Aaron Rosenfeld

Bioinformatics Lead

Perelman School of Medicine, University of Pennsylvania

Biography

I am the Lead Bioinformatician in the Human Immunology Core, Perelman School of Medicine at the University of Pennsylvania.

I write scalable software to analyze large amounts of immunological sequencing data, primarily from B- and T-cells. Additionally I work with clinicians and laboratory staff to develop and implement new tools for exploring and visualizing high-dimensional data.

Interests

Bioinformatics
Python
Immunology

Education

MS Computer Science, 2014

Drexel University
BS Computer Science, 2011

Drexel University

Recent Publications

AIRR Community Standardized Representations for Annotated Immune Repertoires

Jason A. Vander Heiden, Susanna Marquez, Nishanth Marthandan, Syed Ahmad Chan Bukhari, Christian E. Busse, Brian Corrie, Uri Hershberg, Steven H. Kleinstein, Frederick A. Matsen, Duncan K. Ralph, Aaron M. Rosenfeld, Chaim A. Schramm, Scott Christley, Uri Laserson

PDF DOI

ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data

Aaron M. Rosenfeld, Wenzhao Meng, Eline T. Luning Prak, U. Hershberg

PDF DOI

Computational Evaluation of B-Cell Clone Sizes in Bulk Populations

Aaron M. Rosenfeld, Wenzhao Meng, Dora Y. Chen, Bochao Zhang, Tomer Granot, Donna L. Farber, Uri Hershberg, Eline T. Luning Prak

DOI

Human Lymph Nodes Maintain TCF-1textsuperscripthi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life

Michelle Miron, Brahma V. Kumar, Wenzhao Meng, Tomer Granot, Dustin J. Carpenter, Takashi Senda, Dora Chen, Aaron M. Rosenfeld, Bochao Zhang, Harvey Lerner, Amy L. Friedman, Uri Hershberg, Yufeng Shen, Adeeb Rahman, Eline T. Luning Prak, Donna L. Farber

DOI

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Encarnita Mariotti-Ferrandiz, Lindsay G Cowell, Corey T Watson, Nishanth Marthandan, William J Faison, Uri Hershberg, Uri Laserson, Brian D Corrie, Mark M Davis, Bjoern Peters, Marie-Paule Lefranc, Jamie K Scott, Felix Breden, The AIRR Community (including Aaron M. Rosenfeld), Eline T Luning Prak, Steven H Kleinstein

DOI

An atlas of B-cell clonal distribution in the human body

Wenzhao Meng, Bochao Zhang, Gregory W Schwartz, Aaron M. Rosenfeld, Daqiu Ren, Joseph J C Thome, Dustin J Carpenter, Nobuhide Matsuoka, Harvey Lerner, Amy L Friedman, Tomer Granot, Donna L Farber, Mark J Shlomchik, Uri Hershberg, Eline T Luning Prak

DOI

Insight into Rhinovirus-Induced Asthma Exacerbation Using High-Throughput Immunosequencing of B-Cell Repertoires

Bryan Wu Yu-Chang, Aaron M. Rosenfeld, Nadine Upton, Jaideep Dhariwal, Uri Hershberg, David Kipling, Sebastian L. Johnston, Hannah J. Gould

DOI

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

Aaron M. Rosenfeld, Wenzhao Meng, Eline T. Luning Prak, Uri Hershberg

DOI

Biopython Update 2016

Christian Brueffera, Tiago Antao, Peter Cock, Eric Talevich, Michiel de Hoon, Wibowo Arindrarto, Leighton Pritchard, Anuj Sharma, Eric Rasche, Aaron M. Rosenfeld, Connor T. Skennerton, Marco Galardini, Markus Piotrowski

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements

Inimary T. Toby, Mikhail K. Levin, Edward A. Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell

DOI

Dynamic Selection of Persistence and Transport Layer Protocols in Challenged Networks

Aaron M. Rosenfeld, Robert N. Lass, William C. Regli, Joseph P. Macker

DOI

A comparison of group-based data persistence techniques in MANETs

Aaron M. Rosenfeld, Robert N. Lass, Dustin S. Ingram, William C. Regli, Joseph P. Macker

DOI

A Gossip-based Synchronization Protocol for State Consistency in Distributed Applications

Aaron M. Rosenfeld, Dara Kusic, Joseph B. Kopena, William C. Regli

NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads

Gail L. Rosen, Erin R. Reichenberger, Aaron M. Rosenfeld

Messaging the Web: Implementing an SMS System in PHP

Aaron M. Rosenfeld

Aaron Rosenfeld

Bioinformatics Lead

Perelman School of Medicine, University of Pennsylvania

Biography

Interests

Education

Experience

Bioinformatics Lead

Human Immunology Core, Perelman School of Medicine, University of Pennsylvania

Bioinformatics Software Engineer

Systems Immunology Lab, School of Biomedical Engineering, Drexel University

Research Assistant

Applied Informatics Group, Drexel University

Visiting Scientist

Czech Technical University

Student Researcher

U.S. Naval Research Laboratory

Research Assistant

Institute for Applied Comment and Information Networking

Web Developer

phillyBurbs.com

Recent Publications

AIRR Community Standardized Representations for Annotated Immune Repertoires

ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data

Computational Evaluation of B-Cell Clone Sizes in Bulk Populations

Human Lymph Nodes Maintain TCF-1textsuperscripthi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

An atlas of B-cell clonal distribution in the human body

Insight into Rhinovirus-Induced Asthma Exacerbation Using High-Throughput Immunosequencing of B-Cell Repertoires

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

Biopython Update 2016

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements

Dynamic Selection of Persistence and Transport Layer Protocols in Challenged Networks

A comparison of group-based data persistence techniques in MANETs

A Gossip-based Synchronization Protocol for State Consistency in Distributed Applications

NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads

Messaging the Web: Implementing an SMS System in PHP