Works by Jiarui Ding

Results: 25

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

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. 2567, doi. 10.1093/bioinformatics/btw227

By:

Ding, Jiarui;
Shah, Sohrab;
Condon, Anne

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 7, p. 907, doi. 10.1093/bioinformatics/bts053

By:

Roth, Andrew;
Ding, Jiarui;
Morin, Ryan;
Crisan, Anamaria;
Ha, Gavin;
Giuliany, Ryan;
Bashashati, Ali;
Hirst, Martin;
Turashvili, Gulisa;
Oloumi, Arusha;
Marra, Marco A.;
Aparicio, Samuel;
Shah, Sohrab P.

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 2, p. 167, doi. 10.1093/bioinformatics/btr629

By:

Ding, Jiarui;
Bashashati, Ali;
Roth, Andrew;
Oloumi, Arusha;
Tse, Kane;
Zeng, Thomas;
Haffari, Gholamreza;
Hirst, Martin;
Marra, Marco A.;
Condon, Anne;
Aparicio, Samuel;
Shah, Sohrab P.

Publication type:

Article

Characterization of a Natural Accession of Elymus sibiricus with In Situ Hybridization and Agronomic Evaluation.

Published in:

Plants (2223-7747), 2025, v. 14, n. 1, p. 75, doi. 10.3390/plants14010075

By:

Liu, Yizhuo;
Ding, Jiarui;
Wu, Chunfei;
Song, Weiwei;
Zhao, Xinyu;
Zhao, Haibin;
Qu, Yunfeng;
Jin, Hui;
Zhang, Rui;
Li, Mingyao;
Yan, Xinyu;
Zhu, Liangyu;
Bao, Yaqi;
Liu, Dianhao;
Li, Xinling;
Cui, Lei;
Li, Hongjie;
Zhang, Yanming

Publication type:

Article

Cytogenetics and genomics analysis of cold‐hardy perennial wheatgrass: insights into agronomic performance, chromosome composition, and gene expression.

Published in:

Plant Journal, 2025, v. 122, n. 3, p. 1, doi. 10.1111/tpj.70179

By:

Zhao, Xinyu;
Zhang, Zhimeng;
Ding, Jiarui;
Wu, Chunfei;
Qu, Yunfeng;
Song, Anning;
Zhao, Haibin;
Song, Weiwei;
Liu, Meng;
Yang, Donghe;
Liu, Yizhuo;
He, Miao;
Xing, Qianyu;
Zhang, Huixin;
Cui, Lei;
Li, Xinling;
Xie, Jingzhong;
Li, Hongjie;
He, Fei;
Zhang, Yanming

Publication type:

Article

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

Published in:

BMC Cancer, 2014, v. 14, n. 1, p. 1, doi. 10.1186/1471-2407-14-982

By:

Tone, Alicia A.;
McConechy, Melissa K.;
Yang, Winnie;
Jiarui Ding;
Yip, Stephen;
Kong, Esther;
Kwong-Kwok Wong;
Gershenson, David M.;
Mackay, Helen;
Shah, Sohrab;
Gilks, Blake;
Tinker, Anna V.;
Clarke, Blaise;
McAlpine, Jessica N.;
Huntsman, David

Publication type:

Article

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

Published in:

2014

By:

Tone, Alicia A;
McConechy, Melissa K;
Yang, Winnie;
Ding, Jiarui;
Yip, Stephen;
Kong, Esther;
Wong, Kwong-Kwok;
Gershenson, David M;
Mackay, Helen;
Shah, Sohrab;
Gilks, Blake;
Tinker, Anna V;
Clarke, Blaise;
McAlpine, Jessica N;
Huntsman, David

Publication type:

journal article

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

Published in:

PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0041551

By:

Crisan, Anamaria;
Goya, Rodrigo;
Ha, Gavin;
Jiarui Ding;
Prentice, Leah M.;
Oloumi, Arusha;
Senz, Janine;
Zeng, Thomas;
Tse, Kane;
Delaney, Allen;
Marra, Marco A.;
Huntsman, David G.;
Hirst, Martin;
Aparicio, Sam;
Shah, Sohrab;
Creighton, Chad

Publication type:

Article

Mechanical behaviour of bridge expansion joint interfaces filled with novel polyurethane-modified asphalt.

