Hugo Y. Lam, Ph.D. - Publications

Affiliations: 
Yale University, New Haven, CT 
Area:
Computational Biology and Bioinformatics

33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
2019 Sahraeian SME, Liu R, Lau B, Podesta K, Mohiyuddin M, Lam HYK. Deep convolutional neural networks for accurate somatic mutation detection. Nature Communications. 10: 1041. PMID 30833567 DOI: 10.1038/s41467-019-09027-x  0.48
2018 Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Research. PMID 29567674 DOI: 10.1101/gr.223693.117  0.48
2018 Møller HD, Mohiyuddin M, Prada-Luengo I, Sailani MR, Halling JF, Plomgaard P, Maretty L, Hansen AJ, Snyder MP, Pilegaard H, Lam HYK, Regenberg B. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nature Communications. 9: 1069. PMID 29540679 DOI: 10.1038/s41467-018-03369-8  0.48
2017 Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nature Communications. 8: 59. PMID 28680106 DOI: 10.1038/s41467-017-00050-4  0.56
2016 Lau B, Mohiyuddin M, Mu JC, Fang LT, Bani Asadi N, Dallett C, Lam HY. LongISLND: In silico Sequencing of Lengthy and Noisy Datatypes. Bioinformatics (Oxford, England). PMID 27667791 DOI: 10.1093/bioinformatics/btw602  0.48
2016 Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M. svclassify: a method to establish benchmark structural variant calls. Bmc Genomics. 17: 64. PMID 26772178 DOI: 10.1186/s12864-016-2366-2  0.36
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Lam HY, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/nature15394  0.36
2015 Mu JC, Tootoonchi Afshar P, Mohiyuddin M, Chen X, Li J, Bani Asadi N, Gerstein MB, Wong WH, Lam HY. Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods. Scientific Reports. 5: 14493. PMID 26412485 DOI: 10.1038/srep14493  0.36
2015 Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biology. 16: 197. PMID 26381235 DOI: 10.1186/s13059-015-0758-2  0.36
2015 Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 6: 8389. PMID 26346554 DOI: 10.1038/ncomms9389  0.56
2015 Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 6: 7256. PMID 26028266 DOI: 10.1038/ncomms8256  0.48
2015 Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics (Oxford, England). PMID 25861968 DOI: 10.1093/bioinformatics/btv204  0.48
2015 Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics (Oxford, England). 31: 1469-71. PMID 25524895 DOI: 10.1093/bioinformatics/btu828  0.48
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  0.56
2012 Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. Detecting and annotating genetic variations using the HugeSeq pipeline. Nature Biotechnology. 30: 226-9. PMID 22398614 DOI: 10.1038/nbt.2134  0.56
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  0.56
2011 Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. Performance comparison of exome DNA sequencing technologies. Nature Biotechnology. 29: 908-14. PMID 21947028 DOI: 10.1038/nbt.1975  0.48
2011 Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, et al. A comprehensive map of mobile element insertion polymorphisms in humans. Plos Genetics. 7: e1002236. PMID 21876680 DOI: 10.1371/journal.pgen.1002236  0.56
2011 Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. Identification of genomic indels and structural variations using split reads. Bmc Genomics. 12: 375. PMID 21787423 DOI: 10.1186/1471-2164-12-375  0.56
2011 Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research. 39: 7058-76. PMID 21596777 DOI: 10.1093/nar/gkr342  0.56
2011 Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, ... ... Lam HY, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/nature09708  0.56
2011 Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. Measuring the evolutionary rewiring of biological networks. Plos Computational Biology. 7: e1001050. PMID 21253555 DOI: 10.1371/journal.pcbi.1001050  0.56
2010 Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Research. 38: 6997-7007. PMID 20615899 DOI: 10.1093/nar/gkq587  0.56
2010 Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB. MOTIPS: automated motif analysis for predicting targets of modular protein domains. Bmc Bioinformatics. 11: 243. PMID 20459839 DOI: 10.1186/1471-2105-11-243  0.56
2010 Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. Plos Genetics. 6: e1000848. PMID 20174564 DOI: 10.1371/journal.pgen.1000848  0.56
2010 Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, et al. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Science Signaling. 3: ra12. PMID 20159853 DOI: 10.1126/scisignal.2000482  0.56
2010 Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology. 28: 47-55. PMID 20037582 DOI: 10.1038/nbt.1600  0.56
2009 Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. Pseudofam: the pseudogene families database. Nucleic Acids Research. 37: D738-43. PMID 18957444 DOI: 10.1093/nar/gkn758  0.56
2008 Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Research. 18: 1865-74. PMID 18842824 DOI: 10.1101/gr.081422.108  0.56
2007 Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY, Lim E, Chen H, Nadkarni P, Migliore M, Miller PL, Shepherd GM. SenseLab: new developments in disseminating neuroscience information. Briefings in Bioinformatics. 8: 150-62. PMID 17510162 DOI: 10.1093/bib/bbm018  0.56
2007 Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biology. 8: R81. PMID 17501994 DOI: 10.1186/gb-2007-8-5-r81  0.48
2007 Lam HY, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH. AlzPharm: integration of neurodegeneration data using RDF. Bmc Bioinformatics. 8: S4. PMID 17493287 DOI: 10.1186/1471-2105-8-S3-S4  0.56
2006 Lam HY, Marenco L, Shepherd GM, Miller PL, Cheung KH. Using web ontology language to integrate heterogeneous databases in the neurosciences. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 464-8. PMID 17238384  0.56
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