About Me
Hello! I am a computational biologist with >6 years of post-PhD experience in building methods for the analysis of large-scale sequencing and proteomics datasets. I thrive in interdisciplinary teams committed to solving complex biological problems with quantitative approaches.
Research Experience
MSK Cancer Center
Senior Computational Biologist I
July 2023 - Present
Manager: Dr. Andrew McPherson
- Led collaborative research between Computational Oncology and Pediatrics to integrate long-read sequencing with proteomics for discovery of non-canonical proteins in large-scale, cancer patient data.
- Developed pipelines for multimodal analysis of cancer genomics, transcriptomics, and proteomics data (Open source software in Nextflow, Snakemake, Python, and R: proteomegenerator3, nanogenome, SVChordinator).
- Helped write a successful NIH U01 grant ($1.5M).
New York University
LSRF Postdoctoral Fellow
Jun 2019 - July 2023
Advisor: Dr. Edo Kussell
- Developed a population genomics method which leverages statistical correlations in large-scale sequencing data to infer recombination rates for RNA viruses (Open source library in Go and Python: viral-mcorr).
- Advanced a population genomics method to infer recombination rates for bacteria by incorporating sequence clustering and regression analysis, enabling large-scale analysis of bacterial pangenome evolution (Open source libraries in Go and Python: mcorr, mcorr-clustering, PangenomeAlignmentGenerator).
- Developed agent-based models to simulate bacterial aggregation (Modeling done with Simbiotics library in Java).
- Awarded an LSRF Fellowship ($196k) and helped write two successful NIH R01 renewals.
California Institute of Technology
NSF Graduate Fellow
Nov 2013 - Apr 2019
Advisor: Dr. Rustem F. Ismagilov
- Developed thermodynamics models to quantify how dietary and host-secreted polymers interact with biomaterials in the gut (Numerical calculations performed using Python and Mathematica).
- Developed experimental methods using confocal microscopy, computational image analysis, and GPC to quantify how dietary polymers interact with biomaterials in the murine gut ex vivo and in vivo.
- Mentored three PhD rotation students resulting in two co-authored publications.
- Awarded an NSF Graduate Research Fellowship, was the student co-lead writer on a successful ARO MURI-ONR grant, and helped write a successful DARPA BRICS grant ($3.5M).
Brandeis University
Research Assistant
Sept 2011 - May 2013
Advisor: Dr. Milos Dolnik (Irv Epstein Group)
- Used a chemical reaction-diffusion system and computational image analysis to study the growth dynamics of Turing patterns (Thesis received highest honors; Image analysis performed using MATLAB).
Projects
Developed a nextflow pipeline for generating sample-specific proteogenomics search databases from long-read RNAseq. The proteogenomics search databases can be used with matched MS proteomics databases from the same sample for the discovery of non-canonical proteins. Preprint here.
Using correlated substitutions to infer recombination rates in RNA viruses
https://github.com/kussell-lab/viral-mcorr
Developed a new computational approach to infer recombination rates in RNA viruses. The approach relies on the measurement of statistical correlations in large-scale sequencing data to infer recombination rates. Our method has improved efficiency compared to Bayesian methods (we can analyze >400k genomes, whereas most Bayesian approaches can only do ~50 genomes) and allows for the recovery of ancestral relationships between viral genomes. Corresponding publication in PNAS.
Education & Training
California Institute of Technology
PhD in Chemistry
Pasadena, CA | Sept 2013 - Apr 2019
Thesis awarded McCoy Award for best thesis in the Division of Chemistry & Chemical Engineering at Caltech.
Brandeis University
B.A. in Chemistry with Highest Honors and B.A. in Physics
Waltham, MA | Sept 2009 - May 2013
summa cum laude
Selected Publications
12 total and 7 first-author; Link to full publication list on Google Scholar; * indicates equal contribution.
Kulej K.*, A. Preska Steinberg*, J. Zhang, G. Casalena, E. Havasov, S.P. Shah, A. McPherson, A. Kentsis. “End-to-end proteogenomics for discovery of cryptic and non-canonical cancer proteoforms using long-read transcriptomics and multi-dimensional proteomics”. bioRxiv 2025, 10.1101/2025.08.23.671943.
A. Preska Steinberg & E. Kussell. “How recombination and clonal evolution shape bacterial lineages and genomes”. Genetics 2025, 231 (3), iyaf115.
A. Preska Steinberg, O.K. Silander, E. Kussell. “Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools”. Proc Natl Acad Sci USA 2023, 120 (5), e2206945119.
Highlighted in PNAS Commentary: “It takes a village to build a virus”
A. Preska Steinberg, M. Lin, E. Kussell. “Core genes can have higher recombination rates than accessory genes within global microbial populations”. eLife 2022, 11:e78533.
A. Preska Steinberg, Z.G. Wang, R.F. Ismagilov. “Food polyelectrolytes compress the colonic mucus hydrogel by a Donnan mechanism”. Biomacromolecules 2019, 20 (7), 2675-2683.
A. Preska Steinberg, S.S. Datta, T. Naragon, J.C. Rolando, S.R. Bogatyrev, R.F. Ismagilov. “High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine”. eLife 2019, 8:e40387.
S.S. Datta, A. Preska Steinberg, R.F. Ismagilov. “Polymers in the gut compress the colonic mucus hydrogel”. Proc Natl Acad Sci USA 2016, 113 (26), 7041-7046.
J. Palacci, S. Sacanna, A. Preska Steinberg, D.J. Pine, P.M. Chaikin. “Living Crystals of Light-Activated Colloidal Surfers”. Science 2013, 339 (6122), 936-940.
Selected Honors, Awards, & Fellowships
- Life Sciences Research Foundation Postdoctoral Fellowship (2020-2023) - Simons Foundation Awardee of the LSRF
- Herbert Newby McCoy Award (2019) - Most outstanding achievements in research by a graduate student in the CCE Division at Caltech
- Caldwell CEMI Graduate Fellowship (2018-2019) - Awarded by Caltech CEMI
- National Science Foundation Graduate Research Fellowship (2013-2018)
- Molly W. and Charles K. Schiff Memorial Award in Science (2013) - Brandeis University
- CRC Press Chemistry Achievement Award (2010) - Brandeis University
Selected Talks & Presentations
>20 presentations at scientific conferences and research organizations
- 2025 Robert Steel Symposium in Developmental Oncology (Talk)
- 2022 AIChE Annual Meeting (Talk & Poster), Molecular Genetics of Bacteria & Phages (Poster), GRC on Microbial Stress Response (Poster), APS March Meeting (Talk)
- 2019 GRC on Molecular Mechanisms in Evolution (Poster), Caltech CCE McCoy Award Symposium (Talk)
- 2018 Frontiers in Soft Matter & Macromolecular Networks (Talk), UCI Mechanobiology Symposium (Talk)
- 2017 Frontiers in Soft Matter & Macromolecular Networks (Talk), APS March Meeting (Talk)