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Lukas Habegger, Ph.D. - Publications

Affiliations: 
Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Sun KY, Bai X, Chen S, Bao S, Zhang C, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, et al. A deep catalogue of protein-coding variation in 983,578 individuals. Nature. PMID 38768635 DOI: 10.1038/s41586-024-07556-0  0.327
2023 Ziyatdinov A, Torres J, Alegre-Díaz J, Backman J, Mbatchou J, Turner M, Gaynor SM, Joseph T, Zou Y, Liu D, Wade R, Staples J, Panea R, Popov A, Bai X, ... ... Habegger L, et al. Genotyping, sequencing and analysis of 140,000 adults from Mexico City. Nature. PMID 37821707 DOI: 10.1038/s41586-023-06595-3  0.368
2023 Sun KY, Bai X, Chen S, Bao S, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, et al. A deep catalog of protein-coding variation in 985,830 individuals. Biorxiv : the Preprint Server For Biology. PMID 37214792 DOI: 10.1101/2023.05.09.539329  0.343
2021 Backman JD, Li AH, Marcketta A, Sun D, Mbatchou J, Kessler MD, Benner C, Liu D, Locke AE, Balasubramanian S, Yadav A, Banerjee N, Gillies C, Damask A, Liu S, ... ... Habegger L, et al. Exome sequencing and analysis of 454,787 UK Biobank participants. Nature. PMID 34662886 DOI: 10.1038/s41586-021-04103-z  0.358
2020 Van Hout CV, Tachmazidou I, Backman JD, Hoffman JD, Liu D, Pandey AK, Gonzaga-Jauregui C, Khalid S, Ye B, Banerjee N, Li AH, O'Dushlaine C, Marcketta A, Staples J, Schurmann C, ... ... Habegger L, et al. Exome sequencing and characterization of 49,960 individuals in the UK Biobank. Nature. PMID 33087929 DOI: 10.1038/s41586-020-2853-0  0.383
2020 Martin CL, Wain KE, Oetjens MT, Tolwinski K, Palen E, Hare-Harris A, Habegger L, Maxwell EK, Reid JG, Walsh LK, Myers SM, Ledbetter DH. Identification of Neuropsychiatric Copy Number Variants in a Health Care System Population. Jama Psychiatry. PMID 32697297 DOI: 10.1001/Jamapsychiatry.2020.2159  0.338
2018 Staples J, Maxwell EK, Gosalia N, Gonzaga-Jauregui C, Snyder C, Hawes A, Penn J, Ulloa R, Bai X, Lopez AE, Van Hout CV, O'Dushlaine C, Teslovich TM, McCarthy SE, Balasubramanian S, ... ... Habegger L, et al. Profiling and Leveraging Relatedness in a Precision Medicine Cohort of 92,455 Exomes. American Journal of Human Genetics. 102: 874-889. PMID 29727688 DOI: 10.1016/J.Ajhg.2018.03.012  0.341
2016 Dewey FE, Murray MF, Overton JD, Habegger L, Leader JB, Fetterolf SN, O'Dushlaine C, Van Hout CV, Staples J, Gonzaga-Jauregui C, Metpally R, Pendergrass SA, Giovanni MA, Kirchner HL, Balasubramanian S, et al. Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science (New York, N.Y.). 354. PMID 28008009 DOI: 10.1126/Science.Aaf6814  0.446
2015 Packer JS, Maxwell EK, O'Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG. CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data. Bioinformatics (Oxford, England). PMID 26382196 DOI: 10.1093/Bioinformatics/Btv547  0.38
2013 Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research. 23: 2042-52. PMID 24026178 DOI: 10.1101/Gr.154625.113  0.609
2013 Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda, Md.). 3: 387-97. PMID 23450794 DOI: 10.1534/G3.112.004812  0.631
2012 Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biology. 13: R51. PMID 22951037 DOI: 10.1186/Gb-2012-13-9-R51  0.734
2012 Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, et al. Regulatory element copy number differences shape primate expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 109: 12656-61. PMID 22797897 DOI: 10.1073/Pnas.1205199109  0.558
2012 Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics (Oxford, England). 28: 2267-9. PMID 22743228 DOI: 10.1093/Bioinformatics/Bts368  0.567
2012 Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 148: 1293-307. PMID 22424236 DOI: 10.1016/J.Cell.2012.02.009  0.67
2012 MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science (New York, N.Y.). 335: 823-8. PMID 22344438 DOI: 10.1126/Science.1215040  0.691
2012 Du J, Leng J, Habegger L, Sboner A, McDermott D, Gerstein M. IQSeq: integrated isoform quantification analysis based on next-generation sequencing. Plos One. 7: e29175. PMID 22238592 DOI: 10.1371/Journal.Pone.0029175  0.647
2012 Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Performance comparison of whole-genome sequencing platforms. Nature Biotechnology. 30: 78-82. PMID 22178993 DOI: 10.1038/Nbt.2065  0.713
2012 Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Erratum: Corrigendum: Performance comparison of whole-genome sequencing platforms Nature Biotechnology. 30: 562-562. DOI: 10.1038/Nbt0612-562E  0.528
2011 Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, et al. The genomic complexity of primary human prostate cancer. Nature. 470: 214-20. PMID 21307934 DOI: 10.1038/Nature09744  0.518
2011 Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Gene inactivation and its implications for annotation in the era of personal genomics. Genes & Development. 25: 1-10. PMID 21205862 DOI: 10.1101/Gad.1968411  0.619
2011 Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics (Oxford, England). 27: 281-3. PMID 21134889 DOI: 10.1093/Bioinformatics/Btq643  0.742
2011 Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin PC, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, et al. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Research. 21: 56-67. PMID 21036922 DOI: 10.1101/Gr.110684.110  0.53
2011 Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, et al. Abstract 3925: Characterization of complex chromosomal aberrations in prostate cancer from whole genome sequencing Cancer Research. 71: 3925-3925. DOI: 10.1158/1538-7445.Am2011-3925  0.51
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, ... ... Habegger L, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914  0.713
2010 Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biology. 11: R104. PMID 20964841 DOI: 10.1186/Gb-2010-11-10-R104  0.607
2010 Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays Bmc Genomics. 11. PMID 20565764 DOI: 10.1186/1471-2164-11-383  0.531
2010 Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, et al. Variation in transcription factor binding among humans. Science (New York, N.Y.). 328: 232-5. PMID 20299548 DOI: 10.1126/science.1183621  0.65
2010 Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proceedings of the National Academy of Sciences of the United States of America. 107: 5254-9. PMID 20194744 DOI: 10.1073/Pnas.0914114107  0.47
2010 Balasubramanian S, Habegger L, Frankish A, MacArthur D, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Defining the human reference protein-coding gene set Genome Biology. 11. DOI: 10.1186/Gb-2010-11-S1-O5  0.601
2010 Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Svensson MA, Lin P, Kitabayashi N, Moss BJ, Tewari AK, Chee MS, Demichelis F, Gerstein MB, Rubin MA. Abstract 2743: Accelerating the exploration of novel gene fusion events in prostate cancer Cancer Research. 70: 2743-2743. DOI: 10.1158/1538-7445.Am10-2743  0.526
2005 Duax WL, Huether R, Pletnev VZ, Langs D, Addlagatta A, Connare S, Habegger L, Gill J. Rational genomics I: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code. Proteins. 61: 900-6. PMID 16245321 DOI: 10.1002/Prot.20687  0.321
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