Curriculum Vitae

1. Click here to download my CV as a PDF

EDUCATION

Duke University, Durham, NC, USA (2008-2013)

Ph.D. in Computational Biology & Bioinformatics

• Analysis of the gene regulatory networks in immune cell types using high-throughput assay for gene expression, chromatin state, and single cell transcriptome.
• Trained in design, execution, and communication of high impact experimental projects in the application of functional genomics to immunology

Duke University, Durham, NC, USA (Summer 2013)

Part-Time Consultant

Worked with Elizabeth Hauser, Department of Medicine

• Performed meta-analysis of expression, familial linkage, and GWAS data sets to identify regions of genomic convergence

Transcriptional Profiling of Synovial Macrophages using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis

Mandelin II AM*, Homan PJ*, Shaffer AM*, Cuda CM, Dominguez ST, Bacalao E, Carns M, Lee J, Aren K, Thakrar A, Montgomery AB, Bridges Jr SL, Bathon JM, Atkinson J, Fox D, Matteson EL, Buckley CD, Pitzalis C, Parks D, Hughes LB², Geraldino-Pardilla L, Ike R, Phillips K, Wright K, Filer A, Kelly S, Ruderman EM, Morgan V, Abdala-Valencia H, Misharin AV, Budinger GS , Bartom ET, Peabody TD, Pope RM**, Perlman H** & Winter DR**. Arthritis & Rheumatology (Accepted)

Bim Suppresses the Development of SLE by Limiting Macrophage Inflammatory Responses.

Tsai F, Homan PJ, Agrawal H, Misharin A, Abdala-Valencia H, Haines III GK, Dominguez S, Bloomfield CL, Saber R, Chan A, Mohan C, Hutcheson J, Davidson A, Budinger GRS, Bouillet P, Dorfleutner A, Stehlik C, Winter DR, Cuda CM, & Perlman H. J Exp Med. November 2017; jem.20170479.

Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner. Deczkowska A, Matcovitch-Natan O, Tsitsou-Kampeli A, Ben-Hamo S, Dvir-Szternfeld R, Spinrad A, Singer O, David E, Winter DR, Smith LK, Kertser A, Baruch K, Rosenzweig N, Terem A, Prinz M, Villeda S, Citri A, Amit I, Schwartz M. Nature Commun. 2017 September; 8(1):717.

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations.

Thaiss CA, Levy M, Korem T, Dohnalová L, Shapiro H, Jaitin DA, David E, Winter DR, Gury-BenAri M, Tatirovsky E, Tuganbaev T, Federici S, Zmora N, Zeevi D, Dori-Bachash M, Pevsner-Fischer M, Kartvelishvily E, Brandis A, Harmelin A, Shibolet O, Halpern Z, Honda K, Amit I, Segal E, Elinav E. Cell. 2016 December; 167(6), 1495-1510.

Extracellular Matrix Proteolysis by MT1-MMP Contributes to Influenza-Related Tissue Damage and Mortality.

Talmi-Frank D, Altboum Z, Solomnov I, Udi Y, Jaitin DA, Klepfish M, David E, Zhuravlev A, Keren-Shaul H, Winter DR, Gat-Viks I, Mandelboim M, Ziv T, Amit I, Sagi I. Cell Host & Microbe. 2016 October; 20(4), 458-470.

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome.

Gury M*, Thaiss CA*, Serafini N, Winter DR, Giladi A, Lara-Astiaso D, Levy M, Salame TM, Weiner A, David E, Shapiro H, Dori-Bachash M, Pevsner-Fischer M, Lorenzo-Vivas E, Keren-Shaul H, Paul F, Harmelin A, Eberl G, Itzkovitz S, Tanay A, DiSanto JP, Elinav E, Amit I.

Cell. 2016 August; 166(5),1231-1246.

Co-ChIP enables genome-wide characterization of histone mark co-occurrence at single molecule resolution.

Weiner A*, Lara-Astiaso D*, Krupalnik V, David E, Winter DR, Hanna JH, Amit I.

Nature Biotechnology. 2016 September; 34(9), 953-961.

Microglia development follows a stepwise program to regulate brain homeostasis.

