Jiarui Ding

发表

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

A. Bashashati, S. Shah, S. Aparicio, 2012, Genome Biology.

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

Gholamreza Haffari, Anne Condon, Sohrab P. Shah, 2011, Bioinform..

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

Anne Condon, Sohrab P. Shah, Jiarui Ding, 2017 .

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

Anne Condon, Sohrab P Shah, Jiarui Ding, 2017, Nature Communications.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

Irmtraud M. Meyer, A. Bashashati, I. Birol, 2012, Nature.

Mutation Discovery in Regions of Segmental Cancer Genome Amplifications with CoNAn-SNV: A Mixture Model for Next Generation Sequencing of Tumors

Allen D. Delaney, M. Marra, M. Hirst, 2012, PloS one.

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

A. Bashashati, M. Marra, M. Hirst, 2012, Genome research.

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.

Steven J. M. Jones, Ryan D. Morin, Richard A. Moore, 2013, Blood.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Sohrab P. Shah, Ali Bashashati, Marco A. Marra, 2014, Genome research.

Pre-processing of tandem mass spectra using machine learning methods

Jiarui Ding, 2009 .

Quality Assessment of Tandem Mass Spectra by Using a Weighted K-Means

Jiarui Ding, Fang-Xiang Wu, Jin-Hong Shi, 2009, Clinical Proteomics.

A novel approach to denoising ion trap tandem mass spectra

Jiarui Ding, Fang-Xiang Wu, G. Poirier, 2009, Proteome Science.

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types

Gary D Bader, A. Condon, A. Bashashati, 2015, Nature Communications.

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

Ali Bashashati, Thomas Zeng, Stephen Yip, 2013, The Journal of pathology.

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

Vinay K. Kartha, Zachary D. Chiang, A. Regev, 2020, Cell.

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses.

A. Regev, R. Xavier, M. Tabaka, 2019, Immunity.

An adaptive approach to denoising tandem mass spectra

Jiarui Ding, Wen-Jun Zhang, Fang-Xiang Wu, 2010, BIBM Workshops.

populations from tumor whole-genome sequence data TITAN : inference of copy number architectures in clonal cell Material Supplemental

A. Bashashati, M. Marra, S. Shah, 2014 .

using whole-genome sequencing Mutational and structural analysis of diffuse large B-cell lymphoma

Ryan D. Morin, Richard A. Moore, R. Gascoyne, 2013 .

Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury

A. Regev, J. Sanes, K. Shekhar, 2022, bioRxiv.

LYMPHOID NEOPLASIA An RCOR1 loss – associated gene expression signature identi ﬁ es a prognostically signi ﬁ cant DLBCL subgroup

Ryan D. Morin, R. Gascoyne, L. Sehn, 2015 .

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Aviv Regev, Nir Hacohen, Alex K. Shalek, 2020, Nature Biotechnology.

densityCut: an efficient and versatile topological approach for automatic clustering of biological data

Anne Condon, Sohrab P. Shah, Jiarui Ding, 2016, Bioinform..

A microRNA expression and regulatory element activity atlas of the mouse immune system

Jason D. Buenrostro, A. Regev, E. Kenigsberg, 2021, Nature Immunology.

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

A. Condon, S. Shah, Jiarui Ding, 2017, bioRxiv.

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

Jiarui Ding, Aviv Regev, A. Regev, 2019, Nature Communications.

Single cell transcriptome analysis reveals disease-defining T cell subsets in the tumor microenvironment of classic Hodgkin lymphoma.

Allen W. Zhang, Lauren C. Chong, D. Scott, 2019, Cancer discovery.

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.

Ryan D. Morin, R. Gascoyne, D. Scott, 2015, Blood.

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

Aviv Regev, Zachary Chiang, Jason D. Buenrostro, 2020, Cell.

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Monika S. Kowalczyk, Sean K. Simmons, Cynthia C. Hession, 2020, Nature Biotechnology.

Systematic comparative analysis of single cell RNA-sequencing methods

Orit Rozenblatt-Rosen, Aviv Regev, Boaz Barak, 2019, bioRxiv.

BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma

Sohrab P Shah, Jiarui Ding, Janine Senz, 2012, Modern Pathology.

ImmGen at 15

Jason D. Buenrostro, E. Amir, A. Regev, 2020, Nature Immunology.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

Sohrab P. Shah, Ali Bashashati, Ryan D. Morin, 2012, Bioinform..

Disruption of the IL-33-ST2-AKT signaling axis impairs neurodevelopment by inhibiting microglial metabolic adaptation and phagocytic function.

A. Regev, O. Rozenblatt-Rosen, Danielle Dionne, 2021, Immunity.

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas

David J. Arenillas, Wyeth W Wasserman, Anthony Mathelier, 2014, Genome Biology.

Use of mutation profiles to refine the classification of endometrial carcinomas

Thomas Zeng, Martin Hirst, Kane Tse, 2012, The Journal of pathology.

The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments

Jason D. Buenrostro, A. Regev, E. Kenigsberg, 2021, Nature Communications.

Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer

W. Lam, C. Collins, S. Shah, 2016, Clinical Epigenetics.

Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles

S. Shah, Jiarui Ding, D. Huntsman, 2014, Modern Pathology.

Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas

A. Tinker, H. Mackay, S. Shah, 2014, BMC Cancer.

Pre-processing of tandem mass spectra using machine learning methods

Jiarui Ding, Jiarui Ding, 2009 .

Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Monika S. Kowalczyk, Sean K. Simmons, Cynthia C. Hession, 2020, Nature Biotechnology.

Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas

A. Tinker, H. Mackay, Jiarui Ding, 2014, BMC Cancer.

Feature Selection for Tandem Mass Spectrum Quality Assessment via Sparse Logistical Regression

Fang-Xiang Wu, Jiarui Ding, Jiarui Ding, 2009, 2009 3rd International Conference on Bioinformatics and Biomedical Engineering.

Quality assessment of tandem mass spectra using support vector machine (SVM)

Fang-Xiang Wu, An-Min Zou, Jiarui Ding, 2009, BMC Bioinformatics.

Charge State Determination of Peptide Tandem Mass Spectra Using Support Vector Machine (SVM)

Fang-Xiang Wu, An-Min Zou, Jin-Hong Shi, 2008, IEEE Transactions on Information Technology in Biomedicine.

Feature Selection for Tandem Mass Spectrum Quality Assessment

Fang-Xiang Wu, An-Min Zou, Jin-Hong Shi, 2008, 2008 IEEE International Conference on Bioinformatics and Biomedicine.

An approach to assessing peptide mass spectral quality without prior information

Fang-Xiang Wu, Jiarui Ding, Guy G. Poirier, 2008, Int. J. Funct. Informatics Pers. Medicine.

A robust hidden semi-Markov model with application to aCGH data processing

Sohrab P. Shah, Jiarui Ding, Jiarui Ding, 2013, Int. J. Data Min. Bioinform..

A Framework for Mass Spectral Quality Assessment without Prior Information

Fang-Xiang Wu, Jiarui Ding, Guy G. Poirier, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes

Jason D. Buenrostro, A. Regev, E. Kenigsberg, 2021, Nature Immunology.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

A. Bashashati, M. Marra, A. McPherson, 2014, Genome research.

Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer Supplemental Material

A. Bashashati, M. Marra, M. Hirst, 2012 .

Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Monika S. Kowalczyk, Sean K. Simmons, Cynthia C. Hession, 2020, Nature Biotechnology.