Mauricio Carneiro
Ph.D. Computational Biology
Harvard University, 2010
M.Sc. Molecular Biology
Oswaldo Cruz Research Institute, Rio de Janeiro - Brazil, June 2005
B.Sc. Computer Engineering
Pontifical Catholic University of Rio de Janeiro, 2003
Google, January 2015 - present
Computational Technology Development Lead
Broad Institute, December 2010 - January 2015
  • Led three teams of computational biologists and software engineers to provide core libraries for tool development, development of computational/statistical methods for disease research and clinical association studies and provide the analytical interface between the Medical and Population Genetics research needs and the Genomics Platform.
  • Managed collaborations between the Broad Institute and Intel, NVidia, IBM, Cray and Alterra.
  • Implemented hardware accelerated libraries and tools, designed parallel (shared memory and distributed) framework for our development environment and helped guide the design of hardware that would cater to our industry's particular needs.
  • Developed key methods in the Genome Analysis Toolkit (GATK) such as DiagnoseTargets, ReduceReads and BaseRecalibrator. Conceptualized and developed a new pooled sequencing framework based on a reference sample that enabled validation in thousands of samples at a cost-effective rate.
  • Defined and standardized the data processing pipeline for resequencing projects.
  • Instituted continuous integration, code review and project management for the team.
  • Led the creation of a user outreach effort, community building, GATK workshops, website and Q&A forum.
Lead Game Architect
M1nd Corporation, November 2004 - May 2006
  • Managed a team of developers at start-up gaming company producing the first location based role-playing game in the world: Alien Revolt.
  • Led the game design and mathematical framework for the role playing and battle components.
  • Managed a team of 50 alpha and beta testers for quality assurance and design feedback.
Junior Researcher in Computer Graphics
TECGRAF/PUC-RIO, March 2000 - March 2003
  • Developed multiplatform tools for computer graphics developers and participated in the development of the LUA language and basic libraries.
Lead Game Programmer
Getulio Vargas Foundation, February 1998 - January 2000
  • Led the development of the first video game created in Brazil: The Adventures of Taina.
  • Developed the game physics, artificial intelligence, sound and video.
  • Managed designers and musicians
Distinction in Teaching Award
Bok Center, Harvard University, Spring 2010
Distinction in Teaching Award
Bok Center, Harvard University, Spring 2008
Programming Excellence Award
ACM Upsilon Pi Epsilon Society, March 2003
1st place of South America - International Collegiate Programming Contest 2003
Association for Computing Machinery, November 2002
4th place of South America - International Collegiate Programming Contest 2002
Association for Computing Machinery, November 2001
Best Mathematics Software Award
Pontifical Catholic University of Rio de Janeiro, July 1998
Reference sample guided pooled sequencing identifies loss-of-function patterns across human populations
Nature Genetics (in review)
Carneiro MO, Eran A, delAngel G, Auwera GV, Lek M, 1000 Genomes Project Consortium, Altshuler D, Gabriel S, DePristo MA, MacArthur D, Banks E
Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus
PLoS Genetics 2015, 11(1): e1004876. doi: 10.1371/journal.pgen.1004876
T2D Consortium
Semiconductor-based DNA sequencing of histone modification states
Nature Communications 2013, 4:2672
Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Rosenthal A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon NJ, Nusbaum C, Chin L, Regev A and Amit I
Integrative annotation of variants from 1092 humans: application to cancer genomics
Science 2013, 342:6154
1000 Genomes Project Consortium
From FastQ data to high confidence variant calls - the Genome Analysis Toolkit best practices pipeline
Current Protocols in Bioinformatics 2013, 43:11.10
Van der Auwera GA, Carneiro MO, Hartl CL, Poplin R, Angel GD, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S and Mark A. DePristo
The advantages of SMRT sequencing
Genome Biology 2013, 14:405
Roberts RJ, Carneiro MC, Schatz MC
An integrated map of genetic variation from 1,092 human genomes
Nature 2012, 491:56-65
1000 Genomes Project Consortium
Pacific biosciences sequencing technology for genotyping and variation discovery in human data
BMC Genomics 2012, 13:375
Carneiro MO, Russ C, Ross MG, Gabriel S, Nusbaum C, DePristo MA
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations
Nature 2012, 488:106-110
Pugh TJ, Weeraratne SD, Archer TC, Krummel DA, Auclair D, Bochicchio J, Carneiro MO, et al.
Model transcriptional networks with continuously varying expression levels
BMC Evolutionary Biology 2011:11:303
Carneiro MO, Taubes CH, Hartl DL
Adaptive landscapes and protein evolution
Proc Natl Acad Sci USA 2010, 107 Suppl 1:1747-51
Carneiro MO, Hartl DL
Population Genomic Inferences from Sparse High-Throughput Sequencing of Two Populations of Drosophila melanogaster
Gen Biol Evol, 2009:449-465
Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro MO, Marth GL, Hartl DL, Clark AG
Reference Sample Based Pooled Hybrid Selection Sequencing Method And Analytics
US Provisional Patent Application No. 61/893,874 filed October 21, 2013.
Carneiro MO, DelAngel G, Fisher S, DePristo MA
Systems and methods for reducing representations of genome sequencing data
US Provisional Patent Application No. 61/611,993 filed March 16, 2012.
PCT Patent PCT/US13/31429, filed March 14, 2013.
Carneiro MO, DePristo MA
Mendelics Genomic Analysis
Scientific Advisory Board
May, 2013 - present