Matcovitch-Natan O*, Winter DR*, Giladi A, Aguilar SV, Spinrad A, Sarrazin S, Ben-Yehuda H, David E, Gonzales FZ, Perrin P, Keren-Shaul H, Gury M, Lara-Asitaso D, Thaiss CA, Cohen M, Halpern KB, Baruch K, Deczkowska A, Lorenzo-Vivas E, Itzkovitz S, Elinav E, Sieweke M, Schwartz M, Amit I.

Science. 2016 August; 353(6301), aad8670.

Transcriptional heterogeneity and lineage commitment in the common myeloid progenitor

Paul F, Arkin Y, Giladi A, Jaitin DA, Kenigsberg E, Keren-Shaul H, Winter D, Lara-Astiaso D, Gury M, Weiner A, David E, Cohen N, Lauridsen FKB, Haas A, Mildner A, Jung S, Trumpp A, Porse BT, Tanay A, Amit I

Cell 2015 December; 163, 1663–1677

Distinct mucosal Langerhans cell subsets develop from pre-DCs and monocytes (Pubmed)

Capucha T, Mizraji G, Segev H, Blecher-Gonen R, Winter D, Khalaileh A, Tabib Y, Attal T, Nasser M, Zelentsova K, Kisos H, Zenke M, Sere K, Hieronymus T, Burstyn-Cohen T, Amit I, Wilensky A, Hovav A.

Immunity. 2015 August 18; 43(2): 369-381

Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment (Pubmed)

Lavin Y*, Winter D*, Blecher-Gonen R*, David E, Keren-Shaul H, Merad M, Jung S, Amit I.

Cell. 2014 Dec 4;159(6):1312-26.

A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (Pubmed)

Bornstein C, Winter D, Barnett-Itzhaki Z, David E, Kadri S, Garber M, & Amit, I

Molecular Cell. 2014 Nov 20; 56:749-762

Immunogenetics. Chromatin state dynamics during blood formation (PubMed)

Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I , Jaitin DA, David E, Keren-Shaul H, Mildner A, Winter D, Jung S, Friedman N, & Amit I.

Science. 2014 Aug 22; 345(6199):943-9

DNase-seq predicts regions of rotational nucleosome stability in diverse human cell types. (PubMed)

Winter DR, Song L, Mukherjee S, Furey TS, & Crawford GE

Genome Research. 2013 Jul;23(7):1118-29. doi: 10.1101/gr.150482.112.

#An integrated encyclopedia of DNA element in the human genome (PubMed)

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green E, Gunter C, Snyder M

Nature. 2012 Sep 6;489(7414):57-74.

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. (PubMed)

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z,

London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke

ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS.

Genome Research. 2011 Oct;21(10):1757-67. .

#A user's guide to the encyclopedia of DNA elements (ENCODE). (PubMed)

ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC,

Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE.

PLoS Biology. 2011 Apr;9(4):e1001046.

Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. (PubMed)

Rach EA*, Winter DR*, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U.

PLoS Genetics. 2011 Jan 13;7(1):e1001274.

#An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. (PubMed)

Winter D*, Vinegar B* , Nahal H , Ammar R , Wilson GV , Provart NJ .

PLoS One. 2007 Aug 8;2(8):e718. [over 900 citations according to Google Scholar]

Review Articles

A Beginner’s Guide to Analysis of RNA-seq Data

Koch CM*, Chiu SF*, Akbarpour M, Bharat A, Ridge KM, Bartom ET**, Winter DR**.

Am J Respir Cell Mol Biol. 2018 Aug;59(2):145-157 (Tutorial)

Thinking BIG Rheumatology: how to make functional genomics data work for you.

Winter DR^¶.

Arthritis Research & Therapy. 2018 February; 20(29).

The role of the local environment and epigenetics in shaping macrophage identities and their effect on tissue homeostasis

Amit I, Winter DR, & Jung S

Nature Immunology 2015 December; 17(1):18-25.

Making the case for chromatin profiling: a new tool to investigate the immune regulatory landscape (Pubmed)

Winter DR^¶, Jung S, & Amit I^¶

Nature Reviews Immunology 2015 Sep; 15(9): 585-94.

