Works by Zheng, W. Jim

Results: 44

Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis.

Published in:

American Journal of Respiratory Cell & Molecular Biology, 2022, v. 66, n. 1, p. 53, doi. 10.1165/rcmb.2020-0437OC

By:

Hanmandlu, Ankit;
Lisha Zhu;
Mertens, Tinne C. J.;
Collum, Scott;
Weizhen Bi;
Feng Xiong;
Ruoyu Wang;
Amirthalingam, Rajarajan T.;
Dewei Ren;
Leng Han;
Jyothula, Soma S. S. K.;
Wenbo Li;
Jim Zheng, W.;
Karmouty-Quintana, Harry

Publication type:

Article

CNGPLD: case–control copy-number analysis using Gaussian process latent difference.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2096, doi. 10.1093/bioinformatics/btac096

By:

Shih, David J H;
Li, Ruoxing;
Müller, Peter;
Zheng, W Jim;
Do, Kim-Anh;
Lin, Shiaw-Yih;
Carter, Scott L

Publication type:

Article

Virome assembly and annotation in brain tissue based on next‐generation sequencing.

Published in:

Cancer Medicine, 2020, v. 9, n. 18, p. 6776, doi. 10.1002/cam4.3325

By:

Yuan, Zihao;
Ye, Xiaohua;
Zhu, Lisha;
Zhang, Ningyan;
An, Zhiqiang;
Zheng, W. Jim

Publication type:

Article

The Yeast Sphingolipid Phospholipase ISC1 Regulates The Spindle Checkpoint In a CDC55-Dependent Mechanism.

Published in:

Molecular & Cellular Biology, 2020, v. 40, n. 12, p. 1, doi. 10.1128/MCB.00340-19

By:

Matmati, Nabil;
Hassan, Bachar H.;
Jihui Ren;
Shamssedine, Ashraf A.;
Eunmi Jeong;
Shariff, Baasil;
Snider, Justin;
Rødkær, Steven V.;
Guocai Chen;
Mohanty, Bidyut K.;
Zheng, W. Jim;
Obeid, Lina M.;
Røssel-Larsen, Martin;
Færgeman, Nils J.;
Hannun, Yusuf A.

Publication type:

Article

PleThora: Pleural effusion and thoracic cavity segmentations in diseased lungs for benchmarking chest CT processing pipelines.

Published in:

Medical Physics, 2020, v. 47, n. 12, p. 1, doi. 10.1002/mp.14807

By:

Kiser, Kendall J.;
Ahmed, Sara;
Stieb, Sonja;
Mohamed, Abdallah S. R.;
Elhalawani, Hesham;
Park, Peter Y. S.;
Doyle, Nathan S.;
Wang, Brandon J.;
Barman, Arko;
Li, Zhao;
Zheng, W. Jim;
Fuller, Clifton D.;
Giancardo, Luca

Publication type:

Article

PleThora: Pleural effusion and thoracic cavity segmentations in diseased lungs for benchmarking chest CT processing pipelines.

Published in:

Medical Physics, 2020, v. 47, n. 11, p. 5941, doi. 10.1002/mp.14424

By:

Kiser, Kendall J.;
Ahmed, Sara;
Stieb, Sonja;
Mohamed, Abdallah S. R.;
Elhalawani, Hesham;
Park, Peter Y. S.;
Doyle, Nathan S.;
Wang, Brandon J.;
Barman, Arko;
Li, Zhao;
Zheng, W. Jim;
Fuller, Clifton D.;
Giancardo, Luca

Publication type:

Article

Object-oriented biological system integration: a SARS coronavirus example.

Published in:

Bioinformatics, 2005, v. 21, n. 10, p. 2502, doi. 10.1093/bioinformatics/bti344

By:

Daniel Shegogue;
W. Jim Zheng

Publication type:

Article

Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases.

