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50 publications found

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Group #1

TitleAuthors (identified)Published InIdentifier(s)TopicPublished DateMatch?
Biomedical term mapping databases[1]Jonathan Wren, [2]Jeffrey T Chang, [3]James Pustejovsky, [4]Eytan Adar, [5]Harold R Garner, [6]Russ Altman [Full author list]Nucleic Acids Research [missing]DOI: 10.1093/NAR/GKI137 [ORCID]
PubMed: 15608198 [ORCID]
2005-01-01
Extracting and characterizing gene-drug relationships from the literature[1]Jeffrey T Chang, [2]Russ Altman [Full author list]Pharmacogenetics and Genomics [missing]DOI: 10.1097/00008571-200409000-00002 [ORCID]
PubMed: 15475731 [ORCID]
2004-09-01
GAPSCORE: finding gene and protein names one word at a time[1]Jeffrey T Chang, [2]Hinrich Schütze, [3]Russ Altman [Full author list]Bioinformatics [missing]DOI: 10.1093/BIOINFORMATICS/BTG393 [ORCID]
PubMed: 14734313 [ORCID]
2004-01-01
The computational analysis of scientific literature to define and recognize gene expression clusters[1]Soumya Raychaudhuri, [2]Jeffrey T Chang, [3]Farhad Imam, [4]Russ Altman [Full author list]Nucleic Acids Research [missing]DOI: 10.1093/NAR/GKG636 [ORCID]
PubMed: 12888516 [ORCID]
scientific literature [missing]2003-08-01
Creating an online dictionary of abbreviations from MEDLINE.[1]Jeffrey T Chang, [2]Hinrich Schütze, [3]Russ Altman [Full author list]Journal of the American Medical Informatics Association [missing]DOI: 10.1197/JAMIA.M1139 [ORCID]
PubMed: 12386112 [ORCID]
MEDLINE [missing]2002-11-01
Promises of text processing: natural language processing meets AI.[1]Jeffrey T Chang, [2]Russ Altman [Full author list]Drug Discovery Today [missing]DOI: 10.1016/S1359-6446(02)02457-1 [ORCID]
PubMed: 12546913 [ORCID]
natural language processing [missing]2002-10-01
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature[1]Soumya Raychaudhuri, [2]Jeffrey T Chang, [3]Patrick D Sutphin, [4]Russ Altman [Full author list]Genome Research [missing]DOI: 10.1101/GR.199701 [ORCID]
PubMed: 11779846 [ORCID]
Gene Ontology [missing]; ontology [missing]2002-01-01