The Role of Chromatin Dynamics in Immune Cell Development [Review] (PubMed)

Winter DR & Amit, I

Immunological Reviews 2014 Sep; 261(1):9-22.

Conferences & Seminars

Keystone Symposium: Transcription & RNA Regulation in Inflammation &Immunity in Tahoe City, CA, USA(February 2019)

“Synovial macrophages demonstrate heterogeneity in their transcriptional response to joint inflammation in mouse models of arthritis”

Annual Meeting of the American College of Rheumatology in Chicago, Illinois, USA

7 Posters Accepted (October 2018)

“A Survey of Blood and Synovial Tissue Myeloid Cells in Rheumatoid Arthritis Patients By Transcriptional Profiling” (*Presenting Author)

“The Distinct Profile of Ly6c^lo Monocytes in the Murine Joint Compared with Those in Circulation Suggests a Unique Role in Inflammatory Arthritis” (Co-Last Author)

“Arthritis and Atherosclerosis in KRN Ag⁷ Mice Involve Distinct Inflammatory Cell Populations and Are Independent of CCR2 ” (Co-Last Author)

“Tissue Resident Macrophages Establish a Niche That Limits Monocyte to Macrophage Differentiation in Synovial Tissue during Homeostasis” (Co-Last Author)

“Loss of Synovial Tissue Resident Macrophages Permits Monocyte to Macrophage Differentiation and Inflammation in HUPO Mice” (Co-Last Author)

“Monocyte Transcriptome Delineates SSc Patients with Functionally Distinct Patterns of Gene Dysregulation That Persist through Differentiation ” (Co-Last Author)

“Dynamics of Transcriptional Signatures from Purified Synovial Macrophage Subsets During Acute and Chronic Murine Models of Inflammatory Arthritis.” (Co-Last Author)

Next-Gen Immunology at Weizmann Institute of Science in Rehovot, Israel (Feb. 2018)

“Transcriptional Profiling of Synovial Macrophages from RA Patients to Capture Disease Heterogeneity”

Annual Meeting of the American College of Rheumatology in San Diego, California, USA

4 Posters Accepted (November 2017)

“Transcriptional Profiling of Synovial Macrophages from RA Patients to Capture Disease Heterogeneity” (*Presenting Author)

“Mapping changes in monocyte/macrophage populations in the synovium: an aging study in arthritic KRN Ag⁷ mice.” (Co-Last Author)

“Classical Monocytes in the Pathogenesis of Early Diffuse Cutaneous Systemic Sclerosis” (Co-Last Author)

“Dynamics of Transcriptional Signatures from Purified Synovial Macrophage Subsets During Acute and Chronic Murine Models of Inflammatory Arthritis.” (Co-Last Author)

Macrophage Biology in the Single-Cell Era at Ghent, Belgium (October 2017)

Poster Entitled: "The transcriptional program of synovial macrophages in rheumatoid arthritis"

EMBO Annual Fellows Meeting (June 2017)

Poster Entitled: "Modeling the Gene Regulatory Networks of Tissue-Resident Macrophages"

Keystone Symposium: MononuclearPhagocytes, Austin, Texas, USA (May 2017)

Session Chair, Speaker: “The transcriptional program of synovial macrophages in rheumatoid arthritis”

Immunogenomics Conference at Hudson-Alpha (September 2016)

Poster Entitled: “Regulatory Factors Specifying Granulopoiesis”

Biology of Genomes at Cold Spring Harbor, New York, USA (May 2016)

Session Co-Chair, Speaker: “Microglia development follows a stepwise program to regulate brain homeostasis”

Invited Speaker: European Bioinformatics Institute, United Kingdom (December 2015)

Seminar Entitled: “The Underlying Architecture of the Immune System”

Immunogenomics Conference at Hudson-Alpha (September 2015)

Invited Talk Entitled: “Microglia development follows a stepwise process to support the developing brain”

Invited Speaker: North Carolina State University (March 2015)

Seminar Entitled “Nature vs. Nurture: The influence of tissue environment on the macrophage epigenome”

Keystone Symposium: Macrophages and Dendritic Cells Reunited – Montreal (March 2015)

Scholarship recipient and poster/oral presentation entitled “Nature vs. Nurture: Chromatin Dynamics in Microglia Development”

