Francisco M. De La Vega, D.Sc.

Consulting Professor

365 Lasuen Street, Room 310, Littlefield Center MC 2069

Email: or

Phone: 1-650-918-7417


I am a geneticist and computational biology scientist with over 15 years of experience in industry overseeing the research, development, and validation of innovative genetic analysis technologies and bioinformatics tools enabling high-throughput biology. I am currently visiting the lab of Carlos Bustamante, Professor of Genetics. The availability of massively parallel sequencing platforms that allow inexpensive sequencing of complete human genomes is enabling studies in genetic susceptibility to disease and evolution not possible before, and is leading to a revolution in personalized medicine enabled by the genome. Challenges include the massive amounts of data, the complex relationships among the types of relevant data, and the need to make the data accessible from different perspectives. The variation in the DNA sequence among the billions of separate copies of extant human genomes can occasionally be of medical significance because it can alter disease susceptibility and reactions to drugs and pathogens. Aspects of the effective collection, representation, and use of the vast " omics" data in the elucidation of the etiology of common disease have been a major theme of my work. I am currently interested in the application of ultra-high throughput sequencing technologies in genetic epidemiology, population studies, and more recently clinical applications, aiming to identify the role of rare and structural variants in complex diseases.

Positions and Employment

Consulting Professor, Dept. of Genetics, Stanford School of Medicine, Stanford, CA, USA, 2015-Present.

Chief Scientific Officer, Annai Systems, Inc., Burlingame, CA, USA. 2/2014-Present.

Visiting Scholar, Dept. of Genetics, Stanford School of Medicine, Stanford, CA, USA, 2013-2014.

Vice President, Genome Science. Real Time Genomics, Inc., San Francisco, CA, USA. 8/2012-2013.

Visiting Instructor, Dept. of Genetics, Stanford School of Medicine, Stanford, CA, USA, 2012-2013.

Visiting Scholar, Dept. of Genetics, Stanford School of Medicine, Stanford, CA, USA, 2011.

Distinguished Scientific Fellow & VP, Advance Genomics Research. Applied Biosystems, Foster City, CA, USA, 2008-2010.

Scientific Fellow & Sr. Director, Computational Genetics. Applied Biosystems, Foster City, CA, USA, 2005-2008.

Director, Computational Genetics. Applied Biosystems. Foster City, CA, USA, 2003-2005.

Senior Manager, Bioinformatics R&D. Applied Biosystems. Foster City, CA, USA, 2001-2002.

Manager, Arrays Bioinformatics R&D. Applied Biosystems. Foster City, CA, USA, 1999-2001.

Staff Scientist. Synthesis and Arrays R&D. PE Biosystems. Foster City, CA, USA, 1998-1999.

Assistant Professor. Department of Genetics. CINVESTAV-IPN, Mexico City, Mexico,1989-1998.

Research Assistant. Department of Genetics. CINVESTAV-IPN, Mexico City, Mexico, 1988-1989.

Auxiliary Professor. Metropolitan Autonomous University (UAM), Mexico City, Mexico, 1985.


Wood-Whelan Research Fellowship, International Union of Biochemistry, 1990.

Candidate to National Researcher, National System of Researchers, Mexico, 1992.

DNA (Demonstrated Noteworthy Achievement) Award. Applera Corporation, 2002.

Bio-IT World's Best Practices Award, Basic Research category, Boston, MA, 2008.

Inaugural Inductee, I2 Society (Invention x Innovation), Life Technologies, 2009.


Doctor of Science (D.Sc.) Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico. 2000.

Master of Science (M.Sc.) Pharmacology, Center for Research and Advanced Studies, Mexico City, Mexico. 1989.

Biologist (B.Sc) Experimental Biology, Metropolitan Autonomous University (UAM), Mexico City, Mexico.1986.

MIT Sloan Executive Certificate in Management and Leadership. Sloan School of Business. Massachusetts Institute of Technology. Cambridge, MA. 2007.

Recent Publications (Google Scholar Citations)

Delaneau O, Marchini J; 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun. 2014 Jun 13;5:3934

Segal MM, Abdellateef M, El-Hattab AW, Hilbush BS, De La Vega FM, Tromp G, Williams MS, Betensky RA, Gleeson J. Clinical Pertinence Metric Enables Hypothesis-Independent Genome-Phenome Analysis for Neurologic Diagnosis. J Child Neurol. 2014 Aug 24.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol. 2014 Jun 30;15(6):R88.

Cleary JG, Braithwaite R, Gaastra K, Hilbush BS, Inglis S, Irvine SA, Jackson A, Littin R, Nohzadeh-Malakshah S, Rathod M, Ware D, Trigg L, De La Vega FM. Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data. J Comput Biol. 2014 Jun;21(6):405-19.

Enroth S, Andersson R, Bysani M, Wallerman O, Termén S, Tuch BB, De La Vega FM, Heldin CH, Moustakas A, Komorowski J, Wadelius C. Nucleosome regulatory dynamics in response to TGFβ. Nucleic Acids Res. 2014 Jun;42(11):6921-34.