Published in:

Human Molecular Genetics, 2024, v. 33, n. 19, p. 1697, doi. 10.1093/hmg/ddae109

By:

Kin, Katherine;
Bhogale, Shounak;
Zhu, Lisha;
Thomas, Derrick;
Bertol, Jessica;
Zheng, W Jim;
Sinha, Saurabh;
Fakhouri, Walid D

Publication type:

Article

evidence-based lexical pattern approach for quality assurance of Gene Ontology relations.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 3, p. 1, doi. 10.1093/bib/bbac122

By:

Abeysinghe, Rashmie;
Yang, Yuntao;
Bartels, Mason;
Zheng, W Jim;
Cui, Licong

Publication type:

Article

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1797-3

By:

Zhandong Liu;
Jim Zheng, W.;
Allen, Genevera I.;
Yin Liu;
Jianhua Ruan;
Zhongming Zhao

Publication type:

Article

Evaluation of genome-wide association study results through development of ontology fingerprints.

Published in:

Bioinformatics, 2009, v. 25, n. 10, p. 1314, doi. 10.1093/bioinformatics/btp158

By:

Lam C. Tsoi;
Michael Boehnke;
Richard L. Klein;
W. Jim Zheng

Publication type:

Article

Ensemble pretrained language models to extract biomedical knowledge from literature.

Published in:

Journal of the American Medical Informatics Association, 2024, v. 31, n. 9, p. 1904, doi. 10.1093/jamia/ocae061

By:

Li, Zhao;
Wei, Qiang;
Huang, Liang-Chin;
Li, Jianfu;
Hu, Yan;
Chuang, Yao-Shun;
He, Jianping;
Das, Avisha;
Keloth, Vipina Kuttichi;
Yang, Yuntao;
Diala, Chiamaka S;
Roberts, Kirk E;
Tao, Cui;
Jiang, Xiaoqian;
Zheng, W Jim;
Xu, Hua

Publication type:

Article

A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System.

Published in:

2020

By:

Zheng, Fengbo;
Shi, Jay;
Yang, Yuntao;
Zheng, W Jim;
Cui, Licong

Publication type:

journal article

Asthma Exacerbation Prediction and Risk Factor Analysis Based on a Time-Sensitive, Attentive Neural Network: Retrospective Cohort Study.

Published in:

2020

By:

Xiang, Yang;
Ji, Hangyu;
Zhou, Yujia;
Li, Fang;
Du, Jingcheng;
Rasmy, Laila;
Wu, Stephen;
Zheng, W Jim;
Xu, Hua;
Zhi, Degui;
Zhang, Yaoyun;
Tao, Cui

Publication type:

journal article

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.

Published in:

2017

By:

Jim Zheng, W.;
Jianhua Ruan;
Hua Xu;
Zhongming Zhao;
Zhangdong Liu

Publication type:

Proceeding

A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case.

Published in:

BMC Systems Biology, 2015, v. 9, p. 1, doi. 10.1186/1752-0509-9-S4-S2

By:

Liang-Chin Huang;
Soysal, Ergin;
Zheng, W. Jim;
Zhongming Zhao;
Hua Xu;
Jingchun Sun

Publication type:

Article

Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network.

Published in:

BMC Systems Biology, 2012, v. 6, n. Suppl 3, p. 1, doi. 10.1186/1752-0509-6-S3-S3

By:

Tingting Qin;
Tsoi, Lam C.;
Sims, Kellie J.;
Xinghua Lu;
Zheng, W. Jim

Publication type:

Article

A statistical framework for biomedical literature mining.

Published in:

2017

By:

Chung, Dongjun;
Lawson, Andrew;
Zheng, W. Jim

Publication type:

journal article

A comparative study of disease genes and drug targets in the human protein interactome.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/1471-2105-16-S5-S1

By:

Jingchun Sun;
Zhu, Kevin;
Zheng, W. Jim;
Hua Xu

Publication type:

Article

Transcriptional signature of durable effector T cells elicited by a replication defective HCMV vaccine.

Published in:

NPJ Vaccines, 2024, v. 9, n. 1, p. 1, doi. 10.1038/s41541-024-00860-w

By:

Ye, Xiaohua;
Shih, David J. H.;
Ku, Zhiqiang;
Hong, Junping;
Barrett, Diane F.;
Rupp, Richard E.;
Zhang, Ningyan;
Fu, Tong-Ming;
Zheng, W. Jim;
An, Zhiqiang

Publication type:

Article

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4018-6

By:

Zhongming Zhao;
Zhandong Liu;
Ken Chen;
Yan Guo;
Allen, Genevera I.;
Jiajie Zhang;
Jim Zheng, W.;
Jianhua Ruan

Publication type:

Article

Genome3D: A viewer-model framework forintegrating and visualizing multi-scaleepigenomic information within athree-dimensional genome.

