Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE.

Lin, Yingxin; Wu, Tung-Yu; Chen, Xi; Wan, Sheng; Chao, Brian; Xin, Jingxue; Yang, Jean Y H; Wong, Wing H; Wang, Y X Rachel.

Genome Res ; 34(1): 119-133, 2024 Feb 07.

Artigo em Inglês | MEDLINE | ID: mdl-38190633

2.

scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data.

Hao, Jie; Zou, Jiawei; Zhang, Jiaqiang; Chen, Ke; Wu, Duojiao; Cao, Wei; Shang, Guoguo; Yang, Jean Y H; Wong-Lin, KongFatt; Sun, Hourong; Zhang, Zhen; Wang, Xiangdong; Chen, Wantao; Zou, Xin.

Brief Bioinform ; 24(2)2023 03 19.

Artigo em Inglês | MEDLINE | ID: mdl-36813563

3.

A field guide to cultivating computational biology.

Way, Gregory P; Greene, Casey S; Carninci, Piero; Carvalho, Benilton S; de Hoon, Michiel; Finley, Stacey D; Gosline, Sara J C; LÈ Cao, Kim-Anh; Lee, Jerry S H; Marchionni, Luigi; Robine, Nicolas; Sindi, Suzanne S; Theis, Fabian J; Yang, Jean Y H; Carpenter, Anne E; Fertig, Elana J.

PLoS Biol ; 19(10): e3001419, 2021 10.

Artigo em Inglês | MEDLINE | ID: mdl-34618807

4.

Scalable workflow for characterization of cell-cell communication in COVID-19 patients.

Lin, Yingxin; Loo, Lipin; Tran, Andy; Lin, David M; Moreno, Cesar; Hesselson, Daniel; Neely, G Gregory; Yang, Jean Y H.

PLoS Comput Biol ; 18(10): e1010495, 2022 10.

Artigo em Inglês | MEDLINE | ID: mdl-36197936

5.

Whole-genome landscapes of major melanoma subtypes.

Hayward, Nicholas K; Wilmott, James S; Waddell, Nicola; Johansson, Peter A; Field, Matthew A; Nones, Katia; Patch, Ann-Marie; Kakavand, Hojabr; Alexandrov, Ludmil B; Burke, Hazel; Jakrot, Valerie; Kazakoff, Stephen; Holmes, Oliver; Leonard, Conrad; Sabarinathan, Radhakrishnan; Mularoni, Loris; Wood, Scott; Xu, Qinying; Waddell, Nick; Tembe, Varsha; Pupo, Gulietta M; De Paoli-Iseppi, Ricardo; Vilain, Ricardo E; Shang, Ping; Lau, Loretta M S; Dagg, Rebecca A; Schramm, Sarah-Jane; Pritchard, Antonia; Dutton-Regester, Ken; Newell, Felicity; Fitzgerald, Anna; Shang, Catherine A; Grimmond, Sean M; Pickett, Hilda A; Yang, Jean Y; Stretch, Jonathan R; Behren, Andreas; Kefford, Richard F; Hersey, Peter; Long, Georgina V; Cebon, Jonathan; Shackleton, Mark; Spillane, Andrew J; Saw, Robyn P M; López-Bigas, Núria; Pearson, John V; Thompson, John F; Scolyer, Richard A; Mann, Graham J.

Nature ; 545(7653): 175-180, 2017 05 11.

Artigo em Inglês | MEDLINE | ID: mdl-28467829

6.

Whole genome duplication in oral squamous cell carcinoma in patients younger than 50 years: implications for prognosis and adverse clinicopathological factors.

Satgunaseelan, Laveniya; Strbenac, Dario; Willet, Cali; Chew, Tracy; Sadsad, Rosemarie; Wykes, James; Low, Tsu-Hui Hubert; Cooper, Wendy A; Lee, C Soon; Palme, Carsten E; Yang, Jean Y H; Clark, Jonathan R; Gupta, Ruta.

Genes Chromosomes Cancer ; 61(9): 561-571, 2022 09.

Artigo em Inglês | MEDLINE | ID: mdl-35670448

7.

Factors Associated With Advanced Colorectal Neoplasia in Patients With CKD.

Au, Eric H; Wong, Germaine; Howard, Kirsten; Chapman, Jeremy R; Castells, Antoni; Roger, Simon D; Bourke, Michael J; Macaskill, Petra; Turner, Robin; Lim, Wai H; Lok, Charmaine E; Diekmann, Fritz; Cross, Nicholas; Sen, Shaundeep; Allen, Richard D; Chadban, Steven J; Pollock, Carol A; Tong, Allison; Teixeira-Pinto, Armando; Yang, Jean Y; Kieu, Anh; James, Laura; Craig, Jonathan C.

Am J Kidney Dis ; 79(4): 549-560, 2022 Apr.

Artigo em Inglês | MEDLINE | ID: mdl-34461168

8.

LC-N2G: a local consistency approach for nutrigenomics data analysis.

Xu, Xiangnan; Solon-Biet, Samantha M; Senior, Alistair; Raubenheimer, David; Simpson, Stephen J; Fontana, Luigi; Mueller, Samuel; Yang, Jean Y H.

BMC Bioinformatics ; 21(1): 530, 2020 Nov 17.

Artigo em Inglês | MEDLINE | ID: mdl-33203358

9.

Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma.