Invited Speaker: University of Toronto (March 2015)

Seminar Entitled “Nature vs. Nurture: The influence of tissue environment on the macrophage epigenome”

I-CORE Meeting: RNA & Chromatin in Gene Regulation at Hebrew University (November 2014)

Talk Entitled "Nature vs. Nurture: The influence of development and environment on chromatin dynamics"

Gene Expression & Signalling in the Immune System at Cold Spring Harbor (April 2014)

Poster Entitled "The chromatin landscape of tissue-resident macrophages is extensively reshaped by the tissue micro-environment"

FISEB/Ilanit: Federation of Israeli Societies for Experimental Biology in Eilat, Israel (February 2014)

Talk Entitled "The 'When', 'What', and 'Who' of Chromatin Dynamics in Macrophage Heterogeneity"

RECOMB: Regulatory Genomics & Systems Biology in San Francisco, California (November 2012)

Talk Entitled "DNase-seq predicts regions of rotational nucleosome stability in diverse human cell types"

Computational Biology Seminar in Duke University, North Carolina (October 2011)

Talk Entitled “Analyzing high resolution nucleosome structure by DNase-seq”

ISCB-ECCB/RECOMB-Bioinformatics Education in Vienna, Austria (July 2011)

Poster Entitled “Analyzing high resolution nucleosome structure by DNase -seq”

Participated in international conference on teaching practices

Biology of Genomes at Cold Spring Harbour (May 2010)

Poster Entitled “Differential patterns of open chromatin suggest alternate modes of gene regulation”

Encode/modENCODE Meeting (March 2010)

Participated in Analysis Working Group meeting

AWARDS

ANRF Scholar (2017-Present)

Dixon Translational Research Young Investigator Award (2017)

US Bone & Joint Initiative (USBJI) Young Investigator (2016-Present)

EMBO

Long Term Fellow (2014-2016)

Azrieli Foundation

Post-Doctoral Fellow (2014-2015)

National Science & Engineering Research Council of Canada

Post-Graduate Scholarship for Doctorate Studies (NSERC PGS-D) (2010-2012)

Post -Graduate Scholarship for Masters Studies (NSERC PGS-M) (2008-2010)

University of Toronto

Gordon Cressy Student Leadership Award (2008)

University of Toronto, University College Merit Award (2008)

Undergraduate Student Research Award (NSERC)

Lab of Jackie Vogel, McGill University, Montreal, Quebec, Canada (Summer 2007)

Lab of Nicholas Provart, University of Toronto, Ontario, Canada (Summer 2006)

Northrop-Frye Research Scholarship

Lab of Spencer Barrett, University of Toronto, Ontario, Canada (Summer 2005)

PROFESSIONAL ORGANIZATIONS

Member of the American College of Rheumatology (ACR) (2016-Present)

Member of the American Heart Association (AHA) (2017-Present)

Member of the American Association for the Advancement of Science (AAAS) (2017-Present)

TEACHING EXPERIENCE

For more information, see my Teaching Portfolio

Northwestern University, Chicago, IL 60657

Guest Lecturer for Data Science for Biomedical Researchers (October 2018)

· Prepared interactive lecture on “Single-Cell RNA-seq” for DGP PhD students which incorporated a practical hands-on programming component

Guest Lecturer for Molecular Biology & Genetics (March 2018)

· Prepared interactive lecture on “Mapping Gene Regulatory Networks” for DGP PhD students, designed practice/exam questions, and graded student responses.

Faculty Moderator for MSTP Journal Club (Winter 2018)

Moderated discussion of article among MD-PhD students

Faculty Moderator for Introduction to Life Science Research (ILS) Journal Club (Spring 2017, 2018)

Moderated discussion of articles among first-year DGP PhD students

Weizmann Institute, Rehovot, Israel

Workshop on Scientific Communication (Summer 2015)

Designed & hosted a 1 hour session including active learning components on reading, writing and presenting in science aimed at beginning scientists.

