An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.

Aik Choon Tan

Xiang Liu Nancy Gillis Chang Jiang Anthony McCofie Timothy I. Shaw Aik Choon Tan Bo Zhao Lixin Wan Derek R. Duckett Mingxiang Teng An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. 2024 February 20 PLoS Comput. Biol. 2 https://doi.org/10.1371/journal.pcbi.1011873 https://www.wikidata.org/entity/Q128162216 db/journals/ploscb/ploscb20.html#LiuGJMSTZWDT24

Alyssa N. Obermayer Darwin Chang Gabrielle Nobles Mingxiang Teng Aik Choon Tan Xuefeng Wang Y. Ann Chen Steven Eschrich Paulo C. Rodriguez G. Daniel Grass Soheil Meshinchi Ahmad Tarhini Dung-Tsa Chen Timothy I. Shaw PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. 266 2023 December 24 BMC Bioinform. 1 https://doi.org/10.1186/s12859-023-05393-y https://www.wikidata.org/entity/Q130500339 db/journals/bmcbi/bmcbi24.html#ObermayerCNTTWCERGMTCS23

Ramin Homayouni Prashanti Manda Aik Choon Tan Zhaohui S. Qin Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference. 2023 January 6 Frontiers Big Data https://doi.org/10.3389/fdata.2023.1156811 db/journals/fdata/fdata6.html#HomayouniMTQ23

Ching-Nung Lin Christine H. Chung Aik Choon Tan NuKit: A deep learning platform for fast nucleus segmentation of histopathological images. 2350002:1-2350002:14 2023 February 21 J. Bioinform. Comput. Biol. 1 https://doi.org/10.1142/S0219720023500026 db/journals/jbcb/jbcb21.html#LinCT23

Mengyu Xie Kyubum Lee John H. Lockhart Scott D. Cukras Rodrigo Carvajal Amer A. Beg Elsa R. Flores Mingxiang Teng Christine H. Chung Aik Choon Tan TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. 3681-3683 2021 37 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btab244 db/journals/bioinformatics/bioinformatics37.html#XieLLCCBFTCT21

Kyubum Lee John H. Lockhart Mengyu Xie Ritu Chaudhary Robbert J. C. Slebos Elsa R. Flores Christine H. Chung Aik Choon Tan Deep Learning of Histopathology Images at the Single Cell Level. 754641 2021 4 Frontiers Artif. Intell. https://doi.org/10.3389/frai.2021.754641 db/journals/frai/frai4.html#LeeLXCSFCT21

Zhaoping Xiong Minji Jeon Robert J. Allaway Jaewoo Kang Donghyeon Park Jinhyuk Lee Hwisang Jeon Miyoung Ko Hualiang Jiang Mingyue Zheng Aik Choon Tan Xindi Guo Multi-Targeting Drug DREAM Challenge Community Kristen K. Dang Alexander Tropsha Chana Hecht Tirtha K. Das Heather A. Carlson Ruben Abagyan Justin Guinney Avner Schlessinger Ross L. Cagan Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. 2021 17 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1009302 https://www.wikidata.org/entity/Q125860030 db/journals/ploscb/ploscb17.html#XiongJAKPLJKJZT21

Minji Jeon Donghyeon Park Jinhyuk Lee Hwisang Jeon Miyoung Ko Sunkyu Kim Yonghwa Choi Aik Choon Tan Jaewoo Kang ReSimNet: drug response similarity prediction using Siamese neural networks. 5249-5256 2019 35 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btz411 https://www.wikidata.org/entity/Q92213979 db/journals/bioinformatics/bioinformatics35.html#JeonPLJKKCTK19

Minjae Yoo Jimin Shin Hyunmin Kim Jihye Kim 0004 Jaewoo Kang Aik Choon Tan Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map. 33-40 2019 174 Comput. Methods Programs Biomed. https://doi.org/10.1016/j.cmpb.2018.04.002 https://www.wikidata.org/entity/Q88344604 db/journals/cmpb/cmpb174.html#YooSKKKT19

Rani K. Powers Andrew Goodspeed Harrison Pielke-Lombardo Aik Choon Tan James C. Costello GSEA-InContext: identifying novel and common patterns in expression experiments. i555-i564 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty271 https://www.wikidata.org/entity/Q55645886 db/journals/bioinformatics/bioinformatics34.html#PowersGPTC18