Group #2

TitleAuthors (identified)Published InIdentifier(s)TopicPublished DateMatch?
The H3K27me3-demethylase KDM6A is suppressed in breast cancer stem-like cells, and enables the resolution of bivalency during the mesenchymal-epithelial transition[1]Joseph H Taube, [2]Nathalie Sphyris, [3]Kelsey S Johnson, [4]Keighley N Reisenauer, [5]Taylor A Nesbit, [6]Robiya Joseph, [7]Geraldine V Vijay, [8]Tapasree R Sarkar, [9]Neeraja A Bhangre, [10]Joon Jin Song, [11]Jeffrey T Chang, [12]Min Gyu Lee, [13]Rama Soundararajan, [14]Sendurai A. Mani [Full author list]Oncotarget [missing]DOI: 10.18632/ONCOTARGET.19214 [ORCID]
PubMed: 29029452 [ORCID]
2017-07-10
Motility and stem cell properties induced by the epithelial-mesenchymal transition require destabilization of lipid rafts[1]Michael J Tisza, [2]Weina Zhao, [3]Jessie S R Fuentes, [4]Sara Prijic, [5]Xiaoling Chen, [6]Ilya Levental, [7]Jeffrey T Chang [Full author list]Oncotarget [missing]DOI: 10.18632/ONCOTARGET.9928 [ORCID]
PubMed: 27303921 [ORCID]
membrane raft [missing]2016-06-09
Candidate Antimetastasis Drugs Suppress the Metastatic Capacity of Breast Cancer Cells by Reducing Membrane Fluidity[1]Weina Zhao, [2]Sara Prijic, [3]Bettina C Urban, [4]Michael J Tisza, [5]Yan Zuo, [6]Lin Li, [7]Zhi Tan, [8]Xiaoling Chen, [9]Sendurai A. Mani, [10]Jeffrey T Chang [Full author list]Cancer Research [missing]DOI: 10.1158/0008-5472.CAN-15-1970 [ORCID]
PubMed: 26825169 [ORCID]
breast cancer [missing]2016-01-29
A novel embryonic plasticity gene signature that predicts metastatic competence and clinical outcome[1]Rama Soundararajan, [2]Anurag N Paranjape, [3]Valentin Barsan, [4]Jeffrey T Chang, [5]Sendurai A. Mani [Full author list]Scientific Reports [missing]DOI: 10.1038/SREP11766 [ORCID]
PubMed: 26123483 [ORCID]
2015-06-30
FOXC2 expression links epithelial-mesenchymal transition and stem cell properties in breast cancer[1]Brett G Hollier, [2]Agata A Tinnirello, [3]Steven J Werden, [4]Kurt W Evans, [5]Joseph H Taube, [6]Tapasree Roy Sarkar, [7]Nathalie Sphyris, [8]Maryam Shariati, [9]Sreedevi V Kumar, [10]Venkata L Battula, [11]Jason I Herschkowitz, [12]Rudy Guerra, [13]Jeffrey T Chang, [14]Naoyuki Miura, [15]Jeffrey M Rosen, [16]Sendurai A. Mani [Full author list]Cancer Research [missing]DOI: 10.1158/0008-5472.CAN-12-2962 [ORCID]
PubMed: 23378344 [ORCID]
2013-02-01
Epigenetic silencing of microRNA-203 is required for EMT and cancer stem cell properties[1]Joseph H Taube, [2]Gabriel G Malouf, [3]Emily Lu, [4]Nathalie Sphyris, [5]Vidya Vijay, [6]Priyanka P Ramachandran, [7]Katumasa R Ueno, [8]Sanchaika Gaur, [9]Milena S Nicoloso, [10]Simona Rossi, [11]Jason I Herschkowitz, [12]Jeffrey M Rosen, [13]Jean-Pierre J Issa, [14]George A. Calin, [15]Jeffrey T Chang, [16]Sendurai A. Mani [Full author list]Scientific Reports [missing]DOI: 10.1038/SREP02687 [ORCID]
PubMed: 24045437 [ORCID]
microRNA [missing]; neoplastic stem cells [missing]2013-01-01

Group #3

TitleAuthors (identified)Published InIdentifier(s)TopicPublished DateMatch?
Genetic heterogeneity of Myc-induced mammary tumors reflecting diverse phenotypes including metastatic potential[1]Eran R Andrechek, [2]Robert Cardiff, [3]Jeffrey T Chang, [4]Michael L Gatza, [5]Chaitanya R Acharya, [6]Anil Potti, [7]Joseph R Nevins [Full author list]Proceedings of the National Academy of Sciences of the United States of America [missing]DOI: 10.1073/PNAS.0901250106 [ORCID]
PubMed: 19805309 [ORCID]
heterogeneity [missing]; metastatic potential [missing]2009-09-04
Utilization of genomic signatures to identify phenotype-specific drugs[1]Seiichi Mori, [2]Jeffrey T Chang, [3]Eran R Andrechek, [4]Anil Potti, [5]Joseph R Nevins [Full author list]PLOS One [missing]DOI: 10.1371/JOURNAL.PONE.0006772 [ORCID]
PubMed: 19714244 [ORCID]
2009-08-28
A genomic strategy to elucidate modules of oncogenic pathway signaling networks[1]Jeffrey T Chang, [2]Carlos Carvalho, [3]Seiichi Mori, [4]Andrea H Bild, [5]Michael L Gatza, [6]Quanli Wang, [7]Joseph E Lucas, [8]Anil Potti, [9]Phillip G Febbo, [10]Mike West, [11]Joseph R Nevins [Full author list]Molecular Cell [missing]DOI: 10.1016/J.MOLCEL.2009.02.030 [ORCID]
PubMed: 19362539 [ORCID]
2009-04-01
Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma[1]Seiichi Mori, [2]Rachel E Rempel, [3]Jeffrey T Chang, [4]Guang Yao, [5]Anand S Lagoo, [6]Anil Potti, [7]Andrea Bild, [8]Joseph R Nevins [Full author list]Cancer Research [missing]DOI: 10.1158/0008-5472.CAN-08-1329 [ORCID]
PubMed: 18922927 [ORCID]
diffuse large B-cell lymphoma [missing]; B-cell lymphoma [missing]2008-10-01
Patterns of cell signaling pathway activation that characterize mammary development[1]Eran R Andrechek, [2]Seiichi Mori, [3]Rachel E Rempel, [4]Jeffrey T Chang, [5]Joseph R Nevins [Full author list]Development [missing]DOI: 10.1242/DEV.019018 [ORCID]
PubMed: 18550711 [ORCID]
2008-06-11
DIG--a system for gene annotation and functional discovery.[1]Mark Delong, [2]Guang Yao, [3]Quanli Wang, [4]Adrian Dobra, [5]Esther P Black, [6]Jeffrey T Chang, [7]Andrea Bild, [8]Mike West, [9]Joseph R Nevins, [10]Holly Dressman [Full author list]Bioinformatics [missing]DOI: 10.1093/BIOINFORMATICS/BTI467 [ORCID]
PubMed: 15870167 [ORCID]
2005-05-03

