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BatchFLEX: feature-level equalization of X-batch.
Published in:
Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae587
By:
- Davis, Joshua T;
- Obermayer, Alyssa N;
- Soupir, Alex C;
- Hesterberg, Rebecca S;
- Duong, Thac;
- Yang, Ching-Yao;
- Dao, Ken Phong;
- Manley, Brandon J;
- Grass, G Daniel;
- Avram, Dorina;
- Rodriguez, Paulo C;
- Fridley, Brooke L;
- Yu, Xiaoqing;
- Teng, Mingxiang;
- Wang, Xuefeng;
- Shaw, Timothy I
Publication type:
Article
Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37438-4
By:
- Liu, Yanling;
- Klein, Jonathon;
- Bajpai, Richa;
- Dong, Li;
- Tran, Quang;
- Kolekar, Pandurang;
- Smith, Jenny L.;
- Ries, Rhonda E.;
- Huang, Benjamin J.;
- Wang, Yi-Cheng;
- Alonzo, Todd A.;
- Tian, Liqing;
- Mulder, Heather L.;
- Shaw, Timothy I.;
- Ma, Jing;
- Walsh, Michael P.;
- Song, Guangchun;
- Westover, Tamara;
- Autry, Robert J.;
- Gout, Alexander M.
Publication type:
Article
JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics.
Published in:
Metabolites (2218-1989), 2020, v. 10, n. 5, p. 190, doi. 10.3390/metabo10050190
By:
- Wang, Xusheng;
- Cho, Ji-Hoon;
- Poudel, Suresh;
- Li, Yuxin;
- Jones, Drew R.;
- Shaw, Timothy I.;
- Tan, Haiyan;
- Xie, Boer;
- Peng, Junmin
Publication type:
Article
HIV N-linked glycosylation site analyzer and its further usage in anchored alignment.
Published in:
Nucleic Acids Research, 2013, v. 41, p. W454, doi. 10.1093/nar/gkt472
By:
- Shaw, Timothy I.;
- Ming Zhang
Publication type:
Article
STRAW: Species TRee Analysis Web server.
Published in:
Nucleic Acids Research, 2013, v. 41, p. W238, doi. 10.1093/nar/gkt377
By:
- Shaw, Timothy I.;
- Ruan, Zheng;
- Glenn, Travis C.;
- Liang Liu
Publication type:
Article
Expression profiling of lymph node cells from deer mice infected with Andes virus.
Published in:
BMC Immunology, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2172-14-18
By:
- Schountz, Tony;
- Shaw, Timothy I.;
- Glenn, Travis C.;
- Feldmann, Heinz;
- Prescott, Joseph
Publication type:
Article
Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children's Oncology Group AREN18B5-Q.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43730-0
By:
- Murphy, Andrew J.;
- Cheng, Changde;
- Williams, Justin;
- Shaw, Timothy I.;
- Pinto, Emilia M.;
- Dieseldorff-Jones, Karissa;
- Brzezinski, Jack;
- Renfro, Lindsay A.;
- Tornwall, Brett;
- Huff, Vicki;
- Hong, Andrew L.;
- Mullen, Elizabeth A.;
- Crompton, Brian;
- Dome, Jeffrey S.;
- Fernandez, Conrad V.;
- Geller, James I.;
- Ehrlich, Peter F.;
- Mulder, Heather;
- Oak, Ninad;
- Maciezsek, Jamie
Publication type:
Article
Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis).
Published in:
PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0048472
By:
- Shaw, Timothy I.;
- Srivastava, Anuj;
- Wen-Chi Chou;
- Liang Liu;
- Hawkinson, Ann;
- Glenn, Travis C.;
- Adams, Rick;
- Schountz, Tony
Publication type:
Article
PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing.
Published in:
BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05393-y
By:
- Obermayer, Alyssa N.;
- Chang, Darwin;
- Nobles, Gabrielle;
- Teng, Mingxiang;
- Tan, Aik-Choon;
- Wang, Xuefeng;
- Chen, Y. Ann;
- Eschrich, Steven;
- Rodriguez, Paulo C.;
- Grass, G. Daniel;
- Meshinchi, Soheil;
- Tarhini, Ahmad;
- Chen, Dung-tsa;
- Shaw, Timothy I.
Publication type:
Article
Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11661-4
By:
- Wang, Hong;
- Diaz, Alexander K.;
- Shaw, Timothy I.;
- Li, Yuxin;
- Niu, Mingming;
- Cho, Ji-Hoon;
- Paugh, Barbara S.;
- Zhang, Yang;
- Sifford, Jeffrey;
- Bai, Bing;
- Wu, Zhiping;
- Tan, Haiyan;
- Zhou, Suiping;
- Hover, Laura D.;
- Tillman, Heather S.;
- Shirinifard, Abbas;
- Thiagarajan, Suresh;
- Sablauer, Andras;
- Pagala, Vishwajeeth;
- High, Anthony A.
