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Computational Biology Bioinformatics Genomics Genetics Data Science

Location:
Stamford, Connecticut, United States
Posted:
March 09, 2018

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MATTHEW D HEALY, PhD.

linkedin.com/in/matthewdhealy/

ac4q7t@r.postjobfree.com

203-***-****

COMPUTATIONAL BIOLOGY FROM DISCOVERY TO THE CLINIC

Leveraged large amounts of Genomic and Genetic Data to enable Drug Discovery and Development Programs. Data analyses were essential for getting four now-approved drugs from Early Discovery to the Clinic. Gained deep knowledge of Biotech and Pharma Pipeline at all phases, on both Small Molecules and Biologics. Skills:

• Genomics/Genetics •Data Science • Cross-functional teams

• Metabolic Pathways • High-Dimensional Data • Data Mining & Visualization

• Gene Expression Data • Microbial Genomics • Immunology

• Bioinformatics databases • Inventor on US Patent • Neuroscience

• Reporting and collaboration • Genetic Associations • Regulatory Requirements

AWARD-WINNING ACCOMPLISHMENTS

Analysis of Preclinical and Clinical Resistance Mutation Data was essential for progressing multiple HIV and Hepatitis C Virus drugs from Early Discovery to Clinical Trials and in four cases Regulatory Approval. Several other drugs in Clinical Trials.

Built and maintained pipelines for mining of Bacterial and Fungal Genomes.

Inventor on US Patent for Novel Microbial Drug Targets

Identified the first known essential methyltransferase gene in bacteria

Spearheaded the first Next-Generation Sequencing Pilot Study at BMS: selected potential vendors, organized presentations, obtained buy-in from stakeholders across the organization, helped design the study, built analysis pipeline from scratch, and delivered comprehensive reports on the results and their strategic implications.

Given BMS Presidential Award of $1000 for Genomic Dossiers which enabled stakeholders in multiple departments to make better decisions about Target Genes.

Given internal BMS award for rapidly and accurately organizing analysis of data from Phase 1 and Phase 2a clinical trials of an HIV compound, thus “accelerating Phase 2B start” and speeding progress through Human Clinical Trials

Given internal BMS award for helping the “team turn a potentially difficult situation into a successful outcome” by delivering a rapid response for multiple stakeholders to an FDA post-market data request on the HIV drug Efavirenz. “This work involved late nights and weekends as well as tight collaboration across functional areas.”

Note: words in quotation marks above are verbatim quotes by colleagues who made nominations for the BMS internal awards.

EXPERIENCE

Regeneron Genetics Center, Tarrytown, NY 2016 – 2017

Senior Manager Genomic Targeting Information, Translational Genetics

Integrated internal and external Omics and Genetics data for strategic intelligence around proposed targets identified in Human Genetics data mining.

Bristol-Myers Squibb, Wallingford, CT 1998 – 2015

Senior Research Investigator, Translational Bioinformatics 2006-2015

Research Investigator, Translational Bioinformatics 1998-2006

Spearheaded Bioinformatics support of Infectious Diseases Drug Discovery and Development at Bristol-Myers Squibb. Made critical contributions to every antiviral drug BMS brought to market during this period, at every stage of the pipeline from Early Discovery to Clinical Development, and even post-market studies of approved drugs. Many analyses were needed by stakeholders in Exploratory Working Groups, Discovery Working Groups, and Biomarker Working Groups in Microbiology, Immuno-Oncology, Virology, and Neuroscience Drug Discovery and Development to make major decisions.

Maintained large-scale databases and analysis pipelines for Microbial Genomics project which identified a number of novel targets for antibacterial and antifungal drug discovery. Inventor on US Patent for Novel Antifungal Drug Targets

Helped Lead Discovery identify cell lines expressing proteins of interest

TECHNICAL SKILLS

Database Management, Database Curation, Data Integration, Experimental Design, Clinical Data, FDA Data Formats, Extract-Transform-Load (ETL), ICD-9, ICD9, ICD-10, ICD10, SNOMED, BIOVIA Discovery Studio, Designed Analysis Pipelines, BLAST, FASTA, CLUSTAL, ANOVA, PAUP, Excel, Principal Components Analysis (PCA), NCBI, Ensembl, dbSNP, Regression, Hypergeometric Test, False Discovery Rate, R, Perl, Java, SQL, Sybase, Oracle, Postgres, Partek Discovery Suite, Partek Genomics Suite, Omicsoft Array Studio, DAVID, GeneGo, Ingenuity Pathway Analysis, Gene-Finding tools, CGI Scripting, and TimeLogic DeCypher FPGA server, Unix, Linux, Windows, Postgres, Microsoft Office, Word, Excel, Regulatory Documents, Journal Publications, Systems Biology Analysis, Microbial Systems, Virology, Biology, Access, Bioconductor, GSEA, GeneGo, Ingenuity Pathways, Pathway Analysis, Data Visualization, Multivariate Statistics, and PowerPoint