Group #5

TitleAuthors (identified)Published InIdentifier(s)TopicPublished DateMatch?
ω-3 polyunsaturated fatty acids direct differentiation of the membrane phenotype in mesenchymal stem cells to potentiate osteogenesis[1]Kandice R. Levental, [2]Michał A. Surma, [3]Allison D Skinkle, [4]Joseph Lorent, [5]Yong Zhou, [6]Christian Klose, [7]Jeffrey T Chang, [8]John F Hancock, [9]Ilya Levental [Full author list]Science Advances [missing]DOI: 10.1126/SCIADV.AAO1193 [ORCID]
PubMed: 29134198 [ORCID]
mesenchymal stem cell [missing]2017-11-08
Binding of PLD2-Generated Phosphatidic Acid to KIF5B Promotes MT1-MMP Surface Trafficking and Lung Metastasis of Mouse Breast Cancer Cells[1]Ziqing Wang, [2]Feng Zhang, [3]Jingquan He, [4]Ping Wu, [5]Li Wei Rachel Tay, [6]Ming Cai, [7]Weiqi Nian, [8]Yuanyuan Weng, [9]Li Qin, [10]Jeffrey T Chang, [11]Laura B McIntire, [12]Gilbert Di Paolo, [13]Jianming Xu, [14]Junmin Peng, [15]Guangwei Du [Full author list]Developmental Cell [missing]DOI: 10.1016/J.DEVCEL.2017.09.012 [ORCID]
PubMed: 29033361 [ORCID]
lung metastasis [missing]2017-10-11
Lipin-1 regulation of phospholipid synthesis maintains endoplasmic reticulum homeostasis and is critical for triple-negative breast cancer cell survival[1]Jingquan He, [2]Feng Zhang, [3]Li Wei Rachel Tay, [4]Salome Boroda, [5]Weiqi Nian, [6]Kandice R. Levental, [7]Ilya Levental, [8]Thurl E Harris, [9]Jeffrey T Chang, [10]Guangwei Du [Full author list]FASEB Journal [missing]DOI: 10.1096/FJ.201601353R [ORCID]
PubMed: 28347999 [ORCID]
endoplasmic reticulum [missing]; triple-negative breast cancer [missing]2017-03-27

Group #7

TitleAuthors (identified)Published InIdentifier(s)TopicPublished DateMatch?
Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer[1]Nader N El-Chaar, [2]Stephen R Piccolo, [3]Kenneth M Boucher, [4]Adam L Cohen, [5]Jeffrey T Chang, [6]Philip J Moos, [7]Andrea H Bild [Full author list]Molecular Oncology [missing]DOI: 10.1016/J.MOLONC.2014.05.005 [ORCID]
PubMed: 24908424 [ORCID]
2014-05-20
A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment[1]Katrina Steiling, [2]Maarten van den Berge, [3]Kahkeshan Hijazi, [4]Roberta Florido, [5]Joshua D Campbell, [6]Gang Liu, [7]Ji Xiao, [8]Xiaohui Zhang, [9]Grant E Duclos, [10]Eduard Drizik, ..., [21]Peter J Sterk, [22]Wim Timens, [23]Jeffrey T Chang, [24]Paola Sebastiani, [25]George T O'Connor, ... [Full author list]American Journal of Respiratory and Critical Care Medicine [missing]DOI: 10.1164/RCCM.201208-1449OC [ORCID]
PubMed: 23471465 [ORCID]
chronic obstructive pulmonary disease [missing]2013-05-01
A pharmacogenomic method for individualized prediction of drug sensitivity[1]Adam L Cohen, [2]Raffaella Soldi, [3]Haiyu Zhang, [4]Adam M Gustafson, [5]Ryan Wilcox, [6]Bryan E Welm, [7]Jeffrey T Chang, [8]Evan Johnson, [9]Avrum Spira, [10]Stefanie S Jeffrey, [11]Andrea H Bild [Full author list]Molecular Systems Biology [missing]DOI: 10.1038/MSB.2011.47 [ORCID]
PubMed: 21772261 [ORCID]
pharmacogenomics [missing]2011-07-19