Published in:

Road Materials & Pavement Design, 2025, v. 26, n. 5, p. 921, doi. 10.1080/14680629.2024.2389430

By:

Lu, Pengzhen;
Wang, Jiahao;
Ding, Jiarui;
Wu, Ying;
Yang, Liu;
Gu, Zhihui

Publication type:

Article

A novel approach to denoising ion trap tandem mass spectra.

Published in:

Proteome Science, 2009, v. 7, p. 1, doi. 10.1186/1477-5956-7-9

By:

Jiarui Ding;
Jinhong Shi;
Poirier, Guy G.;
Fang-Xiang Wu

Publication type:

Article

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

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04368-5

By:

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

Publication type:

Article

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

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22851-4

By:

Ding, Jiarui;
Regev, Aviv

Publication type:

Article

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

Published in:

Clinical Epigenetics, 2016, v. 8, p. 1, doi. 10.1186/s13148-016-0182-9

By:

Amy Zhang;
Wang, James Z. L.;
Parolia, Abhijit;
Rebecca Wu;
Hui Xue;
Yuwei Wang;
Clermont, Pier-Luc;
Yan Ting Chiang;
Dong Lin;
Crea, Francesco;
Yuzhuo Wang;
Helgason, Cheryl D.;
Collins, Colin C.;
Jiarui Ding;
Shah, Sohrab P.;
Thu, Kelsie L.;
Lam, Wan L.

Publication type:

Article

The improvement of agronomic performances in the cold weather conditions for perennial wheatgrass by crossing Thinopyrum intermedium with wheat-Th. intermedium partial amphiploids.

Published in:

Frontiers in Plant Science, 2023, p. 01, doi. 10.3389/fpls.2023.1207078

By:

Yizhuo Liu;
Weiwei Song;
Anning Song;
Chunfei Wu;
Jiarui Ding;
Xiaoning Yu;
Jia Song;
Miaomiao Liu;
Xinyuan Yang;
Changtong Jiang;
Haibin Zhao;
Weifu Song;
Dongjun Liu;
Xuefeng Yang;
Qingjie Song;
Xinling Li;
Lei Cui;
Hongjie Li;
Yanming Zhang

Publication type:

Article

An adaptive approach to denoising tandem mass spectra.

Published in:

Proteomics, 2011, v. 11, n. 19, p. 3773, doi. 10.1002/pmic.201100145

By:

Lin, Wenjun;
Wu, Fang-Xiang;
Shi, Jinhong;
Ding, Jiarui;
Zhang, Wenjun

Publication type:

Article

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

Published in:

Nature Communications, 2015, v. 6, n. 10, p. 8554, doi. 10.1038/ncomms9554

By:

Ding, Jiarui;
McConechy, Melissa K.;
Horlings, Hugo M.;
Ha, Gavin;
Chun Chan, Fong;
Funnell, Tyler;
Mullaly, Sarah C.;
Reimand, Jüri;
Bashashati, Ali;
Bader, Gary D.;
Huntsman, David;
Aparicio, Samuel;
Condon, Anne;
Shah, Sohrab P.

Publication type:

Article

Efficacy comparison of optimal natural orifice specimen extraction for robotic middle rectal cancer resection in women: transanal or transvaginal orifice.

Published in:

World Journal of Surgical Oncology, 2025, p. 1, doi. 10.1186/s12957-024-03630-z

By:

Yao, Yao;
Ding, Jiarui;
Ju, Houqiong;
Yang, Lingling;
Liu, Yang;
Liang, Yahang;
Yuan, Yuli;
Li, Taiyuan;
Lei, Xiong

Publication type:

Article

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

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0648-7

By:

Mathelier, Anthony;
Lefebvre, Calvin;
Zhang, Allen W.;
Arenillas, David J.;
Ding, Jiarui;
Wasserman, Wyeth W.;
Shah, Sohrab P.

Publication type:

Article

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

Published in:

Genome Biology, 2012, v. 13, n. 12, p. 1, doi. 10.1186/gb-2012-13-12-r124

By:

Bashashati, Ali;
Haffari, Gholamreza;
Ding, Jiarui;
Ha, Gavin;
Lui, Kenneth;
Rosner, Jamie;
Huntsman, David G.;
Caldas, Carlos;
Aparicio, Samuel A.;
Shah, Sohrab P.

