プロフィール詳細

プロジェクトを作成

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Dr. Alex F.に依頼

United States

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

プロフィール概要

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

専門分野

• ★ Genetics
• ★ Data Science
• ☆ Drug Development

サービス

• Research
• Data & AI

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

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

職務経験

Co-Founder and CEO

Talus Bio

6月 2020 - 現在

Senior Data Scientist

Navigating Cancer

7月 2019 - 現在

Postdoctoral Fellow

Altius Institute for Biomedical Research

2016 - 7月 2019

学歴

Ph.D. (Chemical Biology)

Harvard University

2011 - 2015

B.S. (Chemistry, Cell Biology)

University of Rochester

2007 - 2011

認定資格

• 認定資格の詳細は未入力です。

出版物

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). Microsoft.AspNetCore.Mvc.Localization.LocalizedHtmlString 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