Hugo Lam, Ph.D.
Seasoned executive and principle investigator specialized in computational biology, bioinformatics, and AI
Dedicated to enabling people to solve today’s big data challenge
R&D Highlights
HypaHub in the top Analytics Startups funded by Y Combinator, April 2024.
Our quantum computing drug design workflow, HypaCADD, was highlighted on the "Quantum Machine Learning in Drug Discovery: Current State and Challenges" article published in the ACM proceedings.
Pharma Tech Outlook has recognized HypaHub as top Biotech Startup-2022.
NeuSomatic, the first convolutional neural network approach for somatic mutation detection we published in Nature Communications, was featured in the Editors’ Highlights in March on machine learning and selected by the NIH HPC staff to make available on their Biowulf.
The "Tiny Mummy’s ‘Alien’ Appearance Finally Explained" by our research teams, reported by National Geographic and published in Genome Research.
Our research published in Nature Communications found that Circular DNA is Common in Healthy Human Tissue, which was also reported by GenomeWeb.
Our comprehensive RNA-seq analysis protocol and computational pipeline, RNACocktail, was published in Nature Communications and presented at the Precision Medicine World Conference 2018.
Our Bioinformatics was selected by CIOApplications for the "Top 20 Bioinformatics Providers in 2017" - Roche Sequencing Solutions: Breaking the Barriers to Personalized Healthcare.
Our Roche team was recognized in the PrecisionFDA's Truth Challenge for HIGH-SNP-PERFORMANCE (achieving a SNP F-score of 99.920% or higher) and HIGH-INDEL-PERFORMANCE (achieving an indel F-score of 99.310% or higher).
Our SomaticSeq pipeline using a machine learning approach has scored #1 in somatic Indel and #2 in somatic SNV detections in Stage 5 of the ICGC-TCGA Dream Mutation Calling Challenge. The achievement was announced in the Press Release of Roche Sequencing and the method was published in Genome Biology.
Our HugeSeq pipeline for detecting and annotating genetic variations was published in Nature Biotechnology and reported by GenomeWeb.
Our performance analysis of sequencing platforms was published in Nature Biotechnology and selected by Faculty of 1000 (F1000).
Our personal omics profiling analysis was reported by Stanford News and Science News, and published in Cell .
Our junction mapping algorithm, BreakSeq, for identifying structural variants was reported by Yale News and published in Nature Biotechnology.
Publications
The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology. 2024 Feb 22;25(1):53. [Pubmed]
Lau B, Emani PS, Chapman J, Yao L, Lam T, Merrill P, Warrell J, Gerstein MB, Lam HYK. Insights from Incorporating Quantum Computing into Drug Design Workflows. Bioinformatics. 2023 Jan, btac789 [Pubmed] [Notebooks]
Yao L, Rey DA, Bulgarelli L, Kast R, Osborn J, Van Ark E, Fang LT, Lau B, Lam HYK, Teixeira LM, Neto AS, Bellomo R, Deliberato RO. Gene Expression Scoring of Immune Activity Levels for Precision Use of Hydrocortisone In Vasodilatory Shock. Shock. 2022 Jan 25. doi: 10.1097/SHK.0000000000001910 [PubMed]
Fang et al. & The Somatic Working Group of SEQC-II Consortium. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol. 2021 Sep; 39(9): 1151–1160. doi: 10.1038/s41587-021-00993-6 [Pubmed]
Lei I, Huang W, Ward PA, Pober JS, Tellides G, Ailawadi G, Pagani FD, Landstrom AP, Wang Z, Mortensen RM, Cascalho M, Platt J, Eugene Chen Y, Lam HYK, Tang PC. Differential inflammatory responses of the native left and right ventricle associated with donor heart preservation. Physiol Rep. 2021 Sep;9(17):e15004. doi: 10.14814/phy2.15004 [PubMed]
Lei I, Wang Z, Chen YE, Ma PX, Huang W, Kim E, Lam HYK, Goldstein DR, Aaronson KD, Pagani FD, Tang PC. "The Secret Life of Human Donor Hearts": An Examination of Transcriptomic Events During Cold Storage. Circ Heart Fail. 2020 Apr;13(4):e006409. doi: 10.1161/CIRCHEARTFAILURE.119.006409 [Pubmed]
Yao L, Fu Y, Mohiyuddin M, Lam HYK. ecTMB: a robust method to estimate and classify tumor mutational burden. Scientific Reports. 2020 Mar 18;10(1):4983. doi:10.1038/s41598-020-61575-1 [Pubmed]