Misc

TitleAuthors (identified)Published InIdentifier(s)TopicPublished DateMatch?
PCSK9 deficiency reduces atherosclerosis, apolipoprotein B secretion, and endothelial dysfunction.[1]Hua Sun, [2]Ronald M Krauss, [3]Jeffrey T Chang, [4]Ba-Bie Teng [Full author list]Journal of Lipid Research [missing]DOI: 10.1194/JLR.M078360 [ORCID]
PubMed: 29180444 [ORCID]
atherosclerosis [missing]2017-11-27
Mechanisms and clinical implications of tumor heterogeneity and convergence on recurrent phenotypes[1]Jasmine A McQuerry, [2]Jeffrey T Chang, [3]David Bowtell, [4]Adam Cohen, [5]Andrea H Bild [Full author list]Journal of Molecular Medicine [missing]DOI: 10.1007/S00109-017-1587-4 [ORCID]
PubMed: 28871446 [ORCID]
2017-09-04
Planning bioinformatics workflows using an expert system[1]Xiaoling Chen, [2]Jeffrey T Chang [Full author list]Bioinformatics [missing]DOI: 10.1093/BIOINFORMATICS/BTW817 [ORCID]
PubMed: 28052928 [ORCID]
bioinformatics [missing]; workflow [missing]2017-04-01
Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes[1]Greg Boyle, [2]Kerstin Richter, [3]Henry D Priest, [4]David Traver, [5]Todd C Mockler, [6]Jeffrey T Chang, [7]Steve A Kay, [8]Ghislain Breton [Full author list]PLOS One [missing]DOI: 10.1371/JOURNAL.PONE.0169923 [ORCID]
PubMed: 28076377 [ORCID]
circadian rhythm [missing]2017-01-11
MiR-26 down-regulates TNF-α/NF-κB signalling and IL-6 expression by silencing HMGA1 and MALT1.[1]Chyi-Ying A Chen, [2]Jeffrey T Chang, [3]Yi-Fang Ho, [4]Ann-Bin Shyu [Full author list]Nucleic Acids Research [missing]DOI: 10.1093/NAR/GKW205 [ORCID]
PubMed: 27025651 [ORCID]
NF-κB [missing]2016-03-28
Euglycemia Restoration by Central Leptin in Type 1 Diabetes Requires STAT3 Signaling but Not Fast-Acting Neurotransmitter Release[1]Yuanzhong Xu, [2]Jeffrey T Chang, [3]Martin G Myers, [4]Yong Xu, [5]Qingchun Tong [Full author list]Diabetes [missing]DOI: 10.2337/DB15-1160 [ORCID]
PubMed: 26822087 [ORCID]
type-1 diabetes [missing]; neurotransmitter [missing]2016-01-28
Phospholipase C Beta 1: a Candidate Signature Gene for Proneural Subtype High-Grade Glioma[1]Guangrong Lu, [2]Jeffrey T Chang, [3]Zheyu Liu, [4]Yong Chen, [5]Min Li, [6]Jay-Jiguang Zhu [Full author list]Molecular Neurobiology [missing]DOI: 10.1007/S12035-015-9518-2 [ORCID]
PubMed: 26614510 [ORCID]
RNA sequencing [missing]2015-11-28
Identification of a Novel Coregulator, SH3YL1, That Interacts With the Androgen Receptor N-Terminus[1]Alicia M. Blessing, [2]Sathya Ganesan, [3]Kimal Rajapakshe, [4]Ying Ying Sung, [5]Lakshmi Reddy Bollu, [6]Yan Shi, [7]Edwin Cheung, [8]Cristian Coarfa, [9]Jeffrey T Chang, [10]Donald P McDonnell, [11]Daniel E Frigo [Full author list]Molecular Endocrinology [missing]DOI: 10.1210/ME.2015-1079 [ORCID]
PubMed: 26305679 [ORCID]
SH3 domain [missing]2015-08-25
Dissecting the heterogeneity of skin gene expression patterns in systemic sclerosis[1]Shervin Assassi, [2]William R Swindell, [3]Minghua Wu, [4]Filemon D Tan, [5]Dinesh Khanna, [6]Daniel E Furst, [7]Donald P Tashkin, [8]Richard R Jahan-Tigh, [9]Maureen D Mayes, [10]Johann E Gudjonsson, [11]Jeffrey T Chang [Full author list]Arthritis & Rheumatology [missing]DOI: 10.1002/ART.39289 [ORCID]
