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  1. Research: Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia
    • Xiao Gou,
    • Zhen Wang,
    • Ning Li,
    • Feng Qiu,
    • Ze Xu,
    • Dawei Yan,
    • Shuli Yang,
    • Jia Jia,
    • Xiaoyan Kong,
    • Zehui Wei,
    • Shaoxiong Lu,
    • Linsheng Lian,
    • Changxin Wu,
    • Xueyan Wang,
    • Guozhi Li,
    • Teng Ma,
    • Qiang Jiang,
    • Xue Zhao,
    • Jiaqiang Yang,
    • Baohong Liu,
    • Dongkai Wei,
    • Hong Li,
    • Jianfa Yang,
    • Yulin Yan,
    • Guiying Zhao,
    • Xinxing Dong,
    • Mingli Li,
    • Weidong Deng,
    • Jing Leng,
    • Chaochun Wei,
    • Chuan Wang,
    • Huaming Mao,
    • Hao Zhang,
    • Guohui Ding,
    • and Yixue Li
    Genome Res. August 2014 24: 1308-1315; Published in Advance April 10, 2014, doi:10.1101/gr.171876.113
    ...for Science and Technology Grant (2008BAI64B01), Chinese High-Tech R&D Program (863) (2013AA102503, 2009AA02Z304, 2012AA020404), China Postdoctoral Science Foundation (2013M531226), Shanghai Postdoctoral Scientific Program (13R21417300), and the SA-SIBS Scholarship Program. References Akey JM, Ruhe AL, Akey ...
  2. Method: Bayesian-based noninvasive prenatal diagnosis of single-gene disorders
    • Tom Rabinowitz,
    • Avital Polsky,
    • David Golan,
    • Artem Danilevsky,
    • Guy Shapira,
    • Chen Raff,
    • Lina Basel-Salmon,
    • Reut Tomashov Matar,
    • and Noam Shomron
    Genome Res. March 2019 29: 428-438; Published in Advance February 20, 2019, doi:10.1101/gr.235796.118
    ..., Zhang J, He W, Dharmadhikari AV, Qu C, et al. 2017. Use of exome sequencing for infants in intensive care units: ascertainment of severe single-gene disorders and effect on medical management. JAMA Pediatr 171: e173438. doi:10.1001/jamapediatrics.2017.3438 Minon JM, Gerard C, Senterre JM, Schaaps JP ...
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  3. Research: Most chromatin interactions are not in linkage disequilibrium
    • Sean Whalen and
    • Katherine S. Pollard
    Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
    ...in humans. N Engl J Med 373: 895907. doi:10.1056/NEJMoa1502214 Corradin O, Cohen AJ, Luppino JM, Bayles IM, Schumacher FR, Scacheri PC. 2016. Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nat Genet 48: 13131320. doi:10 ...
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  4. Research: Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations
    • Joanna Kaplanis,
    • Nadia Akawi,
    • Giuseppe Gallone,
    • Jeremy F. McRae,
    • Elena Prigmore,
    • Caroline F. Wright,
    • David R. Fitzpatrick,
    • Helen V. Firth,
    • Jeffrey C. Barrett,
    • Matthew E. Hurles,
    • and on behalf of the Deciphering Developmental Disorders study
    Genome Res. July 2019 29: 1047-1056; Published in Advance June 21, 2019, doi:10.1101/gr.239756.118
    .... doi:10.1371/journal.pgen.1006315 Chen JM, Frec C, Cooper DN. 2015. Complex multiple-nucleotide substitution mutations causing human inherited disease reveal novel insights into the action of translesion synthesis DNA polymerases. Hum Mutat 36: 10341038. doi:10.1002/humu.22831 Deciphering ...
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  5. Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
    • Meng Chen,
    • Ran Wei,
    • Gang Wei,
    • Mingqing Xu,
    • Zhixi Su,
    • Chen Zhao,
    • and Ting Ni
    Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
    ...1056. doi:10.1111/j.1474-9726.2010.00631.x Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 2836. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. 2000. Patterns of variant polyadenylation ...
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  6. Perspective: Short arms of human acrocentric chromosomes and the completion of the human genome sequence
    • Stylianos E. Antonarakis
    Genome Res. April 2022 32: 599-607; Published in Advance March 31, 2022, doi:10.1101/gr.275350.121
    ...and fractionation. Pediatr Res 7: 512. doi:10.1203/00006450-197301000-00002 Schmickel RD, Gonzalez IL, Erickson JM. 1985. Nucleolus organizing genes on chromosome 21: recombination and nondisjunction. Ann N Y Acad Sci 450: 121131. doi:10.1111/j.1749-6632.1985.tb21488.x Scott HS, Kudoh J, Wattenhofer M, Shibuya ...
  7. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...21: 35. doi:10.1186/s13059-020-1941-7 Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Marschall T, Li H, Paten B. 2024. Pan graph construction from alignments with Minigraph-Cactus. Nat Biotechnol 42: 663673. doi:10.1038/s41587-023-01793-w Houwaart T, Scholz S, Pollock NR, Palmer WH ...
  8. Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    • Enzo Battistella,
    • Anant Maheshwari,
    • Barış Ekim,
    • Bonnie Berger,
    • and Victoria Popic
    Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
    ...-telangiectasia with double missense and in frame splice mutations. Am J Med Genet A 126A: 272277. doi:10.1002/ajmg.a.20601 Douglas JA, Boehnke M, Gillanders E, Trent JM, Gruber SB. 2001. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet 28: 361364. doi:10 ...
  9. INSIGHT/OUTLOOK: Opportunities and Challenges Grow from ArabidopsisGenome Sequencing
    • A. Mark Settles and
    • Mary Byrne
    Genome Res. February 1, 1998 8: 83-85; doi:10.1101/gr.8.2.83
    ...: 8145 8150 . Marra M.A. , Kucaba T.A. , Dietrich N.L. , Green E.D. , Brownstein B. , Wilson R.K. , McDonald K.M. , Hillier L.W. , McPherson J.D. , Waterston R.H. ( 1997 ) Genome Res. 7 : 1072 1084 . Palauqui J.C. , Elmayan T. , Pollien J.M. , Vaucheret H. ( 1997 ) EMBO J. 16 : 4738 4745 ...
  10. Method: Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins
    • Sojung Kim,
    • Daesik Kim,
    • Seung Woo Cho,
    • Jungeun Kim,
    • and Jin-Soo Kim
    Genome Res. June 2014 24: 1012-1019; Published in Advance April 2, 2014, doi:10.1101/gr.171322.113
    ...: 1738217387. Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frodin M, Davis GD. 2011. High-frequency editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods 8: 753755. Cho SW, Kim S, Kim JM, Kim JS. 2013a. Targeted engineering in human cells ...
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