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Hire Dr. Alex F.

United States

USD 250 /hr

Data scientist and computational biologist with experience in drug discovery, chromatin and cancer biology

Profile Summary

Google scholar page: https://scholar.google.com/citations?user=0ax4FggAAAAJ&hl=en I'm a scientist interested in understanding how cancer drugs work within complex cellular networks, how doctors can best use the drugs we have and how to discover new drugs most efficiently. In my current role, I'm investigating real-world clinical outcomes and building models to predict oncology patient journeys to improve patient management. In previous research, I've - Developed and released software to model transcriptional networks that has been used for drug re-purposing in cancer and understanding cell of origin for rare cancer types. - Led a small team engineering new gene editing reagents for applications in T cell therapy. - Developed a new, highly scalable proteomics method to to measure DNA-bound protein complexes at a systems level - Characterized the response of human immune cells to next-generation BET inhibitors to prioritize further clinical development - Contributed to the screening, medicinal chemistry and cellular characterization of lead compounds that inhibit the chromatin regulators DOT1L, EZH2, CBX chromodomains, YEATS domain proteins and BET bromodomains Competencies: [Bioinformatics] Gene expression analysis (RNA-seq), epigenomics assays (ChIP-seq, DNAme), genome accessibility (DNaseI-seq, ATAC-seq), nascent transcription (GRO-seq), proteomics (data-independent acquisition, targeted proteomics) [Languages] Python, R, Bash, SQL [Data Science] numpy, scipy, pandas, scikit-learn, PyTorch [Misc] Schrödinger, Adobe Illustrator, Google Cloud, Linux

Subject Matter Expertise

• ★ Genetics
• ★ Data Science
• ☆ Drug Development

Services

• Research
• Data & AI

Research Gray Literature Search, Systematic Literature Review, Secondary Data Collection

Data & AI Statistical Analysis, Algorithm Design-Non ML, Data Visualization

Work Experience

Co-Founder and CEO

Talus Bio

June 2020 - Present

Senior Data Scientist

Navigating Cancer

July 2019 - Present

Postdoctoral Fellow

Altius Institute for Biomedical Research

2016 - July 2019

Education

Ph.D. (Chemical Biology)

Harvard University

2011 - 2015

B.S. (Chemistry, Cell Biology)

University of Rochester

2007 - 2011

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Alexander J. Federation, Vivek Nandakumar, Brian C. Searle, Andrew Stergachis, Hao Wang, Lindsay K. Pino, Gennifer Merrihew, Ying S. Ting, Nicholas Howard, Tanya Kutyavin, et al. (2020). Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins . Cell Reports.

Jingwei Cheng, Denise A. Galloway, Donglim Esther Park, Christian Berrios, Elizabeth A. White, Reety Arora, Rosa Yoon, Timothy Branigan, Tengfei Xiao, Thomas Westerling, et al.(2017). Merkel cell polyomavirus recruits {MYCL} to the {EP}400 complex to promote oncogenesis . {PLOS} Pathogens. 13. (10). p. e1006668. Public Library of Science ({PLoS})

et al.(2016). Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer . Cancer discovery.

(2016). Models of human core transcriptional regulatory circuitries . Genome research.

et al.(2016). MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism . Nature genetics.

et al.(2016). Active medulloblastoma enhancers reveal subgroup-specific cellular origins . Nature.

et al.(2015). RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity . Cell.

et al.(2015). Structure-guided DOT1L probe optimization by label-free ligand displacement . ACS Chemical Biology.

et al.(2014). Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability . Cell.

et al.(2014). NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis . Molecular cell.

(2014). The use of small molecules in somatic-cell reprogramming . Trends in cell biology.

et al.(2012). Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors . Nature communications.

(2011). Tuning β-sheet peptide self-assembly and hydrogelation behavior by modification of sequence hydrophobicity and aromaticity . Biomacromolecules.

OTHER

Alexander J. Federation, Vivek Nandakumar, Hao Wang, Brian C. Searle, Lindsay K. Pino, Gennifer Merrihew, Ying S. Ting, Nicholas Howard, Tanya Kutyavin, Michael J. MacCoss, et al.(2018). Quantification of nuclear protein dynamics reveals chromatin remodeling during acute protein degradation . Cold Spring Harbor Laboratory

Alexander J. Federation, Donald R. Polaski, Christopher J. Ott, Angela Fan, Charles Y. Lin, James E. Bradner(2018). Identification of candidate master transcription factors within enhancer-centric transcriptional regulatory networks . Cold Spring Harbor Laboratory