PubMed: 26238292 [ORCID]
heterogeneity [missing]2015-08-03
CDKL2 promotes epithelial-mesenchymal transition and breast cancer progression[1]Linna Li, [2]Chunping Liu, [3]Robert J Amato, [4]Jeffrey T Chang, [5]Guangwei Du, [6]Wenliang Li [Full author list]Oncotarget [missing]DOI: 10.18632/ONCOTARGET.2535 [ORCID]
PubMed: 25333262 [ORCID]
2014-11-01
Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data[1]Emily Lu, [2]Miguel-Angel Elizondo-Riojas, [3]Jeffrey T Chang, [4]David E. Volk [Full author list]Biochemistry [missing]DOI: 10.1021/BI500443E [ORCID]
PubMed: 24866698 [ORCID]
software [missing]; sequence alignment [missing]2014-05-29
p38 MAPK inhibits breast cancer metastasis through regulation of stromal expansion.[1]Bangxing Hong, [2]Haiyan Li, [3]Mingjun Zhang, [4]Jingda Xu, [5]Yong Lu, [6]Yuhuan Zheng, [7]Jianfei Qian, [8]Jeffrey T Chang, [9]Jing Yang, [10]Qing Yi [Full author list]International Journal of Cancer [missing]DOI: 10.1002/IJC.28958 [ORCID]
PubMed: 24806617 [ORCID]
cancer metastasis [missing]2014-05-16
A field guide to genomics research[1]Andrea H Bild, [2]Jeffrey T Chang, [3]W Evan Johnson, [4]Stephen R Piccolo [Full author list]PLOS Biology [missing]DOI: 10.1371/JOURNAL.PBIO.1001744 [ORCID]
PubMed: 24409093 [ORCID]
genomics [missing]2014-01-01
Cross-platform prediction of gene expression signatures[1]Shu-Hong Lin, [2]Lauren Beane, [3]Dawn Chasse, [4]Kevin Zhu, [5]Bernard Mathey-Prevot, [6]Jeffrey T Chang [Full author list]PLOS One [missing]DOI: 10.1371/JOURNAL.PONE.0079228 [ORCID]
PubMed: 24244455 [ORCID]
2013-11-14
Deriving transcriptional programs and functional processes from gene expression databases[1]Jeffrey T Chang [Full author list]Bioinformatics [missing]DOI: 10.1093/BIOINFORMATICS/BTS112 [ORCID]
PubMed: 22408194 [ORCID]
2012-03-08
Biopython: freely available Python tools for computational molecular biology and bioinformatics[1]Peter J Cock, [2]Tiago Antao, [3]Jeffrey T Chang, [4]Brad Chapman, [5]Cymon John Cox, [6]Andrew Dalke, [7]Iddo Friedberg, [8]Thomas Hamelryck, [9]Frank Kauff, [10]Bartek Wilczynski, [11]Michiel J L de Hoon [Full author list]Bioinformatics [missing]DOI: 10.1093/BIOINFORMATICS/BTP163 [ORCID]
PubMed: 19304878 [ORCID]
molecular biology [missing]; bioinformatics [missing]; computational biology [missing]2009-03-20
GATHER: a systems approach to interpreting genomic signatures.[1]Jeffrey T Chang, [2]Joseph R Nevins [Full author list]Bioinformatics [missing]DOI: 10.1093/BIOINFORMATICS/BTL483 [ORCID]
PubMed: 17000751 [ORCID]
2006-09-25

Potential author items

NameDescriptionAuthored itemsIdentifiersEmployer(s)
Jeffrey Changresearcher (ORCID 0000-0001-8793-6044)1ORCID: 0000-0001-8793-6044
Jeffrey Changresearcher (ORCID 0000-0001-9342-5072)1ORCID: 0000-0001-9342-5072
Stanford University [missing]
Jeffrey Changbadminton player0
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