EDUCATION

PhD, Zoology, Duke University, Durham, North Carolina

Bachelor of Science in Engineering, Purdue University, West Lafayette, Indiana

ADDITIONAL RELEVANT EXPERIENCE

Postdoc at Yale School of Medicine, New Haven, CT

Electrical Engineer at Siemens Energy and Automation in various States

CONTINUING PROFESSIONAL EDUCATION

Database Coursework, Oracle Corporation, New York City Training Center

Coursework in Biostatistics and Computer Science, Quinnipiac University, Hamden, CT

Online Coursework in Data Science from Johns Hopkins University via Coursera

Publications by Matthew D Healy, Ph.D.

US Patent

US 7465568 B2. Novel essential fungal polynucleotides, polypeptides, and methods of use.

Inventors: Ying-Kai Wang, Mengping Liu, Brian A. Dougherty, Matthew D. Healy, Daniel B.

Davison, Charles E. Mazzucco, & Trina C. Maurice. USPTO Priority Date: Apr 26, 2002

Publications

A novel LDL-lowering missense variant in B4GALT1 identifies novel biological

connection between protein glycosylation and cardiovascular risk factors in human. M.

Montasser; C. Van Hout; G. Della Gatta; M. Puurunen; J. Reid; J. Overton; A. Baras;

A. Economides; M. Healy; N. Zaghloul; C. Sztalryd-Woodle; E. Streeten; B. Mitchell;

S. Taylor; J. O'Connell; A. Shuldiner. Presented at the American Society of Human

Genetics Meeting in October 2017. Abstract number 2681, which can be viewed on the meeting website

http://www.ashg.org/2017meeting/listing/PosterSessions.shtml

Search within this page for B4GALT1, then click the link to see the abstract

Identification and Characterization of BMS-955176, a Second-Generation HIV-1 Maturation

Inhibitor with Improved Potency, Antiviral Spectrum, and Gag Polymorphic Coverage.

Nowicka-Sans B, Protack T, Lin Z, Li Z, Zhang S, Sun Y, Samanta H, Terry B, Liu Z, Chen Y, Sin

N, Sit SY, Swidorski JJ, Chen J, Venables BL, Healy MD, Meanwell NA, Cockett M,

Hanumegowda U, Regueiro-Ren A, Krystal M, Dicker IB. Antimicrobila Agents &

Chemotherapy. 2016 Jun 20;60(7):3956-69. doi: 10.1128/AAC.02560-15. Print 2016 Jul.

Genotypic correlates of susceptibility to HIV-1 attachment inhibitor BMS-626529, the active

agent of the prodrug BMS-663068. Nannan Zhou, Beata Nowicka-Sans, Brian McAuliffe,

Neelanjana Ray, Betsy Eggers, Hua Fang, Li Fan, Matthew Healy, David R Langley, Carey

Hwang, Max Lataillade, George J Hanna, & Mark Krystal. Journal of Antimicrobial

Chemotherapy 10/2013; 69(3).

Prediction of virologic response and assessment of resistance emergence to the HIV-1

attachment inhibitor BMS-626529 during 8-day monotherapy with its prodrug BMS-663068.

Neelanjana Ray, Carey Hwang, Matthew D Healy, Jeannette Whitcomb, Max Lataillade,

Megan Wind-Rotolo, Mark Krystal, & George J Hanna. JAIDS Journal of Acquired Immune

Deficiency Syndromes 04/2013

Geno- and phenotypic correlates of virologic response to the attachment inhibitor BMS-

626529 in an 8-day monotherapy study of its prodrug BMS-663068. Nannan Zhou,

Neelanjana Ray, Matthew Healy, David Langley, Carey Hwang, Max Lataillade, George

Hanna, & Mark Krystal . Journal of the International AIDS Society 11/2012; 15(6):18270.

Matthew D Healy ac4q7t@r.postjobfree.com C: 203-***-**** Page 2

Inhibition of influenza virus replication via small molecules that induce the formation of

higher-order nucleoprotein oligomers. Samuel W Gerritz, Christopher Cianci, Sean Kim,

Bradley C Pearce, Carol Deminie, Linda Discotto, Brian McAuliffe, Beatrice F Minassian,

Shuhao Shi, Shirong Zhu, Weixu Zhai, Annapurna Pendri, Guo Li, Michael A. Poss, Suzanne

Edavettal, Patricia A. McDonnell, Hal A. Lewis, Klaus Maskos, Mario Mörtl, Reiner

Kiefersauer, Stefan Steinbacher, Eric T. Baldwin, William Metzler, James Bryson, Matthew D

Healy, Thomas Philip, Mary Zoeckler, Richard Schartman, Michael Sinz, Victor H Leyva-

Grado, Hans-Heinrich Hoffmann, David R Langley, Nicholas A Meanwell, & Mark Krystal.

