Binbin Chen

Binbin Chen

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Binbin Chen

Division of Oncology, Department of Medicine, Stanford University, Stanford, USA

Research Focus & Metrics

Academic Career Length

16Years (2011-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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18 January 2018
Verified
Book Chapter
Closed access
PDF file
BCBinbin Chen
Binbin Chen
MKMichael S. Khodadoust
Michael S. Khodadoust
CLChih Long Liu
Chih Long Liu
ANAaron M. Newman
Aaron M. Newman
AAAsh A Alizadeh
Ash A Alizadeh

25 March 2020 in Nature
Verified
Journal Article
Closed access
PDF file
JCJacob J. Chabon
Jacob J. Chabon
EHEmily G. Hamilton
Emily G. Hamilton
DKDavid M. Kurtz
David M. Kurtz
MEMohammad S. Esfahani
Mohammad S. Esfahani
EMEverett J. Moding
Everett J. Moding
MDMaximilian Diehn
Maximilian Diehn

22 July 2021 in Nature Biotechnology
Verified
Journal Article
Closed access
PDF file
DKDavid M. Kurtz
David M. Kurtz
JSJoanne Soo
Joanne Soo
LKLyron Co Ting Keh
Lyron Co Ting Keh
SAStefan Alig
Stefan Alig
JCJacob J. Chabon
Jacob J. Chabon
AAAsh A Alizadeh
Ash A Alizadeh

14 October 2019 in Nature Biotechnology
Verified
Journal Article
Closed access
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BCBinbin Chen
Binbin Chen
MKMichael S. Khodadoust
Michael S. Khodadoust
NONiclas Olsson
Niclas Olsson
LWLisa E. Wagar
Lisa E. Wagar
EFEthan Fast
Ethan Fast
AAAsh A Alizadeh
Ash A Alizadeh

7 May 2016
Verified
Conference Paper
Open access
EFEthan Fast
Ethan Fast
BCBinbin Chen
Binbin Chen
MBMichael S. Bernstein
Michael S. Bernstein
Human language is colored by a broad range of topics, but existing text analysis tools only focus on a small number of them. We present Empath, a tool that can generate and validate new lexical categories on demand from a small set of seed terms (like \"bleed\" and \"punch\" to generate the category violence). Empath draws connotations between words and phrases by deep learning a neural embedding across more than 1.8 billion words of modern fiction. Given a small set of seed words that characterize a category, Empath uses its neural embedding to discover new related terms, then validates the category with a crowd-powered filter. Empath also analyzes text across 200 built-in, pre-validated categories we have generated from common topics in our web dataset, like neglect, government, and social media. We show that Empath's data-driven, human validated categories are highly correlated (r=0.906) with similar categories in LIWC.

22 March 2017 in Nature
Verified
Journal Article
Open access
PDF file
MKMichael S. Khodadoust
Michael S. Khodadoust
NONiclas Olsson
Niclas Olsson
LWLisa E. Wagar
Lisa E. Wagar
OHOle A. W. Haabeth
Ole A. W. Haabeth
BCBinbin Chen
Binbin Chen
AAAsh A Alizadeh
Ash A Alizadeh
Evidence for the abundant presentation of class II neoantigens by a human B-cell lymphoma. Neoantigens created by cancer somatic mutations can distinguish between malignant and normal cells, but the challenge lies in their personalized identification and verification. Michael Khodadoust et al. provide evidence for the abundant presentation of MHC class II restricted neoantigens in human B cell lymphomas. Using an integrated genomic and proteomic strategy, they find that mutated tumour antigens are derived from the lymphoma immunoglobulin heavy and light chains and that they drive CD4 T-cell mediated cytotoxicity. Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells1,2,3,4,5,6,7. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4+ T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.