Published in:

2010

By:

Asbury, Thomas M.;
Mitman, Matt;
Jijun Tang;
Zheng, W. Jim

Publication type:

Product Review

Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

Published in:

BMC Bioinformatics, 2006, v. 7, p. 1, doi. 10.1186/1471-2105-7-S4-S21

By:

Mao, Linyong;
Zheng, W. Jim

Publication type:

Article

Integration of the Gene Ontology into an object-oriented architecture.

Published in:

BMC Bioinformatics, 2005, v. 6, p. 113, doi. 10.1186/1471-2105-6-113

By:

Shegogue, Daniel;
Zheng, W. Jim

Publication type:

Article

Aging- and alcohol-associated spatial transcriptomic signature in mouse acute pancreatitis reveals heterogeneity of inflammation and potential pathogenic factors.

Published in:

Journal of Molecular Medicine, 2024, v. 102, n. 8, p. 1051, doi. 10.1007/s00109-024-02460-6

By:

Tindall, Rachel R.;
Yang, Yuntao;
Hernandez, Isabella;
Qin, Amy;
Li, Jiajing;
Zhang, Yinjie;
Gomez, Thomas H.;
Younes, Mamoun;
Shen, Qiang;
Bailey-Lundberg, Jennifer M.;
Zhao, Zhongming;
Kraushaar, Daniel;
Castro, Patricia;
Cao, Yanna;
Zheng, W. Jim;
Ko, Tien C.

Publication type:

Article

Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate.

Published in:

Human Genetics, 2020, v. 139, n. 10, p. 1261, doi. 10.1007/s00439-020-02169-9

By:

Morris, Vershanna E.;
Hashmi, S. Shahrukh;
Zhu, Lisha;
Maili, Lorena;
Urbina, Christian;
Blackwell, Steven;
Greives, Matthew R.;
Buchanan, Edward P.;
Mulliken, John B.;
Blanton, Susan H.;
Zheng, W. Jim;
Hecht, Jacqueline T.;
Letra, Ariadne

Publication type:

Article

Subgingival Microbiome and Specialized Pro-Resolving Lipid Mediator Pathway Profiles Are Correlated in Periodontal Inflammation.

Published in:

Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.691216

By:

Lee, Chun-Teh;
Li, Ruoxing;
Zhu, Lisha;
Tribble, Gena D.;
Zheng, W. Jim;
Ferguson, Brittney;
Maddipati, Krishna Rao;
Angelov, Nikola;
Van Dyke, Thomas E.

Publication type:

Article

ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D331, doi. 10.1093/nar/gkae1018

By:

Yang, Yuntao;
Kumar, Himansu;
Xie, Yuhan;
Li, Zhao;
Li, Rongbin;
Chen, Wenbo;
Diala, Chiamaka S;
Ali, Meer A;
Xu, Yi;
Wu, Albon;
Hosseini, Sayed-Rzgar;
Bi, Erfei;
Zhao, Hongyu;
Kim, Pora;
Zheng, W Jim

Publication type:

Article

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.

Published in:

Nucleic Acids Research, 2014, v. 42, n. 18, p. e138, doi. 10.1093/nar/gku678

By:

Qin, Tingting;
Matmati, Nabil;
Tsoi, Lam C.;
Mohanty, Bidyut K.;
Gao, Nan;
Tang, Jijun;
Lawson, Andrew B.;
Hannun, Yusuf A.;
Zheng, W. Jim

Publication type:

Article

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03113-2

By:

Yan Zhang;
Lin An;
Jie Xu;
Bo Zhang;
Jim Zheng, W.;
Ming Hu;
Jijun Tang;
Feng Yue

Publication type:

Article

Informatics, Data Science, and Artificial Intelligence.

Published in:

2018

By:

Zhu, Lisha;
Zheng, W. Jim

Publication type:

journal article

Presence of complete murine viral genome sequences in patient-derived xenografts.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22200-5

By:

Yuan, Zihao;
Fan, Xuejun;
Zhu, Jay-Jiguang;
Fu, Tong-Ming;
Wu, Jiaqian;
Xu, Hua;
Zhang, Ningyan;
An, Zhiqiang;
Zheng, W. Jim

Publication type:

Article

An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.

