Twelve years of SAMtools and BCFtools

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

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247

A draft human pangenome reference.

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Byrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094

The complete sequence of a human Y chromosome

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature · doi:10.1038/s41586-023-06457-y · Cited by 471

A complete reference genome improves analysis of human genetic variation

Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441

Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration

Moiseeva, V., Cisneros, A., Sica, V., Deryagin, O., Lai, Y., Jung, S., Andrés, E., An, J., Segalés, J., Ortet, L., et al. (2023) · Nature · doi:10.1038/s41586-022-05535-x · Cited by 423

HTSlib: C library for reading/writing high-throughput sequencing data

(2021) · doi:10.1093/gigascience/giab007 · Cited by 413

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Avsec, Ž., Latysheva, N., Cheng, J., Novati, G., Taylor, K. R., Ward, T., Bycroft, C., Nicolaisen, L., Arvaniti, E., Pan, J., et al. (2025) · doi:10.1101/2025.06.25.661532 · Cited by 395

Advancing regulatory variant effect prediction with AlphaGenome

Avsec, Ž., Latysheva, N., Cheng, J., Novati, G., Taylor, K. R., Ward, T., Bycroft, C., Nicolaisen, L., Arvaniti, E., Pan, J., et al. (2026) · Nature · doi:10.1038/s41586-025-10014-0 · Cited by 373

Pangenome graph construction from genome alignments with Minigraph-Cactus

Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Asri, M., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01793-w · Cited by 343

A reference human induced pluripotent stem cell line for large-scale collaborative studies

Pantazis, C. B., Yang, A., Lara, E., McDonough, J. A., Blauwendraat, C., Peng, L., Oguro, H., Kanaujiya, J., Zou, J., Sebesta, D., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2022.11.004 · Cited by 310

Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297

Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota

Akagbosu, B., Tayyebi, Z., Shibu, G., Paucar Iza, Y. A., Deep, D., Parisotto, Y. F., Fisher, L., Pasolli, H. A., Thevin, V., Elmentaite, R., et al. (2022) · Nature · doi:10.1038/s41586-022-05309-5 · Cited by 273

Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase

Patterson, A., Rimal, B., Collins, S., Granda, M., Koo, I., Solanka, S., Hoque, N., Gentry, E., Yan, T., Bisanz, J., et al. (2022) · doi:10.21203/rs.3.rs-2050120/v1 · Cited by 252

Truvari: refined structural variant comparison preserves allelic diversity

English, A. C., Menon, V. K., Gibbs, R. A., Metcalf, G. A., & Sedlazeck, F. J. (2022) · Genome Biology · doi:10.1186/s13059-022-02840-6 · Cited by 236

Deeply conserved synteny and the evolution of metazoan chromosomes

Simakov, O., Bredeson, J., Berkoff, K., Marletaz, F., Mitros, T., Schultz, D. T., O’Connell, B. L., Dear, P., Martinez, D. E., Steele, R. E., et al. (2022) · Science Advances · doi:10.1126/sciadv.abi5884 · Cited by 197

Macrophage-mediated myelin recycling fuels brain cancer malignancy

Kloosterman, D. J., Erbani, J., Boon, M., Farber, M., Handgraaf, S. M., Ando-Kuri, M., Sánchez-López, E., Fontein, B., Mertz, M., Nieuwland, M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.030 · Cited by 231

A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

Pozniak, J., Pedri, D., Landeloos, E., Van Herck, Y., Antoranz, A., Vanwynsberghe, L., Nowosad, A., Roda, N., Makhzami, S., Bervoets, G., et al. (2024) · Cell · doi:10.1016/j.cell.2023.11.037 · Cited by 199

Single-cell DNA methylation and 3D genome architecture in the human brain

Tian, W., Zhou, J., Bartlett, A., Zeng, Q., Liu, H., Castanon, R. G., Kenworthy, M., Altshul, J., Valadon, C., Aldridge, A., et al. (2023) · Science · doi:10.1126/science.adf5357 · Cited by 154

Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes

Humphrey, J., Venkatesh, S., Hasan, R., Herb, J. T., de Paiva Lopes, K., Küçükali, F., Byrska-Bishop, M., Evani, U. S., Narzisi, G., Fagegaltier, D., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-022-01205-3 · Cited by 138

NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells

Chen, A. F., Parks, B., Kathiria, A. S., Ober-Reynolds, B., Goronzy, J. J., & Greenleaf, W. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01461-y · Cited by 139

Personal transcriptome variation is poorly explained by current genomic deep learning models

Huang, C., Shuai, R. W., Baokar, P., Chung, R., Rastogi, R., Kathail, P., & Ioannidis, N. M. (2023) · Nature Genetics · doi:10.1038/s41588-023-01574-w · Cited by 127

Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors

Nassar, A. H., Adib, E., Abou Alaiwi, S., El Zarif, T., Groha, S., Akl, E. W., Nuzzo, P. V., Mouhieddine, T. H., Perea-Chamblee, T., Taraszka, K., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.08.022 · Cited by 121

Increased mutation and gene conversion within human segmental duplications

Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Human Pangenome Reference Consortium, et al. (2023) · Nature · doi:10.1038/s41586-023-05895-y · Cited by 104

RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis

Zou, Z., Dou, X., Li, Y., Zhang, Z., Wang, J., Gao, B., Xiao, Y., Wang, Y., Zhao, L., Sun, C., et al. (2024) · Nature · doi:10.1038/s41586-024-07969-x · Cited by 103

Exercise-induced microbiota metabolite enhances CD8 T cell antitumor immunity promoting immunotherapy efficacy

Phelps, C. M., Willis, N. B., Duan, T., Lee, A. H., Zhang, Y., Rodriguez J, D. M., Pandey, S. P., Laughlin, C. R., Rosen, A. B. I., McPherson, A. C., et al. (2025) · Cell · doi:10.1016/j.cell.2025.06.018 · Cited by 91

Atezolizumab plus anthracycline-based chemotherapy in metastatic triple-negative breast cancer: the randomized, double-blind phase 2b ALICE trial

Røssevold, A. H., Andresen, N. K., Bjerre, C. A., Gilje, B., Jakobsen, E. H., Raj, S. X., Falk, R. S., Russnes, H. G., Jahr, T., Mathiesen, R. R., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-02126-1 · Cited by 89

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

Sibbesen, J. A., Eizenga, J. M., Novak, A. M., Sirén, J., Chang, X., Garrison, E., & Paten, B. (2023) · Nature Methods · doi:10.1038/s41592-022-01731-9 · Cited by 83

Colibactin-driven colon cancer requires adhesin-mediated epithelial binding

Jans, M., Kolata, M., Blancke, G., D’Hondt, A., Gräf, C., Ciers, M., Sze, M., Thiran, A., Petta, I., Andries, V., et al. (2024) · Nature · doi:10.1038/s41586-024-08135-z · Cited by 84

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration

Little, A. S., Younker, I. T., Schechter, M. S., Bernardino, P. N., Méheust, R., Stemczynski, J., Scorza, K., Mullowney, M. W., Sharan, D., Waligurski, E., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01560-2 · Cited by 80

Next-generation data filtering in the genomics era

Hemstrom, W., Grummer, J. A., Luikart, G., & Christie, M. R. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00738-6 · Cited by 77

Mpox virus infection and drug treatment modelled in human skin organoids

Li, P., Pachis, S. T., Xu, G., Schraauwen, R., Incitti, R., de Vries, A. C., Bruno, M. J., Peppelenbosch, M. P., Alam, I., Raymond, K., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01489-6 · Cited by 77

Individualized patient tumor organoids faithfully preserve human brain tumor ecosystems and predict patient response to therapy

Peng, T., Ma, X., Hua, W., Wang, C., Chu, Y., Sun, M., Fermi, V., Hamelmann, S., Lindner, K., Shao, C., et al. (2025) · Cell Stem Cell · doi:10.1016/j.stem.2025.01.002 · Cited by 86

GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia

Shade, L. M. P., Katsumata, Y., Abner, E. L., Aung, K. Z., Claas, S. A., Qiao, Q., Heberle, B. A., Brandon, J. A., Page, M. L., Hohman, T. J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01939-9 · Cited by 72