Kyubum Lee Byounggun Kim Yonghwa Choi Sunkyu Kim Won-Ho Shin Sunwon Lee Sungjoon Park Seongsoon Kim Aik Choon Tan Jaewoo Kang Deep learning of mutation-gene-drug relations from the literature. 21:1-21:13 2018 19 BMC Bioinform. 1 https://doi.org/10.1186/s12859-018-2029-1 https://www.wikidata.org/entity/Q49449222 db/journals/bmcbi/bmcbi19.html#LeeKCKSLPKTK18

Zongliang Yue Qi Zheng Michael T. Neylon Minjae Yoo Jimin Shin Zhiying Zhao Aik Choon Tan Jake Y. Chen PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. D668-D676 2018 46 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkx1040 https://www.wikidata.org/entity/Q47138916 db/journals/nar/nar46.html#YueZNYSZTC18

Kyubum Lee Sunwon Lee Sungjoon Park Sunkyu Kim Suhkyung Kim Kwanghun Choi Aik Choon Tan Jaewoo Kang BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. 2016 2016 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baw043 https://www.wikidata.org/entity/Q36794964 db/journals/biodb/biodb2016.html#LeeLPKKCTK16

Kyubum Lee Won-Ho Shin Byounggun Kim Sunwon Lee Yonghwa Choi Sunkyu Kim Minji Jeon Aik Choon Tan Jaewoo Kang HiPub: translating PubMed and PMC texts to networks for knowledge discovery. 2886-2888 2016 32 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btw511 https://www.wikidata.org/entity/Q39531508 db/journals/bioinformatics/bioinformatics32.html#LeeSKLCKJTK16

Jennifer Hintzsche Jihye Kim 0004 Vinod Kumar Yadav Carol Amato Steven E. Robinson Eric Seelenfreund Yiqun Shellman Joshua Wisell Allison Applegate Martin McCarter Neil Box John Tentler Subhajyoti De William A. Robinson Aik Choon Tan IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. 721-730 2016 23 J. Am. Medical Informatics Assoc. 4 https://doi.org/10.1093/jamia/ocw022 https://www.wikidata.org/entity/Q37051433 db/journals/jamia/jamia23.html#HintzscheKYARSS16

Minjae Yoo Jimin Shin Jihye Kim 0004 Karen A. Ryall Kyubum Lee Sunwon Lee Minji Jeon Jaewoo Kang Aik Choon Tan DSigDB: drug signatures database for gene set analysis. 3069-3071 2015 31 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btv313 https://www.wikidata.org/entity/Q36344536 db/journals/bioinformatics/bioinformatics31.html#YooSKRLLJKT15

Karen A. Ryall Jimin Shin Minjae Yoo Trista K. Hinz Jihye Kim 0004 Jaewoo Kang Lynn E. Heasley Aik Choon Tan Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. 3799-3806 2015 31 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btv427 https://www.wikidata.org/entity/Q30982375 db/journals/bioinformatics/bioinformatics31.html#RyallSYHKKHT15

Karen A. Ryall Aik Choon Tan Systems biology approaches for advancing the discovery of effective drug combinations. 7 2015 7 J. Cheminformatics https://doi.org/10.1186/s13321-015-0055-9 https://www.wikidata.org/entity/Q27702922 db/journals/jcheminf/jcheminf7.html#RyallT15

Minji Jeon Sunwon Lee Kyubum Lee Aik Choon Tan Jaewoo Kang BEReX: Biomedical Entity-Relationship eXplorer. 135-136 2014 30 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btt598 https://www.wikidata.org/entity/Q35024137 db/journals/bioinformatics/bioinformatics30.html#JeonLLTK14

Jihye Kim 0004 Vihas T. Vasu Rangnath Mishra Katherine R. Singleton Minjae Yoo Sonia M. Leach Eveline Farias-Hesson Robert J. Mason Jaewoo Kang Preveen Ramamoorthy Jeffrey A. Kern Lynn E. Heasley James H. Finigan Aik Choon Tan Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. 2393-2398 2014 30 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btu323 https://www.wikidata.org/entity/Q34103108 db/journals/bioinformatics/bioinformatics30.html#KimVMSYLFMKRKHFT14

Lei Xu 0014 Aik Choon Tan Raimond L. Winslow Donald Geman Merging microarray data from separate breast cancer studies provides a robust prognostic test. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-125 https://www.wikidata.org/entity/Q31147871 db/journals/bmcbi/bmcbi9.html#XuTWG08