Publication type:
Article
Metabolomic and transcriptomic analysis reveals endogenous substrates and metabolic adaptation in rats lacking Abcg2 and Abcb1a transporters.
Published in:
PLoS ONE, 2021, v. 16, n. 7, p. 1, doi. 10.1371/journal.pone.0253852
By:
- Ganguly, Samit;
- Finkelstein, David;
- Shaw, Timothy I.;
- Michalek, Ryan D.;
- Zorn, Kimberly M.;
- Ekins, Sean;
- Yasuda, Kazuto;
- Fukuda, Yu;
- Schuetz, John D.;
- Mukherjee, Kamalika;
- Schuetz, Erin G.
Publication type:
Article
Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds.
Published in:
BMC Bioinformatics, 2012, v. 13, n. Suppl 5, p. 1, doi. 10.1186/1471-2105-13-S5-S1
By:
- Wang, Yingfeng;
- Manzour, Amir;
- Shareghi, Pooya;
- Shaw, Timothy I;
- Li, Ying-Wai;
- Malmberg, Russell L;
- Cai, Liming
Publication type:
Article
Cell-surface antigen profiling of pediatric brain tumors: B7-H3 is consistently expressed and can be targeted via local or systemic CAR T-cell delivery.
Published in:
Neuro-Oncology, 2021, v. 23, n. 6, p. 999, doi. 10.1093/neuonc/noaa278
By:
- Haydar, Dalia;
- Houke, Haley;
- Chiang, Jason;
- Yi, Zhongzhen;
- Odé, Zelda;
- Caldwell, Kenneth;
- Zhu, Xiaoyan;
- Mercer, Kimberly S;
- Stripay, Jennifer L;
- Shaw, Timothy I;
- Vogel, Peter;
- DeRenzo, Christopher;
- Baker, Suzanne J;
- Roussel, Martine F;
- Gottschalk, Stephen;
- Krenciute, Giedre
Publication type:
Article
The landscape of coding RNA editing events in pediatric cancer.
Published in:
2021
By:
- Wen, Ji;
- Rusch, Michael;
- Brady, Samuel W.;
- Shao, Ying;
- Edmonson, Michael N.;
- Shaw, Timothy I.;
- Powers, Brent B.;
- Tian, Liqing;
- Easton, John;
- Mullighan, Charles G.;
- Gruber, Tanja;
- Ellison, David;
- Zhang, Jinghui
Publication type:
journal article
Bcl11b sustains multipotency and restricts effector programs of intestinal-resident memory CD8<sup>+</sup> T cells.
Published in:
Science Immunology, 2023, v. 8, n. 82, p. 1, doi. 10.1126/sciimmunol.abn0484
By:
- Helm, Eric Y.;
- Zelenka, Tomas;
- Cismasiu, Valeriu B.;
- Islam, Shamima;
- Silvane, Leonardo;
- Zitti, Beatrice;
- Holmes, Tim D.;
- Drashansky, Theodore T.;
- Kwiatkowski, Alexander J.;
- Tao, Christine;
- Dean, Joseph;
- Obermayer, Alyssa N.;
- Chen, Xianghong;
- Keselowsky, Benjamin G.;
- Zhang, Weizhou;
- Huo, Zhiguang;
- Zhou, Liang;
- Sheridan, Brian S.;
- Conejo-Garcia, Jose R.;
- Shaw, Timothy I.
Publication type:
Article
Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL).
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-84647-2
By:
- Shaw, Timothy I.;
- Dong, Li;
- Tian, Liqing;
- Qian, Chenxi;
- Liu, Yu;
- Ju, Bensheng;
- High, Anthony;
- Kavdia, Kanisha;
- Pagala, Vishwajeeth R.;
- Shaner, Bridget;
- Pei, Deqing;
- Easton, John;
- Janke, Laura J.;
- Porter, Shaina N.;
- Ma, Xiaotu;
- Cheng, Cheng;
- Pruett-Miller, Shondra M.;
- Choi, John;
- Yu, Jiyang;
- Peng, Junmin
Publication type:
Article
DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets.
Published in:
Biology (2079-7737), 2022, v. 11, n. 2, p. 260, doi. 10.3390/biology11020260
By:
- Obermayer, Alyssa;
- Dong, Li;
- Hu, Qianqian;
- Golden, Michael;
- Noble, Jerald D.;
- Rodriguez, Paulo;
- Robinson, Timothy J.;
- Teng, Mingxiang;
- Tan, Aik-Choon;
- Shaw, Timothy I.
Publication type:
Article
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.
Published in:
PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011873
By:
- Liu, Xiang;
- Gillis, Nancy;
- Jiang, Chang;
- McCofie, Anthony;
- Shaw, Timothy I.;
- Tan, Aik-Choon;
- Zhao, Bo;
- Wan, Lixin;
- Duckett, Derek R.;
- Teng, Mingxiang
Publication type:
Article
Correction to: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo.