Sahraeian SME, Liu R, Lau B, Podesta K, Mohiyuddin M, Lam HYK. Deep convolutional neural networks for accurate somatic mutation detection. Nature Communications. 2019 Mar 4;10(1):1041. doi: 10.1038/s41467-019-09027-x [Pubmed]
Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Bani Asadi N, Lachman RS, Lam HY, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Research. 2018 Mar 22; doi:10.1101/gr.223693.117 [Pubmed]
Møller HD, Mohiyuddin M, Prada-Luengo I, Sailani MR, Halling JF, Plomgaard P, Maretty L, Hansen AJ, Snyder MP, Pilegaard H, Lam HY & Regenberg B. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nature Communications. 2018 Mar 14;9(1):1069. doi: 10.1038/s41467-018-03369-8. [PubMed]
Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HY. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nature Communications. 2017 Jul 5;8(1):59. doi: 10.1038/s41467-017-00050-4. [PubMed] [Website]
Chandonia JM, Adhikari A, Carraro M, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, Lam HYK et al. Lessons from the CAGI-4 Hopkins clinical panel challenge. Human Mutation. 2017 Apr 11. doi: 10.1002/humu.23225. [PubMed] [Website]
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. 2016 Dec 15;32(24):3829-3832. [PubMed] [Website]
Parikh H, Mohiyuddin M, Lam HY et. al. svclassify: a method to establish benchmark structural variant calls. BMC Genomics. 2016 Jan 16;17(1):64. doi: 10.1186/s12864-016-2366-2. [PubMed] [Website]
Sudmant PH et. al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526:75–81. doi:10.1038/nature15394. [PubMed]
The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015 Oct 1;526:68–74. doi:10.1038/nature15393. [PubMed]
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. 2015; 5:14493. doi:10.1038/srep14493. [PubMed] [Website]
Fang L* & Tootoonchi Afshar P* et. al. & Lam HY. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biology. 2015;16:197. doi:10.1186/s13059-015-0758-2. [PubMed] [Website]
Abyzov A, Li S, Kim D, Mohiyuddin M, Stuetz a, Parrish A, Mu XJ, Clark W, Chen Ken, Hurles M, Korbel J, Lam HY, Lee C, Gerstein M. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nature Communications. 2015 Jun 1;6:7256. doi: 10.1038/ncomms8256. [PubMed] [Website | BreakSeq2]
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. 2015 Apr 10. pii: btv204. [PubMed] [Website]
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. 2014 Dec 17. pii: btu828. [PubMed] [Website]
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489:57-74. [PubMed]
Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY et. al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012 Mar 16;148(6):1293-307. [PubMed]
Lam HY et. al. Detecting and Annotating Genetic Variations Using the HugeSeq Pipeline. Nature Biotechnology. 2012 Mar 7;30(3):226-9. [PubMed] [Website]
Lam HY et. al. Performance comparison of whole-genome sequencing platforms. Nature Biotechnology. 2011 Dec 18;30(1):78-82. [PubMed]
Clark M, Chen R, Lam HY et. al. Performance comparison of exome DNA sequencing technologies. Nature Biotechnology. 2011 Sep 25;29(10):908-14. [PubMed]
Stewart C, Kural D, Strömberg M, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY et. al. A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PloS Genetics. 2011 Aug 20;7(8): e1002236. [PubMed]
Zhang ZD, Du J, Lam HY et. al. Identification of genomic indels and structural variations using split reads. BMC Genomics. 2011 Jul 25;12(1):375. [PubMed]
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 Res. 2011 May 19. [PubMed]
ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. [PubMed]
Mills R et al. & 1000 Genomes Project. Mapping copy number variation by population scale genome sequencing. Nature. 2011 Feb 3;470(7332):59-65. [PubMed] [Website]
Shou C, Bhardwaj N, Lam HY et. al. Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol. 2011 Jan 6;7(1):e1001050. [PubMed]
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. [PubMed] [Website]
Khurana E, Lam HY et. al. Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res. 2010 Jul 8. [PubMed]
Lam HY et al. Motips: An Automated Motif Analysis Pipeline for Predicting Domain Targets. BMC Bioinformatics. 2010 May 11;11(1):243. [PubMed] [Website]