Brownstein CA, et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 2014 Mar 25;15(3):R53.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 4;342(6154):1235587.

Craig DW, O'Shaughnessy JA, Kiefer JA, Aldrich J, Sinari S, Moses TM, Wong S, Dinh J, Christoforides A,Blum JL, Aitelli CL, Osborne CR, Izatt T, Kurdoglu A, Baker A, Koeman J, Barbacioru C, Sakarya O, De La Vega FM, Siddiqui A, Hoang L, Billings PR, Salhia B, Tolcher AW, Trent JM, Mousses S, Von Hoff D, Carpten JD. Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities.Mol Cancer Ther. 2013 Jan;12(1):104-16.

1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65.

Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, Degenhardt JD, Brisbin A, Sheth V, Chen R, McLaughlin SF, Peckham HE, Omberg L, Bormann Chung CA, Stanley S, Pearlstein K, Levandowsky E, Acevedo-Acevedo S, Auton A, Keinan A, Acuña-Alonzo V, Barquera-Lozano R, Canizales-Quinteros S, Eng C, Burchard EG, Russell A, Reynolds A, Clark AG, Reese MG, Lincoln SE, Butte AJ, De La Vega FM, Bustamante CD. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variatio. Am J Hum Genet. 2012 Oct 5;91(4):660-71.

Gusev A, Shah MJ, Kenny EE, Ramachandran A, Lowe JK, Salit J, Lee CC, Levandowsky EC, Weaver TN, Doan QC, Peckham HE, McLaughlin SF, Lyons MR, Sheth VN, Stoffel M, De La Vega FM, Friedman JM, Breslow JL, Pe'er I. Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population. Genetics. 2012 Feb;190(2):679-89.

Bustamante CD, Burchard EG, De la Vega FM. Genomics for the world. Nature. 2011 Jul 13;475(7355):163-5.

Gordon D, Finch S.J., and De La Vega FM. A new expectation-maximization statistical test for case-control association studies considering rare variants obtained by high-throughput sequencing. Human Heredity, 2011, Hum Hered. 2011;71(2):113-25..

Moore B, Hu H Singleton M, De La Vega FM, Reese MG, and Yandel M. Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole-genome-based clinical diagnostics. Genetics in Medicine, 2011, 13(3):210-217.

Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK. Analyses of 128 ancestry informative SNPs (AISNPs) in a global set of 119 population samples. Investigative Genetics, 2011, 2:1.

Mitrovich QM, Tuch BB, De La Vega FM, Guthrie C, Johnson AD. Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss. Science. 2010 Nov 5;330(6005):838-41.

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project (..De La Vega, FM..), Eichler EE. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6.

1000 Genomes Project Consortium (.. De La Vega FM..), Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

Tuch BB, Mitrovich QM, Homann OR, Hernday AD, Monighetti CK, De La Vega FM, Johnson AD. The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation. PLoS Genetics, 2010 Aug 19;6(8):e1001070.

Londono D, Haynes C, De La Vega FM, Finch SJ, Gordon D. A Cost-Effective Statistical Method to Correct for Differential Genotype Misclassification When Performing Case-Control Genetic Association. Human Heredity, 2010 Jul 3;70(2):102-108.

Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, Antipova A, Lee C, McKernan K, De La Vega FM, Kinzler KW, Vogelstein B, Diaz LA Jr, Velculescu VE. Development of personalized tumor biomarkers using massively parallel sequencing. Science Translational Med. 2010 Feb 24;2(20):20ra14.

Tuch BB, Laborde RR, Xu X, Gu J, Chung CB, Monighetti CK, Stanley SJ, Olsen KD, Kasperbauer JL, Moore EJ, Broomer AJ, Tan R, Brzoska PM, Muller MW, Siddiqui AS, Asmann YW, Sun Y, Kuersten S, Barker MA, De La Vega FM, Smith DI. Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PLoS One. 2010 Feb 19;5(2):e9317.

McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research, 2009 Sep;19(9):1527-41.

Kosoy R, Nassir N, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW, De La Vega FM, and Seldin MF. (2008) Ancestry Informative Marker Sets for Determining Continental Origin and Admixture Proportions in Common Populations in America. Human Mutation, Jan;30(1):69-78.

Hellmann I, Mang Y, Gu Z, Li P, De La Vega FM, Clark AG, Nielsen R. (2008) Population genetic analysis of shotgun assemblies of genomic sequence from multiple individuals. Genome Research, 18(7):1020-9.

Welch RA, Lazaruk K, Haque KA, Hyland FCL, Xiao N, Wronka L, Burdett L, Chanock SJ, Ingber D, De La Vega FM, Yeager M. (2008) Validation of the Performance of a Comprehensive Genotyping Assay Panel of Single Nucleotide Polymorphisms in Drug Metabolism Enzyme Genes. Human Mutation, 29(5):750-6.

Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Gunther S, Prescott NJ, Onnie CM, Hasler R, Sipos B, Folsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nature Genetics, 39(2):207-11.