Donald Geman Bahman Afsari Aik Choon Tan Daniel Q. Naiman Microarray Classification from Several Two-Gene Expression Comparisons. 583-585 2008 ICMLA https://doi.org/10.1109/ICMLA.2008.152 https://doi.ieeecomputersociety.org/10.1109/ICMLA.2008.152 conf/icmla/2008 db/conf/icmla/icmla2008.html#GemanATN08

Aik Choon Tan Daniel Q. Naiman Lei Xu 0014 Raimond L. Winslow Donald Geman Simple decision rules for classifying human cancers from gene expression profiles. 3896-3904 2005 21 Bioinform. 20 https://doi.org/10.1093/bioinformatics/bti631 https://www.wikidata.org/entity/Q41735339 db/journals/bioinformatics/bioinformatics21.html#TanNXWG05

Lei Xu 0014 Aik Choon Tan Daniel Q. Naiman Donald Geman Raimond L. Winslow Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. 3905-3911 2005 21 Bioinform. 20 https://doi.org/10.1093/bioinformatics/bti647 https://www.wikidata.org/entity/Q31002200 db/journals/bioinformatics/bioinformatics21.html#XuTNGW05

Ali Al-Shahib Chao He Aik Choon Tan Mark A. Girolami David R. Gilbert An Assessment of Feature Relevance in Predicting Protein Function from Sequence. 52-57 https://doi.org/10.1007/978-3-540-28651-6_8 2004 conf/ideal/2004 IDEAL db/conf/ideal/ideal2004.html#Al-ShahibHTGG04 Aik Choon Tan David R. Gilbert An Empirical Comparison of Supervised Machine Learning Techniques in Bioinformatics. 219-222 2003 conf/apbc/2003 APBC http://crpit.scem.westernsydney.edu.au/abstracts/CRPITV19Tan.html db/conf/apbc/apbc2003.html#TanG03 Aik Choon Tan David R. Gilbert Yves Deville Integrative machine learning approach for multi-class SCOP protein fold classification. 153-159 2003 conf/gcb/2003 German Conference on Bioinformatics db/conf/gcb/gcb2003.html#TanGD03 Ruben Abagyan Bahman Afsari Ali Al-Shahib Robert J. Allaway Carol Amato Allison Applegate Amer A. Beg Neil Box Ross L. Cagan Heather A. Carlson Rodrigo Carvajal Darwin Chang Ritu Chaudhary Dung-Tsa Chen Jake Yue ChenJake Y. Chen Y. Ann Chen Kwanghun Choi Yonghwa Choi Christine H. Chung Multi-Targeting Drug DREAM Challenge Community James C. Costello Scott D. Cukras Kristen K. Dang Tirtha K. Das Subhajyoti De Yves Deville Derek R. Duckett Steven Eschrich Eveline Farias-Hesson James H. Finigan Elsa R. Flores Donald Geman David R. Gilbert Nancy Gillis Mark A. Girolami Andrew Goodspeed G. Daniel Grass Justin Guinney Xindi Guo Chao He Lynn E. Heasley Chana Hecht Jennifer Hintzsche Trista K. Hinz Ramin Homayouni Hwisang Jeon Minji Jeon Chang Jiang Hualiang Jiang Jaewoo Kang Jeffrey A. Kern Byounggun Kim Hyunmin Kim Jihye Kim 0004 Seongsoon Kim Suhkyung Kim Sunkyu Kim Miyoung Ko Sonia M. Leach Jinhyuk Lee Kyubum Lee Sunwon Lee Ching-Nung Lin Xiang Liu John H. Lockhart Prashanti Manda Robert J. Mason Martin McCarter Anthony McCofie Soheil MeschinchiSoheil Meshinchi Rangnath Mishra Daniel Q. Naiman Michael T. Neylon Gabrielle Nobles Alyssa N. Obermayer Donghyeon Park Sungjoon Park Harrison Pielke-Lombardo Rani K. Powers Zhaohui S. Qin Preveen Ramamoorthy Steven E. Robinson William A. Robinson Paulo C. Rodriguez Karen A. Ryall Avner Schlessinger Eric Seelenfreund Timothy I. Shaw Yiqun Shellman Jimin Shin Won-Ho Shin Katherine R. Singleton Robbert J. C. Slebos Ahmad Tarhini Mingxiang Teng John Tentler Alexander Tropsha Vihas T. Vasu Lixin Wan Xuefeng Wang Raimond L. Winslow Joshua Wisell Mengyu Xie Zhaoping Xiong Lei Xu 0014 Vinod Kumar Yadav Minjae Yoo Zongliang Yue Bo Zhao Zhiying Zhao Mingyue Zheng Qi Zheng