Mauricio Carneiro's Professional Resume

EDUCATION:

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

PROFESSIONAL
EXPERIENCE:

Google[x]

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

AWARDS:

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

SELECTED
PUBLICATIONS:

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

PATENTS:

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

ADVISORY
BOARD:

Mendelics Genomic Analysis

Scientific Advisory Board

May, 2013 - present

EDUCATION:	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
PROFESSIONAL EXPERIENCE:	Google[x] 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
AWARDS:	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
SELECTED PUBLICATIONS:	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
PATENTS:	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
ADVISORY BOARD:	Mendelics Genomic Analysis Scientific Advisory Board May, 2013 - present