Publication type:

Article

An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-47647-0

By:

Ding, Jiarui;
Garber, John J.;
Uchida, Amiko;
Lefkovith, Ariel;
Carter, Grace T.;
Vimalathas, Praveen;
Canha, Lauren;
Dougan, Michael;
Staller, Kyle;
Yarze, Joseph;
Delorey, Toni M.;
Rozenblatt-Rosen, Orit;
Ashenberg, Orr;
Graham, Daniel B.;
Deguine, Jacques;
Regev, Aviv;
Xavier, Ramnik J.

Publication type:

Article

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

Published in:

Journal of Pathology, 2013, v. 231, n. 1, p. 21, doi. 10.1002/path.4230

By:

Bashashati, Ali;
Ha, Gavin;
Tone, Alicia;
Ding, Jiarui;
Prentice, Leah M;
Roth, Andrew;
Rosner, Jamie;
Shumansky, Karey;
Kalloger, Steve;
Senz, Janine;
Yang, Winnie;
McConechy, Melissa;
Melnyk, Nataliya;
Anglesio, Michael;
Luk, Margaret TY;
Tse, Kane;
Zeng, Thomas;
Moore, Richard;
Zhao, Yongjun;
Marra, Marco A

Publication type:

Article

Use of mutation profiles to refine the classification of endometrial carcinomas.

Published in:

Journal of Pathology, 2012, v. 228, n. 1, p. 20, doi. 10.1002/path.4056

By:

McConechy, Melissa K;
Ding, Jiarui;
Cheang, Maggie CU;
Wiegand, Kimberly C;
Senz, Janine;
Tone, Alicia A;
Yang, Winnie;
Prentice, Leah M;
Tse, Kane;
Zeng, Thomas;
McDonald, Helen;
Schmidt, Amy P;
Mutch, David G;
McAlpine, Jessica N;
Hirst, Martin;
Shah, Sohrab P;
Lee, Cheng-Han;
Goodfellow, Paul J;
Gilks, C Blake;
Huntsman, David G

Publication type:

Article

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

Published in:

Nature, 2012, v. 486, n. 7403, p. 395, doi. 10.1038/nature10933

By:

Shah, Sohrab P.;
Roth, Andrew;
Goya, Rodrigo;
Oloumi, Arusha;
Ha, Gavin;
Zhao, Yongjun;
Turashvili, Gulisa;
Ding, Jiarui;
Tse, Kane;
Haffari, Gholamreza;
Bashashati, Ali;
Prentice, Leah M.;
Khattra, Jaswinder;
Burleigh, Angela;
Yap, Damian;
Bernard, Virginie;
McPherson, Andrew;
Shumansky, Karey;
Crisan, Anamaria;
Giuliany, Ryan

Publication type:

Article

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

Published in:

2020

By:

Ding, Jiarui;
Adiconis, Xian;
Simmons, Sean K.;
Kowalczyk, Monika S.;
Hession, Cynthia C.;
Marjanovic, Nemanja D.;
Hughes, Travis K.;
Wadsworth, Marc H.;
Burks, Tyler;
Nguyen, Lan T.;
Kwon, John Y. H.;
Barak, Boaz;
Ge, William;
Kedaigle, Amanda J.;
Carroll, Shaina;
Li, Shuqiang;
Hacohen, Nir;
Rozenblatt-Rosen, Orit;
Shalek, Alex K.;
Villani, Alexandra-Chloé

Publication type:

Correction Notice

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

Published in:

Nature Biotechnology, 2020, v. 38, n. 6, p. 737, doi. 10.1038/s41587-020-0465-8

By:

Ding, Jiarui;
Adiconis, Xian;
Simmons, Sean K.;
Kowalczyk, Monika S.;
Hession, Cynthia C.;
Marjanovic, Nemanja D.;
Hughes, Travis K.;
Wadsworth, Marc H.;
Burks, Tyler;
Nguyen, Lan T.;
Kwon, John Y. H.;
Barak, Boaz;
Ge, William;
Kedaigle, Amanda J.;
Carroll, Shaina;
Li, Shuqiang;
Hacohen, Nir;
Rozenblatt-Rosen, Orit;
Shalek, Alex K.;
Villani, Alexandra-Chloé

Publication type:

Article