Jake Conway

1

2

5

Ph.D.
NIH NRSA F31 Fellow
Sep 2016 - 2021

B.S.
Sep 2012 - May 2016
Concentration
Minor
Honors

6

Senior Biomedical Data Scientist
Nov 2022 - Present

Biomedical Data Scientist
Jul 2021 - Nov 2022

7

Ph.D. Candidate
Jul 2017 - 2021

Undergraduate Researcher
Jun 2014 - Aug 2014

Undergraduate Researcher
May 2015 - Aug 2015

8

Teaching Assistant
2020

Teaching Assistant
2018 - 2020

Teaching Assistant
2017

Teaching Assistant
2014

Tutor
2014 - 2015

9

Predoctoral
2019 - 2021

Predoctoral
2016 - 2019

10

2023
break
break

2021
break
break

2020
break

2020
break
break

2019
break

2018
break

2017
break

10

Poster
2019

Poster
2018

Invited Speaker
2016

Invited Speaker
2014

12

R Package
1.4M Downloads

Shiny App
break

12

Phase II
2019

Jake Conway

Current Position

Senior Biomedical Data Scientist, PathAI

Education

Harvard University, Cambridge, MA, USA
Van Allen Lab, Dana-Farber Cancer Institute and The Broad Institute of Harvard and MIT
Division of Medical Sciences, Bioinformatics and Integrative Genomics Program

UMass Lowell, Lowell, MA, USA
Department of Biological Sciences: Biology
Bioinformatics
Mathematics
Summa Cum Laude

Work Experience

Biomedical Sciences
PathAI, Boston, MA, USA

Machine Learning R&D
PathAI, Boston, MA, USA

Academic Research Experience

Bioinformatics and Integrative Genomics Program (Van Allen Lab)
Harvard Medical School, Boston, MA, USA

Department of Biomedical Informatics (Gehlenborg Lab)
Harvard Medical School, Boston, MA, USA

Department of Biostatistics (Tchetgen Tchetgen Lab)
Harvard School of Public Health, Boston, MA, USA

Teaching

Computational Statistics for Biomedical Informatics (BMI 715; Instructors: Nathalie Vladis, Ph.D.)
Harvard Medical School, Boston, MA, USA

Computing Skills for Biomedical Informatics (BMI 713; Instructors: Nils Gehlenborg, Ph.D.)
Harvard Medical School, Boston, MA, USA

Concepts in Genome Analysis (BMIF 201; Instructors: Shamil Sunyaev, Ph.D., Michael Baym, Ph.D., CZ Zhang, Ph.D.)
Harvard Medical School, Boston, MA, USA

Principles of Molecular Biology (BCMP 200; Instructor: Joseph Loparo, Ph.D.)
Harvard Medical School, Boston, MA, USA

Principles of Cell and Molecular Biology (BIOL.2200; Instructor: Carol Myers, Ph.D.)
UMass Lowell, Lowell, MA, USA

Genetics (BIOL.2350; Instructor: Wesley Savage, Ph.D.)
UMass Lowell, Lowell, MA, USA

Principles of Biology II (BIOL.1120; Instructor: Naomi Wernick, Ph.D.)
UMass Lowell, Lowell, MA, USA

Principles of Biology I (BIOL.1110; Instructor: Naomi Wernick, Ph.D.)
UMass Lowell, Lowell, MA, USA

Calculus I-III, Discrete Structures I, Introduction to Statistics, and Linear Algebra I (Mathematics Department)
UMass Lowell, Lowell, MA, USA

Fellowships and Funding

Redefining the Molecular Landscape of Melanoma
$121,188 NIH Ruth L. Kirschstein Predoctoral Individual National Research Service Award (F31; NCI 1F31CA239347-01)

Training in Bioinformatics and Integrative Genomics
$112,470 NIH/NHGRI Institutional National Research Service Award (T32; 4T32HG002295-14; PI: Park)

Publications (Considerable Contributions)

Conway JR,, Tewari AK, Camp SY, Han S, Crowdis J, He MX, Nyame YA, AlDubayan SH, Schultz N, Szallasi Z, Pomerantz MM, Freedman ML, Fong L, Nelson PS, Brown M, Salari K, Van Allen EM. Analysis of evolutionary dynamics and clonal architecture in prostate cancer. bioRxiv (2023). DOI: 10.1101/2023.03.23.533974

Conway JR, Pouryahya M, Gindin Y, Pan DZ, Carrasco-Zevallos OM, Mountain V, Subramanian GM, Montalto MC, Resnick M, Beck AH, Huss RS, Myers RP, Taylor-Weiner A, Wapinski I, Chung C. Integration of deep learning-based histopathology and transcriptomics reveals key genes associated with fibrogenesis in patients with advanced NASH. Cell Reports Medicine (2023) 4(4):101016. PMID: 37075704. DOI: 10.1016/j.xcrm.2023.101016.