Published in:

Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baaa074

By:

Patra, Braja Gopal;
Soltanalizadeh, Babak;
Deng, Nan;
Wu, Leqing;
Maroufy, Vahed;
Wu, Canglin;
Zheng, W Jim;
Roberts, Kirk;
Wu, Hulin;
Yaseen, Ashraf

Publication type:

Article

Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.

Published in:

Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/bay145

By:

Chen, Guocai;
Ramírez, Juan Camilo;
Deng, Nan;
Qiu, Xing;
Wu, Canglin;
Zheng, W Jim;
Wu, Hulin

Publication type:

Article

Colorectal cancer drug target prediction using ontology-based inference and network analysis.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav015

By:

Cui Tao;
Jingchun Sun;
W. Jim Zheng;
Junjie Chen;
Hua Xu

Publication type:

Article

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav034

By:

Guocai Chen;
Jieyi Zhao;
Cohen, Trevor;
Cui Tao;
Jingchun Sun;
Hua Xu;
Bernstam, Elmer V.;
Lawson, Andrew;
Jia Zeng;
Johnson, Amber M.;
Holla, Vijaykumar;
Bailey, Ann M.;
Lara-Guerra, Humberto;
Litzenburger, Beate;
Meric-Bernstam, Funda;
Zheng, W. Jim

Publication type:

Article

Molecular Profiling of Multiple Human Cancers Defines an Inflammatory Cancer-Associated Molecular Pattern and Uncovers KPNA2 as a Uniform Poor Prognostic Cancer Marker.

Published in:

PLoS ONE, 2013, v. 8, n. 3, p. 1, doi. 10.1371/journal.pone.0057911

By:

Rachidi, Saleh M.;
Qin, Tingting;
Sun, Shaoli;
Zheng, W. Jim;
Li, Zihai

Publication type:

Article

Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files.

Published in:

PLoS ONE, 2011, v. 6, n. 12, p. 1, doi. 10.1371/journal.pone.0028251

By:

Sakib, Muhammad Nazmus;
Jijun Tang;
Zheng, W. Jim;
Chin-Tser Huang

Publication type:

Article

Cellular Morphogenesis Under Stress Is Influenced by the Sphingolipid Pathway Gene ISC1 and DNA Integrity Checkpoint Genes in Saccharomyces cerevisiae.

Published in:

Genetics, 2011, v. 189, n. 2, p. 533, doi. 10.1534/genetics.111.132092

By:

Tripathi, Kaushlendra;
Matmati, Nabil;
Zheng, W. Jim;
Hannun, Yusuf A.;
Mohanty, Bidyut K.

Publication type:

Article

Distinct Profiles of Specialized Pro-resolving Lipid Mediators and Corresponding Receptor Gene Expression in Periodontal Inflammation.

Published in:

Frontiers in Immunology, 2020, v. 11, p. 1, doi. 10.3389/fimmu.2020.01307

By:

Ferguson, Brittney;
Bokka, Nishantha R.;
Maddipati, Krishna Rao;
Ayilavarapu, Srinivas;
Weltman, Robin;
Zhu, Lisha;
Chen, Wanqi;
Zheng, W. Jim;
Angelov, Nikola;
Van Dyke, Thomas E.;
Lee, Chun-Teh

Publication type:

Article

Statistical Methods in Bioinformatics: An Introduction (2nd ed.).

Published in:

2006

By:

Zheng, W. Jim

Publication type:

Book Review

Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD.

Published in:

2019

By:

Chen, Guocai;
Jia, Yuxi;
Zhu, Lisha;
Li, Ping;
Zhang, Lin;
Tao, Cui;
Jim Zheng, W.

Publication type:

journal article

SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05873-9

By:

Tang, Yi-Ching;
Li, Rongbin;
Tang, Jing;
Zheng, W. Jim;
Jiang, Xiaoqian

Publication type:

Article

Use artificial neural network to align biological ontologies.

Published in:

BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-S2-S16

By:

Jingshan Huang;
Jiangbo Dang;
Huhns, Michael N.;
Zheng, W. Jim

Publication type:

Article