille, E. R., O’Connor, M., Lan, X., Whetstone, H., Coutinho, F. J., Vanner, R. J., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.06.004 · Cited by 218

Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution

Chaw, S., Liu, Y.-C., Wu, Y., Wang, H.-Y., Lin, C. I., Wu, C., Ke, H., Chang, L., Hsu, C.-Y., Yang, H.-T., et al. (2019) · Nature Plants · doi:10.1038/s41477-018-0337-0 · Cited by 214

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

Venturini, L., Caim, S., Kaithakottil, G., Mapleson, D., & Swarbreck, D. (2018) · GigaScience · doi:10.1093/gigascience/giy093 · Cited by 215

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

Gate, R. E., Cheng, C. S., Aiden, A. P., Siba, A., Tabaka, M., Lituiev, D., Machol, I., Gordon, M. G., Subramaniam, M., Shamim, M., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0156-2 · Cited by 181

Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity

Karmaus, P. W. F., Chen, X., Lim, S. A., Herrada, A. A., Nguyen, T.-L. M., Xu, B., Dhungana, Y., Rankin, S., Chen, W., Rosencrance, C., et al. (2019) · Nature · doi:10.1038/s41586-018-0806-7 · Cited by 215

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

Martin, P., McGovern, A., Orozco, G., Duffus, K., Yarwood, A., Schoenfelder, S., Cooper, N. J., Barton, A., Wallace, C., Fraser, P., et al. (2015) · Nature Communications · doi:10.1038/ncomms10069 · Cited by 213

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Abascal, F., Corvelo, A., Cruz, F., Villanueva‐Cañas, J. L., Vlasova, A. V., Marcet‐Houben, M., Martínez‐Cruz, B., Cheng, J. Y., Prieto, P., Quesada, V., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1090-1 · Cited by 221

The evolutionary history of bears is characterized by gene flow across species

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