Publications

Articles

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

Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe B├╝rckert, 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, Eline T Luning Prak, Steven H Kleinstein

Nature Immunology 2017

doi:10.1038/ni.3873 | pdf

Reproducibility and reuse of adaptive immune receptor repertoire data

Felix Breden, Eline T Luning Prak, Bjoern Peters, Florian Rubelt, Chaim A Schramm, Christian E Busse, Jason A Vander Heiden, Scott Christley, Syed Ahmad Chan Bukhari, Adrian Thorogood, Frederick A Matsen IV, Yariv Wine, Uri Laserson, David Klatzmann, Daniel C Douek, Marie-Paule Lefranc, Andrew M Collins, Tania Bubela, Steven H Kleinstein, Corey T Watson, Lindsay G Cowell, Jamie K Scott, Thomas B Kepler

Frontiers in Immunology 2017

doi:10.3389/fimmu.2017.01418 | pdf

Rethinking data-intensive science using scalable analytics systems

Frank Austin Nothaft, Matt Massie, Timothy Danford, Zhao Zhang, Uri Laserson, Carl Yeksigian, Jey Kottalam, Arun Ahuja, Jeff Hammerbacher, Michael Linderman, Michael J Franklin, Anthony D Joseph, David A Patterson

SIGMOD15--Proceedings of the 2015 ACM SIGMOD International Conference on Management of Data 2015

doi:10.1145/2723372.2742787 | pdf

Two classes of broadly neutralizing antibodies within a single lineage directed to the high-mannose patch of HIV envelope

Katie J Doores, Leopold Kong, Stefanie A Krumm, Khoa M Le, Devin Sok, Uri Laserson, Fernando Garces, Pascal Poignard, Ian A Wilson, Dennis R Burton

Journal of Virology 2015

doi:10.1128/JVI.02905-14 | pdf

High-resolution antibody dynamics of vaccine-induced immune responses

Uri Laserson*, Francois Vigneault*, Daniel Gadala-Maria, Gur Yaari, Mohamed Uduman, Jason A Vander Heiden, William Kelton, Sang Taek Jung, Yi Liu, Jonathan Laserson, Raj Chari, Je-Hyuk Lee, Ido Bachelet, Brendan Hickey, Erez Lieberman-Aiden, Bozena Hanczaruk, Birgitte B Simen, Michael Egholm, Daphne Koller, George Georgiou, Steven H Kleinstein, George M Church

PNAS 2014

doi:10.1073/pnas.1323862111 | pdf

Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data

Gur Yaari, Jason A Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Namita Gupta, Joel N H Stern, Kevin C O'Connor, David A Hafler, Uri Laserson, Francois Vigneault, Steven H Kleinstein

Frontiers in Immunology 2013

doi:10.3389/fimmu.2013.00358 | pdf

The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies

Devin Sok*, Uri Laserson*, Jonathan Laserson*, Yi Liu*, Francois Vigneault, Jean-Philippe Julien, Bryan Briney, Alejandra Ramos, Karen F Saye, Khoa Le, Alison Mahan, Shenshen Wang, Mehran Kardar, Gur Yaari, Laura M Walker, Birgitte B Simen, Elizabeth P St John, Po-Ying Chan-Hui, Kristine Swiderek, Stephen H Kleinstein, Galit Alter, Michael S Seaman, Arup K Chakraborty, Daphne Koller, Ian A Wilson, George M Church, Dennis R Burton, Pascal Poignard

PLoS Pathogens 2013

doi:10.1371/journal.ppat.1003754 | pdf

PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis

H. Benjamin Larman, Uri Laserson, Luis Querol, Katrijn Verhaeghen, Nicole L Solimini, George Jing Xu, Paul L Klarenbeek, George M Church, David A Hafler, Robert M Plenge, Peter A Nigrovic, Philip L De Jager, Ilse Weets, Geert A Martens, Kevin C O'Connor, Stephen J Elledge

Journal of Autoimmunity 2013

doi:10.1016/j.jaut.2013.01.013 | pdf

Protein interaction discovery using parallel analysis of translated ORFs (PLATO)

Jian Zhu, H Benjamin Larman, Geng Gao, Romel Somwar, Zijuan Zhang, Uri Laserson, Alberto Ciccia, Natalya Pavlova, George M Church, Wei Zhang, Santosh Kesari, Stephen J Elledge

Nature Biotech 2013

doi:10.1038/nbt.2539 | pdf

Autoantigen discovery with a synthetic human peptidome

H Benjamin Larman, Zhenming Zhao, Uri Laserson, Mamie Z Li, Alberto Ciccia, M Angelica Martinez Gakidis, George M Church, Santosh Kesari, Emily M LeProust, Nicole L Solimini, Stephen J Elledge

Nature Biotech 2011

doi:10.1038/nbt.1856 | pdf

Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs

Uri Laserson, Hin Hark Gan, Tamar Schlick

Nucleic Acids Research 2005

doi:10.1093/nar/gki911 | pdf

Searching for 2D RNA geometries in bacterial genomes

Uri Laserson, Hin Hark Gan, Tamar Schlick

SCG--Proceedings of the 20th annual symposium on computational geometry 2004

doi:10.1145/997817.997819 | pdf

RAG: RNA-As-Graphs web resource

Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick

BMC Bioinformatics 2004

doi:10.1186/1471-2105-5-88 | pdf

RAG: RNA-As-Graphs database--concepts, analysis, and features

Hin Hark Gan, Daniela Fera, Julie Zorn, Nahum Shiffeldrim, Michael Tang, Uri Laserson, Namhee Kim, Tamar Schlick

Bioinformatics 2004

doi:10.1093/bioinformatics/bth084 | pdf

Patents

High-Throughput Immune Sequencing

George M Church, Francois Vigneault, Uri Laserson, Ido Bachelet

2011

PCT/US2011/055801 | pdf

Methods and compositions for evaluating genetic markers

Gregory Porreca, Uri Laserson, Jin Billy Li, E Robert Wassman

2010

PCT/US2010/001293 | pdf

Books

Advanced Analytics with Spark: Patterns for Learning from Data at Scale

Sandy Ryza, Uri Laserson, Sean Owen, Josh Wills

O'Reilly2015

http://shop.oreilly.com/product/0636920035091.do

Book Articles

Reading the antibody repertoire against viruses, microbes, and the self

Uri Laserson

Evolutionary Biology of the Virome, and Impacts in Human Health and Disease (2017 Old Herborn University Seminar No. 31)2017

doi: | pdf

Exploring the connection between synthetic and natural RNAs in genomes: a novel computational approach

Uri Laserson, Hin Hark Gan, Tamar Schlick

New Algorithms for Macromolecular Simulation2006

doi:10.1007/3-540-31618-3_3 | pdf

Theses

Thesis: High-throughput methods for characterizing the immune repertoire

Uri Laserson

2012

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