Community-wide genome sequencing reveals 30 years of Darwin’s finch evolution

Enbody, E. D., Sendell-Price, A. T., Sprehn, C. G., Rubin, C.-J., Visscher, P. M., Grant, B. R., Grant, P. R., & Andersson, L. (2023) · Science · doi:10.1126/science.adf6218 · Cited by 75

Analysis and benchmarking of small and large genomic variants across tandem repeats

English, A. C., Dolzhenko, E., Ziaei Jam, H., McKenzie, S. K., Olson, N. D., De Coster, W., Park, J., Gu, B., Wagner, J., Eberle, M. A., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02225-z · Cited by 68

UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability

Tsai, J. M., Aguirre, J. D., Li, Y.-D., Brown, J., Focht, V., Kater, L., Kempf, G., Sandoval, B., Schmitt, S., Rutter, J. C., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.028 · Cited by 68

HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy

Jiang, Q., Braun, D. A., Clauser, K. R., Ramesh, V., Shirole, N. H., Duke-Cohan, J. E., Nabilsi, N., Kramer, N. J., Forman, C., Lippincott, I. E., et al. (2025) · Cell · doi:10.1016/j.cell.2025.01.046 · Cited by 68

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome

Laso-Pérez, R., Wu, F., Crémière, A., Speth, D. R., Magyar, J. S., Zhao, K., Krupovic, M., & Orphan, V. J. (2023) · Nature Microbiology · doi:10.1038/s41564-022-01297-4 · Cited by 68

Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding

Blumer, M., Brown, T., Freitas, M. B., Destro, A. L., Oliveira, J. A., Morales, A. E., Schell, T., Greve, C., Pippel, M., Jebb, D., et al. (2022) · Science Advances · doi:10.1126/sciadv.abm6494 · Cited by 65

Comparative studies of 2168 plasma proteins measured by two affinity-based platforms in 4000 Chinese adults

Wang, B., Pozarickij, A., Mazidi, M., Wright, N., Yao, P., Said, S., Iona, A., Kartsonaki, C., Fry, H., Lin, K., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56935-2 · Cited by 64

Decreased echinocandin susceptibility in Candida parapsilosis causing candidemia and emergence of a pan-echinocandin resistant case in China

Ning, Y., Xiao, M., Perlin, D. S., Zhao, Y., Lu, M., Li, Y., Luo, Z., Dai, R., Li, S., Xu, J., et al. (2023) · Emerging Microbes & Infections · doi:10.1080/22221751.2022.2153086 · Cited by 63

Transposon-encoded nucleases use guide RNAs to promote their selfish spread

Meers, C., Le, H. C., Pesari, S. R., Hoffmann, F. T., Walker, M. W. G., Gezelle, J., Tang, S., & Sternberg, S. H. (2023) · Nature · doi:10.1038/s41586-023-06597-1 · Cited by 60

Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

Xu, Z., Sziraki, A., Lee, J., Zhou, W., & Cao, J. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01948-9 · Cited by 52

Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis

(2023) · doi:10.1038/s41467-023-43702-4 · Cited by 55

Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases

Kumbhari, A., Cheng, T. N. H., Ananthakrishnan, A. N., Kochar, B., Burke, K. E., Shannon, K., Lau, H., Xavier, R. J., & Smillie, C. S. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.022 · Cited by 54

A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure

(2021) · doi:10.1371/journal.pone.0259871 · Cited by 54

Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment

Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Rocafort, M., Bowen, J. K., Hassing, B., Cox, M. P., McGreal, B., de la Rosa, S., Plummer, K. M., Bradshaw, R. E., & Mesarich, C. H. (2022) · BMC Biology · doi:10.1186/s12915-022-01442-9 · Cited by 52

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation

Lin, L., DeMartino, J., Wang, D., van Son, G. J. F., van der Linden, R., Begthel, H., Korving, J., Andersson-Rolf, A., van den Brink, S., Lopez-Iglesias, C., et al. (2023) · Science · doi:10.1126/science.adi2246 · Cited by 50

Structural basis of LRPPRC–SLIRP-dependent translation by the mitoribosome

Singh, V., Moran, J. C., Itoh, Y., Soto, I. C., Fontanesi, F., Couvillion, M., Huynen, M. A., Churchman, L. S., Barrientos, A., & Amunts, A. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01365-9 · Cited by 49

Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction

Femerling, G., van Oosterhout, C., Feng, S., Bristol, R. M., Zhang, G., Groombridge, J., P. Gilbert, M. T., & Morales, H. E. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad256 · Cited by 49

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

Badrane, H., Cheng, S., Dupont, C., Hao, B., Driscoll, E., Morder, K., Liu, G., Newbrough, A., Fleres, G., Kaul, D., et al. (2023) · doi:10.21203/rs.3.rs-2706400/v1 · Cited by 48

STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair

(2024) · doi:10.1016/j.cell.2024.10.018 · Cited by 44

A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., et al. (2023) · Genome Research · doi:10.1101/gr.277481.122 · Cited by 43

FOXP3 recognizes microsatellites and bridges DNA through multimerization

Zhang, W., Leng, F., Wang, X., Ramirez, R. N., Park, J., Benoist, C., & Hur, S. (2023) · Nature · doi:10.1038/s41586-023-06793-z · Cited by 42

Transient mitochondria dysfunction confers fungal cross-resistance against phagocytic killing and fluconazole

Siscar-Lewin, S., Gabaldón, T., Aldejohann, A. M., Kurzai, O., Hube, B., & Brunke, S. (2021) · mBio · doi:10.1128/mbio.01128-21 · Cited by 36

CRISPR/Cas9 Screen in Gastric Cancer Patient‐Derived Organoids Reveals KDM1A‐NDRG1 Axis as a Targetable Vulnerability

Mircetic, J., Camgöz, A., Abohawya, M., Ding, L., Dietzel, J., Tobar, S. G., Paszkowski‐Rogacz, M., Seidlitz, T., Schmäche, T., Mehnert, M., et al. (2023) · Small Methods · doi:10.1002/smtd.202201605 · Cited by 40

Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers

Owens, G. L., Huang, K., Todesco, M., & Rieseberg, L. H. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad013 · Cited by 39

A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

Chen, C., Jost, M., Outram, M. A., Friendship, D., Chen, J., Wang, A., Periyannan, S., Bartoš, J., Holušová, K., Doležel, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41021-2 · Cited by 38

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

Hickey, G., Monlong, J., Ebler, J., Novak, A., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Marschall, T., Li, H., & Paten, B. (2022) · doi:10.1101/2022.10.06.511217 · Cited by 345

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.

Kiu, R., Darby, E. M., Alcon-Giner, C., Acuna-Gonzalez, A., Camargo, A., Lamberte, L. E., Phillips, S., Sim, K., Shaw, A. G., Clarke, P., et al. (2025) · Nature communications · doi:10.1038/s41467-025-62584-2 · Cited by 36

TREX reveals proteins that bind to specific RNA regions in living cells

(2024) · doi:10.1038/s41592-024-02181-1 · Cited by 36

Mammalian PIWI–piRNA–target complexes reveal features for broad and efficient target silencing

Li, Z., Li, Z., Zhang, Y., Zhou, L., Xu, Q., Li, L., Zeng, L., Xue, J., Niu, H., Zhong, J., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01287-6 · Cited by 35

Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

(2023) · doi:10.7554/elife.80489 · Cited by 34

The Genomic Natural History of the Aurochs

Rossi, C., Sinding, M.-H. S., Mullin, V. E., Scheu, A., Erven, J. A. M., Verdugo, M. P., Daly, K. G., Ciucani, M. M., Mattiangeli, V., Teasdale, M. D., et al. (2024) · Nature · doi:10.1038/s41586-024-08112-6 · Cited by 32

Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

Rajan, S., Zaccaria, S., Cannon, M. V., Cam, M., Gross, A. C., Raphael, B. J., & Roberts, R. D. (2021) · doi:10.1101/2021.08.30.458268 · Cited by 33

Bringing the genetically minimal cell to life on a computer in 4D

Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44

Association of SPI1 haplotypes with altered SPI1 gene expression and Alzheimer’s disease risk

Cao, H., Initiative, A. D. N., Zhou, X., Chen, Y., Ip, F. C. F., Chen, Y., Lai, N. C. H., Lo, R. M. N., Tong, E. P. S., Mok, V. C. T., et al. (2022) · Journal of Alzheimer s Disease · doi:10.3233/jad-215311 · Cited by 28

