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

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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