Duke University, Durham, NC, USA

TA & Guest Lecturer – “Seminar in Quantitative Genomics” (Fall 2010)

Assisted in developing course structure, helped integrate lectures from various

professors, taught section on genome databases with related assignment,

administered regular quizzes, conducted review session, and took charge of

grading

TA & Guest Lecturer – “Introduction to Computational Genomics” (Spring 2010)

Shared grading responsibilities, held office hours, and guest -lectured class on

network motifs

Various Guest Lectures (2009-2011)

Guest lectured for classes on various topics including computational biology,

genome browsers, and heuristic sequence aligners (i.e. BLAST & FASTA)

see Teaching: Practical Teaching Experience for more information

Teaching Classes & Seminars Attended

Introduction to College Teaching, Fall 2009

Seminar in Teaching College Biology, Fall 2010

Teaching Ideas Workshops, (2009-2012)

see Teaching: Courses and Workshops for more information

TRAINEES

Northwestern University, Chicago, IL 60657

Preceptor for Immunology and Molecular Pathogenesis (IMP) Program 2019-Present

Accepted as mentor for postdoc and graduate students on NIH Training Grant

Co-Advisor to DGP Informatics PhD Student in Winter/Ridge Lab 2018-Present

Kishore Anekalla working on functional genomic analysis of pulmonary disease

Preceptor for Cellular & Molecular Basis of Disease (CMBD) Program 2018-Present

· Accepted as mentor for graduate students on NIH Training Grant

Advisor to DGP PhD Student in Winter Lab 2017-Present

Anna Woo (CMBD grantee) working on gene regulatory networks in aging immunity

Advisor to DGP PhD Student in Winter Lab 2017-Present

Shang-Yang (Sam) Chen working on analysis of genomic experiments in aging and modeling of chromatin data

Awarded American Heart Association (AHA) Predoctoral Award

Co-Advisor to Postdoc in Winter/Perlman Lab 2017-2018

Julia Dunn working on computational analysis of the transcriptional program of myeloid cells in Systemic Sclerosis

Co-Advisor to Postdoc in Winter/Perlman Lab 2016-2018

Philip Homan working on design and analysis of genomic experiments to understand RA pathogenesis using patient samples and mouse models

Thesis Committee Member to MSTP Student in Hauser Lab 2017-Present

Nathan Pincus is working to identify genomic components of P. aeruginosa that contribute to

virulence and patient mortality using machine learning and experimental approaches

Rotation Mentor to DGP PhD Students in Winter Lab

Garrett Eickelberg developing models to predict clinical phenotypes of SSc from transcriptional data (Fall 2017)

Anna Woo working on genomic approach to study aging monocytes (Spring 2017)

Chang Zeng working on RNA-seq & ATAC-seq analysis in scleroderma patient samples (Winter 2017)

Shang-Yang (Sam) Chen working on inferring cell lineage from enhancer profiles (Fall 2016)

Weizmann Institute, Rehovot, Israel

Rotation Mentor to Masters Student in Amit Lab Spring 2015

Advised Amit Spinrad working on single cell RNA-seq analysis in microglia development

In-Lab Mentor for International Summer Science Institute (ISSI) Summer 2014

Designed and supervised a research project for 2 post-high school students

Duke University, Durham, NC, USA

Out-of-Lab Mentor for Institute of Genome Science & Policy Fellows Summers 2010-2012

Offered general guidance and support to undergraduates doing summer research

RELATED EXPERIENCE

Weizmann Institute, Rehovot, Israel

Co-Leader of FacultyQuantBio Lunches at Northwestern 2017-Present

Facilitated monthly lunch discussions on various topics in Quantitative Biology

Contributor to Bioinformatics Community at Northwestern 2016-Present

-Attend weekly meetings

-Regularly present at meetings, including an ongoing series entitled “Primer on Bioinformatics” and a 2-part discussion of single-cell analysis techniques

-Instructor at Bioinformatics Workshop for Beginners (August 2017)

Annual Summer Training Course in Experimental Aging Research June 2017

Training on the status of the aging field and grant writing for NIA in Seattle, WA, USA

Reviewer for Northwestern KL2 Grant Summer 2017

Reviewed an application for the Career Development grant

Reviewer for “Certificate in Management for Scientists and Engineers” Spring 2017

Reviewed applications and rated candidates for certificate program jointly offered by the Graduate School and Kellogg School of Management to current PhDs at Northwestern