Tewari AK, Cheung ATM, Crowdis J, Conway JR, Camp SY, Wankowicz SA, Livitz D, Park J, Lis RT, Bosma-Moody A, He MX, AlDubayan SH, Zhang Z, McKay RR, Leshchiner I, Balk S, Getz G, Taplin ME, Van Allen EM. Molecular features of exceptional response to neoadjuvant anti-androgen therapy in poor-risk localized prostate cancer. Cell Reports (2021) 36(10):109665. PMID: 34496240. DOI: 10.1016/j.celrep.2021.109665.

Conway JR, Taylor-Weiner A, Braun D, Bakouny Z, Choueiri TK, Van Allen EM. PBRM1 loss-of-function mutations and response to immune checkpoint blockade in clear cell renal cell carcinoma. medRxiv (2020). DOI: 10.1101/2020.10.30.20222356.

Conway JR, Dietlein F, Taylor-Weiner A, AlDubayan SH, Vokes N, Keenan T, Reardon B, He MX, Margolis CA, Weirather J, Haq R, Schilling B, Hodi FS, Schadendorf D, Liu D, Van Allen EM. Integrated molecular drivers coordinate biological and clinical states in melanoma. Nature Genetics (2020) 52(12):1373-1383. PMID: 33230298. DOI: 10.1038/s41588-020-00739-1.

AlDubayan SH, Conway JR, Witkowski L, Kofman E, Reardon B, Camp SY, Han S, Elmarakeby H, Al-Rubaish AM, Al-Sulaiman AA, Al-Ali AK, Taylor-Weiner A, Van Allen EM. Detection of Pathogenic Variants with Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients with Prostate Cancer and Melanoma. JAMA (2020) 324(19):1957-1969. PMID: 33201204. DOI: 10.1001/jama.2020.20457.

Conway JR, Warner JL, Rubinstein WS, Miller RS. Next-Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action. JCO Precision Oncology (2019) (3): 1-10. PMID: 32923847. DOI: 10.1200/PO.19.00232.

Conway JR, Kofman E, Mo SS, Elmarakeby H, Van Allen E. Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine. Genome Medicine (2018) 10(1):93. PMID: 30497521. DOI: 10.1186/s13073-018-0605-7.

Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics (2017) 33(18):2938-2940. PMID: 28645171. DOI: 10.1093/bioinformatics/btx364.

Presentations

The secondary genomic architecture of melanoma
Applications of Cancer Computational Biology, AACR Annual Meeting, Atlanta, GA, USA

Whole-exome analysis of 1,135 melanomas reveals significantly mutated cancer genes and copy number alterations
Application of Bioinformatics to Cancer Biology Session, AACR Annual Meeting, Chicago, IL, USA

Evaluation of Gene-Environment Interactions for Ovarian Cancer
Pipelines into Biostatistics Annual Symposium, Dana-Farber Cancer Institute, Boston, MA, USA

UpSetR: A novel R package for visualizing intersecting sets and their attributes
Pipelines into Biostatistics Annual Symposium, Dana-Farber Cancer Institute, Boston, MA, USA

Software

UpSetR
A novel R package for visualizing intersecting sets and their attributes

UpSetR Shiny App
A Shiny wrapper for the UpSetR R package

Clinical Trial Experience

A phase II study of cisplatin and the Wee1 inhibitor adavosertib in metastatic triple-negative breast cancer (mTNBC)
Keenan TE, Tan-Wasielewski Z, Trippa L, Kochupurakkal B, Guerriero JL, Tahara RK, Winship G, Osmani W, Andrews C, Conway JR, He MX, Pastorello R, Tracy A, Godin RE, Overmoyer BA, Winer EP, Mittendorf EA, Shapiro GI, Van Allen EM, Tolaney SM