A structured coalescent model reveals deep ancestral structure shared by all modern humans

Cousins, T., Scally, A., & Durbin, R. (2025) · Nature Genetics · doi:10.1038/s41588-025-02117-1 · Cited by 27

Bone marrow breakout lesions act as key sites for tumor-immune cell diversification in multiple myeloma

Lutz, R., Poos, A. M., Solé-Boldo, L., John, L., Wagner, J., Prokoph, N., Baertsch, M. A., Vonficht, D., Palit, S., Brobeil, A., et al. (2025) · Science Immunology · doi:10.1126/sciimmunol.adp6667 · Cited by 25

Human-specific gene expansions contribute to brain evolution

(2025) · doi:10.1016/j.cell.2025.06.037 · Cited by 25

The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

Peyrégne, S., Kelso, J., Peter, B. M., & Pääbo, S. (2022) · eLife · doi:10.7554/elife.75464 · Cited by 24

The origin of hepatocellular carcinoma depends on metabolic zonation

Guo, J., Liang, R., Chung, A., Li, Z., Li, B., Chen, E., Li, L., Wang, J., Hsieh, M.-H., Fang, I. X., et al. (2026) · Science · doi:10.1126/science.adv7129 · Cited by 24

Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity

Barrault, M., Chabelskaya, S., Coronel-Tellez, R. H., Toffano-Nioche, C., Jacquet, E., & Bouloc, P. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae506 · Cited by 20

A multi-ancestry GWAS of Fuchs corneal dystrophy highlights the contributions of laminins, collagen, and endothelial cell regulation

Gorman, B. R., Francis, M., Nealon, C. L., Halladay, C. W., Duro, N., Markianos, K., Genovese, G., Hysi, P. G., Choquet, H., Afshari, N. A., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-06046-3 · Cited by 23

Polymerization of ZBTB transcription factors regulates chromatin occupancy

Park, P. M. C., Park, J., Brown, J., Hunkeler, M., Roy Burman, S. S., Donovan, K. A., Yoon, H., Nowak, R. P., Słabicki, M., Ebert, B. L., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.06.010 · Cited by 22

Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing

Jensvold, Z. D., Flood, J. R., Christenson, A. E., & Lewis, P. W. (2024) · Nature Communications · doi:10.1038/s41467-024-53761-w · Cited by 22

Paneth-like transition drives resistance to dual targeting of KRAS and EGFR in colorectal cancer

Zhang, Y., Chen, J., She, Y., Fang, Z., Zhang, Y., Ruan, D., Guo, W., Liao, J., Zhou, W., Lao, J., et al. (2026) · Cancer Cell · doi:10.1016/j.ccell.2025.10.010 · Cited by 23

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Cardiello, J. F., Joven Araus, A., Giatrellis, S., Helsens, C., Simon, A., & Leigh, N. D. (2023) · Life Science Alliance · doi:10.26508/lsa.202301979 · Cited by 21

Baricitinib attenuates the proinflammatory phase of COVID-19 driven by lung-infiltrating monocytes

Dobosh, B., Zandi, K., Giraldo, D. M., Goh, S. L., Musall, K., Aldeco, M., LeCher, J., Giacalone, V. D., Yang, J., Eddins, D. J., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110945 · Cited by 19

Positive and negative feedback regulation of the TGF-β1 explains two equilibrium states in skin aging

Haga, M., Iida, K., & Okada, M. (2024) · iScience · doi:10.1016/j.isci.2024.109708 · Cited by 19

Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes

Badonyi, M., & Marsh, J. A. (2025) · Nature Communications · doi:10.1038/s41467-025-63234-3 · Cited by 19

Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9

Zhang, J., Nirmala, J., Chen, S., Jost, M., Steuernagel, B., Karafiatova, M., Hewitt, T., Li, H., Edae, E., Sharma, K., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42747-9 · Cited by 19

Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle

Ward, J. A., Ng'ang'a, S. I., Randhawa, I. A. S., McHugo, G. P., O'Grady, J. F., Flórez, J. M., Browne, J. A., Pérez O’Brien, A. M., Landaeta-Hernández, A. J., Garcia, J. F., et al. (2024) · Royal Society Open Science · doi:10.1098/rsos.231388 · Cited by 17