American Association of Immunologists (AAI) Advanced Course in Immunology August 2016

Attended intensive course directed toward advanced trainees and scientists in Boston, MA, USA

European Molecular Biology Organization (EMBO) Lab Management Course March 2016

Management training for postdocs and group leaders addressing key skills in Leimen, Germany

Scientific Communication Consultant (Spring 2015)

Volunteered to write & edit material for Davidson Institute Science Education

Systems Biology Symposium Organizer (2014-2015)

Worked in a team to plan the student-run conference at Weizmann in March 2015

Computational Biology Seminar Committee (2009-2011)

Helped organize weekly seminar and recruit visiting speakers

RESEARCH EXPERIENCE BY ADVISOR

see Research for more information about gene regulation and specific projects

Ido Amit, Post-Doctoral Researcher, Weizmann Institute (2013-2016)

• Studying gene regulation in immunology through analysis of regulatory networks in immune cells using expression, chromatin, and single cell data
• Trained in design, execution, and communication of high impact experimental projects in the application of functional genomics to immunology
• Specific Projects addressing the impact of environment on tissue-resident macrophages, microglia development, transcription factors in hematopoiesis, dendritic cell fates, the effect of dysbiosis on ILCs, and granulocyte differentiation

Beth Hauser, Part-Time Consultant, Duke University (Summer 2013)

• Performed bioinformatic analysis of several data sets, including expression, familial linkage, and GWAS to identify regions of genomic convergence

Terry Furey & Greg Crawford, Ph.D Thesis, Duke University (2008-2013)

• Alignability: Generated Uniqueness Track on UCSC Browser that assigns probability that a read from a high-throughput assay will be assigned to each base of the human genome
• DNASE-FAIRE Comparison: Investigated similarities and differences in regions called by two complementary assays that both detect regions of open chromatin
• DARNS: Designed HMM to annotate nucleosomes through the ~10bp period of digestion

Uwe Ohler, Ph. D Rotation, Duke University (Summer 2009)

• Demonstrated that promoters, when grouped by the distribution of their transcription start sites (TSSs), have distinct chromatin profiles that suggest variable initiation strategies

Ryan Lilien, Independent Research Project, U Toronto (2007 – 2008)

• Using online databases and bioinformatics tools, explored the hypothesis that the active sites of proteins can be inferred from regions of high sequence homology among protein families

Jackie Vogel, NSERC Undergraduate Research Award, McGill University (Summer 2007)

• Gained wet-lab experience with S. cerevisiae including molecular genetics and cell biology; developed software to cluster the results of high-throughput synthetic lethality experiments

Nicholas Provart, NSERC Undergraduate Research Award, U Toronto (Summer 2006)

• Augmented and developed innovative features for the electronic Fluorescent Pictograph (eFP) Browser (http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi) that visualizes cross-experiment microarray results from an online SQL database
• Led to patent and licensing of software as well as highly used and cited software

Spencer Barrett, Northrop-Frye Research Scholarship, U Toronto (Summer 2005)

• Assisted lab members with botany research extending from molecular biology protocols, such as phenotype assays, to greenhouse and fieldwork.

SKILLS & TRAINING

(Courses taken at University of Toronto unless otherwise indicated)

Biology Courses

Cell & Molecular Biology

Biochemistry

Concepts in Genetics

Microbiology I

Chemical Genomics

Eukaryotic Molecular Biology

Germ Cell Biology

Genome Tools & Technologies (Duke)

Interdisciplinary

Computational Genomics & Bioinformatics

Applied Bioinformatics

Computational Systems Biology

Algorithms in Computational Systems Biology (Duke)

Statistical Methods for Computational Biology (Duke)

Core Concepts in Genomic & Computational Biology (Duke)

Computational Sequence Biology (Duke - Audited)

Quantitative Courses

Probability with Computer Applications

Statistics for Computer Scientists

Introduction to Databases

Enriched Algorithm Design & Analysis

Enriched Data Structures & Analysis

Machine Learning & Data Mining

Numerical Methods

Computational Complexity & Computability

Introduction to Statistical Methods (Duke)

Applications

Fluent with Perl, Python, C, C++, Java, R, Matlab, SQL, IGV, & UCSC Genome Browser