Zhong M, Niu W, Lu Z, Sarov M, Murray J, Janette J, Raha D, Sheaffer K, Lam HY et. al. Genome-wide identification of binding sites defines distinct functions for C. elegans PHA-4/FOXA in development and environmental response. PloS Genetics. 2010 Feb 19;6(2):e1000848. [PubMed]
Mok J, Kim PM, Lam HY et. al. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation motifs. Science Signaling. 2010 Feb 16;3(109):ra12. [PubMed]
Lam HY et al. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology. 2010 Jan;28(1):47-55. [PubMed] [Website]
Lam HY et al. Pseudofam: the pseudogene families database. Nucleic Acids Res. 2009 37(Database issue):D738-D743. [PubMed] [Website]
Kim PM* & Lam HY* et. al. 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 Res. 2008 Dec;18(12):1865-74. [PubMed] [Website]
Zhang ZD, Rozowsky J, Lam HY et. al. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol. 2007;8(5):R81. [PubMed]
Crasto CJ1, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY et al. SenseLab: new developments in disseminating neuroscience information. BMC Bioinformatics. Brief Bioinform. 2007 May;8(3):150-62. [PubMed]
Lam HY et al. AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics. 2007 May 9;8 Suppl 3:S4. [PubMed]
Lam HY et al. Using web ontology language to integrate heterogeneous databases in the neurosciences. AMIA Annu Symp Proc. 2006:464-8. [PubMed]
Patents
Lau B, Lee A, Lam T, Merrill P, Lam HY. Computational Method And System For Diagnostic And Therapeutic Prediction From Multimodal Data. Patent Pending. HypaHub, Inc, assignee. [USPTO]
Lam HY, Lau B, Yao L. Hybrid Computational System of Classical and Quantum Computing for Drug Discovery and Methods. Patent Pending. HypaHub, Inc, assignee. [Google Patents]
Rey DA, Teixeira LM, Lam HY, LAU B, YAO L. Biomarker panels for guiding dysregulated host response therapy. Endpoint Health, Inc, assignee. Patent Pending. [Google Patents]
Lam HY, Mohuyuddin M, Yao L. Tumor Classification Based On Predicted Tumor Mutational Burden. Roche Sequencing Solutions, Inc, assignee. Patent Pending. [Google Patents]
Lal P, Lam HY, Lee J, Lovejoy A, Palma J, Rosenthal A, Yao L. Classifying somatic mutations from heterogeneous sample. Roche Sequencing Solutions, Inc, assignee. Patent Pending. [Google Patents]
Lam HY, Mohiyuddin M, Sahraeian SME. Systems and methods for using neural networks for germline and somatic variant calling. Roche Sequencing Solutions, Inc, assignee. Patent Pending. [Google Patents]
Fu Yao, Chhibber A, Mohiyuddin M, Fang LT, Lam HY. Detecting cancer driver genes and pathways. Roche Sequencing Solutions, Inc, assignee. Patent Pending. [Google Patents]
Bartha GT, Chandratillake G, Chen R, Garcia S, Lam HY, Luo S, Pratt MR, West J. Methods and Systems for Genetic Analysis. Personalis, Inc, assignee. Patent 9,128,861. 8 Sept. 2015. Print. [USPTO]
Talks
A Deep Learning Approach For Somatic Mutation Detection. Precision Medicine World Conference. January 22, 2019.
A comprehensive RNA-seq Analysis Protocol & Computational Pipeline. Precision Medicine World Conference. January 23, 2018.
From Gold Standard to Accurate Variant Detection. FDA's SEQC2 Workshop. October 26, 2017.
Using a Machine Learning Algorithm to Detect Accurate Somatic Mutations in Cancer. Artificial Intelligence and Machine Learning Symposium at Genentech. September 29, 2016.
Leveraging TCGA data to generate insights in oncology. Festival of Genomics. September 20, 2016.
NGS informatics and its challenges. Stanford BMI206: Informatics in Industry. April 25, 2016.
Scientific Advancement in Genomics with Bina Technologies. Genomics Program Biotechnology Companies Day. March 18, 2016.
Assessing and improving accuracy of next-generation sequencing informatics. Molecular Medicine Tri-Conference (TriCon 2016). March 7, 2016.
Panel Discussion: Technologies for De Novo Genome Sequence Assembly for Variation Detection. The 16th International Meeting on Human Genome Variation and Complex Genome Analysis (HGV 2015). November 13, 2015.
Big Data Challenge in Genomics. Stanford Pre-collegiate Science Conference (2nd). November 7, 2015.
Bina Technologies: Bioinformatics & Analytics. Seminar at Stanford Center for Genomics and Personalized Medicine. Tuesday, March 24, 2015.