Published in:
2019
By:
- Silveira, André B.;
- Kasper, Lawryn H.;
- Zhu, Xiaoyan;
- Larson, Jon D.;
- Zhang, Junyuan;
- Noyes, Rachel M.;
- Russell, Brent L.;
- Baker, Suzanne J.;
- Fan, Yiping;
- Jin, Hongjian;
- Wu, Gang;
- Shaw, Timothy I.;
- Easton, John;
- Shao, Ying;
- Yergeau, Donald A.;
- Rosencrance, Celeste;
- Boggs, Kristy;
- Rusch, Michael C.;
- Ding, Liang;
- Finkelstein, David
Publication type:
Correction Notice
H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo.
Published in:
Acta Neuropathologica, 2019, v. 137, n. 4, p. 637, doi. 10.1007/s00401-019-01975-4
By:
- Silveira, André B.;
- Kasper, Lawryn H.;
- Zhu, Xiaoyan;
- Larson, Jon D.;
- Zhang, Junyuan;
- Noyes, Rachel M.;
- Russell, Brent L.;
- Baker, Suzanne J.;
- Fan, Yiping;
- Jin, Hongjian;
- Wu, Gang;
- Shaw, Timothy I.;
- Easton, John;
- Shao, Ying;
- Yergeau, Donald A.;
- Rosencrance, Celeste;
- Boggs, Kristy;
- Rusch, Michael C.;
- Ding, Liang;
- Finkelstein, David
Publication type:
Article
Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).
Published in:
PeerJ, 2019, p. 1, doi. 10.7717/peerj.7786
By:
- Glenn, Travis C.;
- Pierson, Todd W.;
- Bayona-Vásquez, Natalia J.;
- Kieran, Troy J.;
- Hoffberg, Sandra L.;
- Thomas IV, Jesse C.;
- Lefever, Daniel E.;
- Finger, John W.;
- Bei Gao;
- Xiaoming Bian;
- Louha, Swarnali;
- Kolli, Ramya T.;
- Bentley, Kerin E.;
- Rushmore, Julie;
- Wong, Kelvin;
- Shaw, Timothy I.;
- Rothrock Jr, Michael J.;
- McKee, Anna M.;
- Guo, Tai L.;
- Mauricio, Rodney
Publication type:
Article
Toxicoproteomic Profiling of hPXR Transgenic Mice Treated with Rifampicin and Isoniazid.
Published in:
Cells (2073-4409), 2020, v. 9, n. 7, p. 1654, doi. 10.3390/cells9071654
By:
- Brewer, Christopher Trent;
- Kodali, Kiran;
- Wu, Jing;
- Shaw, Timothy I.;
- Peng, Junmin;
- Chen, Taosheng
Publication type:
Article
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers.
Published in:
Nucleic Acids Research, 2022, v. 50, n. 6, p. 3115, doi. 10.1093/nar/gkac141
By:
- Liu, Xiang;
- Zhao, Bo;
- Shaw, Timothy I;
- Fridley, Brooke L;
- Duckett, Derek R;
- Tan, Aik Choon;
- Teng, Mingxiang
Publication type:
Article
Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients.
Published in:
Frontiers in Oncology, 2022, v. 12, p. 1, doi. 10.3389/fonc.2022.1051487
By:
- Shaw, Timothy I.;
- Bi Zhao;
- Yuxin Li;
- Hong Wang;
- Liang Wang;
- Manley, Brandon;
- Stewart, Paul A.;
- Karolak, Aleksandra
Publication type:
Article
Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions.
Published in:
Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00500
By:
- Molina, Marirosa;
- Wong, Kelvin;
- Oladeinde, Adelumola;
- Shaw, Timothy I.;
- Glenn, Travis C.;
- Oakley, Brian
Publication type:
Article
ANALYZING MODULAR RNA STRUCTURE REVEALS LOW GLOBAL STRUCTURAL ENTROPY IN MICRORNA SEQUENCE.
Published in:
Journal of Bioinformatics & Computational Biology, 2011, v. 9, n. 2, p. 283, doi. 10.1142/S0219720011005495
By:
- SHAW, TIMOTHY I.;
- MANZOUR, AMIR;
- WANG, YINGFENG;
- MALMBERG, RUSSELL L.;
- CAI, LIMING
Publication type:
Article
Transcriptome Analysis of a North American Songbird, Melospiza melodia.
Published in:
DNA Research, 2012, v. 19, n. 4, p. 325, doi. 10.1093/dnares/dss015
By:
- Srivastava, Anuj;
- Winker, Kevin;
- Shaw, Timothy I.;
- Jones, Kenneth L.;
- Glenn, Travis C.
Publication type:
Article

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