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis

Lim, B., Kamal, A., Gomez Ramos, B., Adrian Segarra, J. M., Ibarra, I. L., Dignas, L., Kindinger, T., Volz, K., Rahbari, M., Rahbari, N., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02081-w · Cited by 17

Parallel gene expansions drive rapid dietary adaptation in herbivorous woodrats

Klure, D. M., Greenhalgh, R., Orr, T. J., Shapiro, M. D., & Dearing, M. D. (2025) · Science · doi:10.1126/science.adp7978 · Cited by 17

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

Marino, A., Debaecker, G., Fiston-Lavier, A.-S., Haudry, A., & Nabholz, B. (2025) · eLife · doi:10.7554/elife.100574 · Cited by 17

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

Hesketh-Best, P. J., Bosco-Santos, A., Garcia, S. L., O’Beirne, M. D., Werne, J. P., Gilhooly, W. P., & Silveira, C. B. (2023) · Communications Earth & Environment · doi:10.1038/s43247-023-00796-4 · Cited by 16

Ancestry diversity in the genetic determinants of the human plasma proteome enhances identification of potential drug targets

Pozarickij, A., Said, S., Lin, K., Morris, S., Edris, A., Iona, A., Kartsonaki, C., Wright, N., Yao, P., Fry, H., et al. (2023) · doi:10.1101/2023.11.13.23298365 · Cited by 16

Rapid, Reference-Free human genotype imputation with denoising autoencoders

Dias, R., Evans, D., Chen, S.-F., Chen, K.-Y., Loguercio, S., Chan, L., & Torkamani, A. (2022) · eLife · doi:10.7554/elife.75600 · Cited by 16

Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle

Milia, S., Leonard, A. S., Mapel, X. M., Bernal Ulloa, S. M., Drögemüller, C., & Pausch, H. (2025) · Genome Research · doi:10.1101/gr.279064.124 · Cited by 22

Proteome-scale prediction of molecular mechanisms underlying dominant genetic diseases

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Exploring the evolution and function of Canoe’s intrinsically disordered region in linking cell-cell junctions to the cytoskeleton during embryonic morphogenesis

Gurley, N. J., Szymanski, R. A., Dowen, R. H., Butcher, T. A., Ishiyama, N., & Peifer, M. (2023) · PLOS ONE · doi:10.1371/journal.pone.0289224 · Cited by 15

Increased matrix stiffness promotes fibrogenesis of hepatic stellate cells through AP-1-induced chromatin priming

Zhao, W., Yuan, W., Dong, T., Qi, W., Feng, Z., Li, C., & Sun, Y. (2025) · Communications Biology · doi:10.1038/s42003-025-08160-2 · Cited by 16

Temporal genomic dynamics shape clinical trajectory in multiple myeloma

Maura, F., Kaddoura, M., Poos, A. M., Baughn, L. B., Ziccheddu, B., Bärtsch, M.-A., Cirrincione, A., Maclachlan, K., Chojnacka, M., Diamond, B., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02292-1 · Cited by 14

Candida albicans’ inorganic phosphate transport and evolutionary adaptation to phosphate scarcity

Acosta-Zaldívar, M., Qi, W., Mishra, A., Roy, U., King, W. R., Li, Y., Patton-Vogt, J., Anderson, M. Z., & Köhler, J. R. (2024) · PLOS Genetics · doi:10.1371/journal.pgen.1011156 · Cited by 14

An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G. G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N. D., Aristilde, L., Huson, D. H., et al. (2023) · iScience · doi:10.1016/j.isci.2023.108016 · Cited by 14

Cross-feeding affects the target of resistance evolution to an antifungal drug

Durand, R., Jalbert-Ross, J., Fijarczyk, A., Dubé, A. K., & Landry, C. R. (2023) · PLOS Genetics · doi:10.1371/journal.pgen.1011002 · Cited by 14

Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans

Guitart, X., Porubsky, D., Yoo, D., Dougherty, M. L., Dishuck, P. C., Munson, K. M., Lewis, A. P., Hoekzema, K., Knuth, J., Chang, S., et al. (2024) · Genome Research · doi:10.1101/gr.279299.124 · Cited by 14