Proceedings of the National Academy of Sciences 09/2011; 108(37):15366-71

Using BLAST for performing sequence alignment. Matthew D Healy. Unit 6.8 of Current

protocols in human genetics. 02/2007

Conserved fungal genes as potential targets for broad-spectrum antifungal drug discovery.

Mengping Liu, Matthew D Healy, Brian A Dougherty, Kim M Esposito, Trina C Maurice,

Charles E Mazzucco, Robert E Bruccoleri, Daniel B Davison, Marybeth Frosco, John F Barrett,

& Ying-Kai Wang. Eukaryotic Cell 05/2006; 5(4):638-49.

Structural and functional characterization of CFE88: evidence that a conserved and essential

bacterial protein is a methyltransferase. Keith L Constantine, Stanley R Krystek, Matthew D

Healy, Michael L Doyle, Nathan O Siemers, Jane Thanassi, Ning Yan, Dianlin Xie, Valentina

Goldfarb, Joseph Yanchunas, Li Tao, Brian A Dougherty, & Bennett T Farmer. Protein

Science 07/2005; 14(6):1472-84

Bioinformatics: not just for sequences anymore. Donald G. Jackson, Matthew D. Healy, &

Daniel B. Davison. BIOSILICO 07/2003; 1(3):103-111

Finding homologs to nucleic acid or protein sequences using the framesearch program.

Matthew Healy. Unit 3.2 of Current protocols in bioinformatics 09/2002

Olfactory Receptor Database: a database of the largest eukaryotic gene family. E Skoufos, M

D Healy, M S Singer, P M Nadkarni, P L Miller, & G M Shepherd. Nucleic Acids Research

02/1999

Matthew D Healy ac4q7t@r.postjobfree.com C: 203-***-**** Page 3

The Human Brain Project: neuroinformatics tools for integrating, searching and modeling

multidisciplinary neuroscience data. Gordon M. Shepherd, Jason S. Mirsky, Matthew D.

Healy, Michael S. Singer, Emmanouil Skoufos, Michael S. Hines, Prakash M. Nadkarni, &

Perry L. Miller. Trends in Neurosciences 12/1998; 21(11):460-8

Database tools for integrating and searching membrane property data correlated with

neuronal morphology. Jason S. Mirsky, Prakash M. Nadkarni, Matthew D. Healy, Perry L.

Miller, & Gordon M. Shepherd. Journal of Neuroscience Methods 08/1998; 82(1):105-21.

Acquiring, Storing and Retrieving Diverse Biomedical Data Using the World-Wide-Web: The

SenseLab Paradigm. Emmanouil Skoufos, Jason S. Mirsky, Matthew D. Healy, Michael S.

Singer, Michael L Hines, Prakash M. Nakardi, Perry L. Miller, & Gordon M Shepherd.

Proceedings of the American Medical Informatics Association, 1998.

Olfactory receptor database (ORDB): a resource for sharing and analyzing published and

unpublished data. M D Healy, J E Smith, M S Singer, P M Nadkarni, E Skoufos, P L Miller, & G

M Shepherd. Chemical Senses 07/1997; 22(3):321-6

Senselab: Modeling Heterogenous Data on the Nervous System. Prakash Nadkarni, Jason

Mirsky, Emmanouil Skoufos, Matthew Healy, Michael Hines, Perry Miller, & Gordon

Shepherd. pp. 21-56 of Neuroinformatics: An Overview of the Human Brain Project, ed.

S.H. Koslow & M.F. Huerta. Lawrence Erlbaum Associates, Inc. Mahwah, NJ: 1997.

ModelDB: an environment for running and storing computational models and their results

applied to neuroscience. B E Peterson, M D Healy, P M Nadkarni, P L Miller, G M Shepherd.

Journal of the American Medical Informatics Association 11/1996; 3(6):389-98

James Bell Pettigrew's Design in nature and D'Arcy Wentworth Thompson's On growth

and form : two early twentieth-century views of functional morphology. Matthew David

Healy. Doctoral Dissertation, Duke University, 1994.

Contributed a chapter on CGI-database programming to the book Special Edition Using CGI,

Que Books, April 1996. This chapter then appeared in revised form in the book Special

Edition Using Perl 5 for Web Programming, Que Books, September 1996.



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