Su, Xianbin; Long, Qi; Bo, Juanjie; Shi, Yi; Zhao, Li-Nan; Lin, Yingxin; Luo, Qing; Ghazanfar, Shila; Zhang, Chao; Liu, Qiang; Wang, Lan; He, Kunyan; He, Jian; Cui, Xiaofang; Yang, Jean Y H; Han, Ze-Guang; Yang, Guoliang; Sha, Jian-Jun.

Prostate ; 80(6): 508-517, 2020 05.

Artigo em Inglês | MEDLINE | ID: mdl-32119131

10.

3D reconstruction of spatial expression.

Lin, Yingxin; Yang, Jean Y H.

Nat Methods ; 19(5): 526-527, 2022 05.

Artigo em Inglês | MEDLINE | ID: mdl-35577956

11.

DCARS: differential correlation across ranked samples.

Ghazanfar, Shila; Strbenac, Dario; Ormerod, John T; Yang, Jean Y H; Patrick, Ellis.

Bioinformatics ; 35(5): 823-829, 2019 03 01.

Artigo em Inglês | MEDLINE | ID: mdl-30102408

12.

bcGST-an interactive bias-correction method to identify over-represented gene-sets in boutique arrays.

Wang, Kevin Y X; Menzies, Alexander M; Silva, Ines P; Wilmott, James S; Yan, Yibing; Wongchenko, Matthew; Kefford, Richard F; Scolyer, Richard A; Long, Georgina V; Tarr, Garth; Mueller, Samuel; Yang, Jean Y H.

Bioinformatics ; 35(8): 1350-1357, 2019 04 15.

Artigo em Inglês | MEDLINE | ID: mdl-30215668

13.

One-Time Fecal Immunochemical Screening for Advanced Colorectal Neoplasia in Patients with CKD (DETECT Study).

Wong, Germaine; Hope, Richard L; Howard, Kirsten; Chapman, Jeremy R; Castells, Antoni; Roger, Simon D; Bourke, Michael J; Macaskill, Petra; Turner, Robin; Williams, Gabrielle; Lim, Wai Hon; Lok, Charmaine E; Diekmann, Fritz; Cross, Nicholas B; Sen, Shaundeep; Allen, Richard D M; Chadban, Steven J; Pollock, Carol A; Tong, Allison; Teixeira-Pinto, Armando; Yang, Jean Y H; Williams, Narelle; Au, Eric Hoi Kit; Kieu, Anh; James, Laura; Craig, Jonathan C.

J Am Soc Nephrol ; 30(6): 1061-1072, 2019 06.

Artigo em Inglês | MEDLINE | ID: mdl-31040191

14.

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis.

Geddes, Thomas A; Kim, Taiyun; Nan, Lihao; Burchfield, James G; Yang, Jean Y H; Tao, Dacheng; Yang, Pengyi.

BMC Bioinformatics ; 20(Suppl 19): 660, 2019 Dec 24.

Artigo em Inglês | MEDLINE | ID: mdl-31870278

15.

scDC: single cell differential composition analysis.

Cao, Yue; Lin, Yingxin; Ormerod, John T; Yang, Pengyi; Yang, Jean Y H; Lo, Kitty K.

BMC Bioinformatics ; 20(Suppl 19): 721, 2019 Dec 24.

Artigo em Inglês | MEDLINE | ID: mdl-31870280

16.

Utilizing state-of-the-art "omics" technology and bioinformatics to identify new biological mechanisms and biomarkers for coronary artery disease.

Vernon, Stephen T; Hansen, Thomas; Kott, Katharine A; Yang, Jean Y; O'Sullivan, John F; Figtree, Gemma A.

Microcirculation ; 26(2): e12488, 2019 02.

Artigo em Inglês | MEDLINE | ID: mdl-29956866

17.

Differential distribution improves gene selection stability and has competitive classification performance for patient survival.

Strbenac, Dario; Mann, Graham J; Yang, Jean Y H; Ormerod, John T.

Nucleic Acids Res ; 44(13): e119, 2016 07 27.

Artigo em Inglês | MEDLINE | ID: mdl-27190235

18.

Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods.

Strbenac, Dario; Zhong, Ling; Raftery, Mark J; Wang, Penghao; Wilson, Susan R; Armstrong, Nicola J; Yang, Jean Y H.

J Proteome Res ; 16(7): 2359-2369, 2017 07 07.

Artigo em Inglês | MEDLINE | ID: mdl-28580786

19.

Hyperactivation of the Insulin Signaling Pathway Improves Intracellular Proteostasis by Coordinately Up-regulating the Proteostatic Machinery in Adipocytes.

Minard, Annabel Y; Wong, Martin K L; Chaudhuri, Rima; Tan, Shi-Xiong; Humphrey, Sean J; Parker, Benjamin L; Yang, Jean Y; Laybutt, D Ross; Cooney, Gregory J; Coster, Adelle C F; Stöckli, Jacqueline; James, David E.

J Biol Chem ; 291(49): 25629-25640, 2016 Dec 02.

Artigo em Inglês | MEDLINE | ID: mdl-27738101

20.

Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development.

Su, Xianbin; Shi, Yi; Zou, Xin; Lu, Zhao-Ning; Xie, Gangcai; Yang, Jean Y H; Wu, Chong-Chao; Cui, Xiao-Fang; He, Kun-Yan; Luo, Qing; Qu, Yu-Lan; Wang, Na; Wang, Lan; Han, Ze-Guang.

BMC Genomics ; 18(1): 946, 2017 Dec 04.

Artigo em Inglês | MEDLINE | ID: mdl-29202695

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