FIRST/CO-FIRST AUTHOR PUBLICATION

  1. Timothy I. Shaw*, Li Dong*, Liqing Tian, Chenxi Qian, Yu Liu, Bensheng Ju, Anthony High, Kanisha Kavdia, Vishwajeeth R. Pagala, Bridget Shaner, Deqing Pei, John Easton, Laura J. Janke, Shaina N. Porter, Xiaotu Ma, Cheng Cheng, Shondra M Pruett-Miller, John Choi, Jiyang Yu, Junmin Peng, Wei Gu, A. Thomas  Look, James R Downing & Jinghui Zhang. Integrative Network Analysis Reveals USP7 Haploinsufficiency Inhibits E-protein Activity in Pediatric T-lineage Acute Lymphoblastic Leukemia (T-ALL). Scientific Reports. Accepted.

 

  1. MingRui Jiaa*, Timothy Shaw*, Xing Zhang, Dong Liu, Ye Shen, Amara E. Ezeamama, Chunfu Yangf, Ming Zhang#. Decoding noises in HIV computational genotyping. Virology.2017 Sep 14;511:249-255. doi: 10.1016/j.virol.2017.08.031.

 

  1. Haiyan Tan*, Kai Yang*, Yuxin Li*, Timothy I. Shaw*, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng#, Hongbo Chi#. Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation. Immunity. 2017 Mar 21;46(3):488-503. doi: 10.1016/j.immuni.2017.02.010.

 

  1. Kelvin Wong*, Timothy I. Shaw*,Adelumola Oladeinde, Travis Glenn, Brian Oakley, Marirosa Molina#. Microbiome changes in freshly deposited cowpats under field conditions. Front Microbiol.2016 Apr 13;7:500. doi: 10.3389/fmicb.2016.00500.

 

  1. Timothy I. Shaw, Ming Zhang#. HIV N-linked Glycosylation Site Analyzer and Its Further Usage as Alignment Anchors. Nucleic Acids Res. 2013 Jul 1;41(Web Server issue):W454-8. doi: 10.1093/nar/gkt472

 

  1. Timothy I. Shaw, Ruan Zheng, Travis Glenn, Liang Liu#. STRAW: Species Tree Analysis Web server. Nucleic Acids Res.2013 Jul 1;41(Web Server issue):W238-41. doi: 10.1093/nar/gkt377

 

  1. Timothy I. Shaw, Anuj Srivastava, Wen-Chi Chou, Liang Liu, Ann Hawkinson, Travis C. Glenn, Rick Adams and Tony Schountz#.  Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis), PLoS One.2012;7(11):e48472. doi: 10.1371/journal.pone.0048472.

 

  1. Timothy I. Shaw#, Amir Manzour, Yingfeng Wang, Russell Malmberg, Liming Cai#. Analyzing modular RNA structure reveals low global structural entropy in microRNA sequence. (Invited) J Bioinform Comput Biol. 2011 Apr;9(2):283-98.

(* Co-First Author; # Corresponding Author)

CONTRIBUTING AUTHOR PUBLICATION

  1. Jessica Wagner, Elizabeth Wickman, Timothy I Shaw, Alejandro Allo Anido, Deanna Langfitt, Jinghui Zhang, Shaina N Porter, Shondra M Pruett-Miller, Heather Tillman, Giedre Krenciute, Stephen Gottschalk. Antitumor effects of CAR T cells redirected to the EDB splice variant of fibronectin.Cancer Immunol Res. 2020 Dec 22;. doi: 10.1158/2326-6066.CIR-20-0280. 

 

  1. Dalia Haydar, Haley Houke, Jason Chiang, Zhongzhen, Zelda Odé, Kenneth Caldwell, Xiaoyun Zhu, Kimberley S Mercer, Jennifer L Stripay, Timothy I Shaw, Peter Vogel, Christopher DeRenzo, Suzanne J Baker, Martine F Roussel, Stephen Gottschalk, Giedre Krenciute.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. Neuro-Oncol. 2020 Dec 15;. doi: 10.1093/neuonc/noaa278. 

 

  1. Christopher Trent Brewer, Kiran Kodali, Jing Wu, Timothy I Shaw, Junmin Peng, Taosheng Chen. Toxicoproteomic Profiling of hPXRTransgenic Mice Treated with Rifampicin and Isoniazid. Cells.2020 Jul 9;9(7). doi: 10.3390/cells9071654. PubMed PMID: 32660103; PubMed Central PMCID: PMC7407182.
  2. Xusheng Wang, Ji-Hoon Cho, Suresh Poudel, Yuxin Li, Drew R Jones, Timothy I Shaw, Haiyan Tan, Boer Xie, Junmin Peng. JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics. Metabolites. 2020 May 12;10(5):190. doi: 10.3390/metabo10050190.

 

  1. Bing Bai, Xusheng Wang, Yuxin Li, Ping-Chung Chen, Kaiwen Yu, Kaushik Kumar Dey, Jay M. Yarbro, Xian Han, Brianna M. Lutz, Shuquan Rao, Yun Jiao, Jeffrey M. Sifford, Jonghee Han, Minghui Wang, Haiyan Tan, Timothy I. Shaw, Ji-Hoon Cho, Suiping Zhou, Hong Wang, Mingming Niu, Ariana Mancieri, Kaitlynn Messler, Xiaojun Sun, Zhiping Wu, Vishwajeeth Pagala, Anthony A. High, Wenjian Bi, Hui Zhang, Hongbo Chi, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Gang Yu and Junmin Peng. Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression. Neuron. 2020 May 20;106(4):700. doi: 10.1016/j.neuron.2020.04.031

 

  1. Travis C. Glenn, Todd W. Pierson, Natalia J. Bayona-Vásquez, Troy J. Kieran, Sandra L. Hoffberg, Jesse C. Thomas IV, Daniel E. Lefever, John W. Finger, Bei Gao, Xiaoming Bian, Swarnali Louha, Ramya T. Kolli, Kerin E. Bentley, Julie Rushmore, Kelvin Wong, Timothy I. Shaw, Michael J. Rothrock Jr, Anna M. McKee, Tai L. Guo, Rodney Mauricio, Marirosa Molina, Brian S. Cummings, Lawrence H. Lash, Kun Lu, Gregory S. Gilbert, Stephen P. Hubbell, Brant C. Faircloth. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ. 2019 Oct 11;7:e7786. doi: 10.7717/peerj.7786. eCollection 2019.

 

  1. Hong Wang, Alexander K. Diaz, Timothy I. Shaw,Yuxin Li, Mingming Niu, Ji-Hoon Cho, Barbara S. Paugh, Yang Zhang, Jeffrey Sifford, Bing Bai, Zhiping Wu, Haiyan Tan, Suiping Zhou, Laura D. Hover, Heather S. Tillman, Abbas Shirinifard, Suresh Thiagarajan, Andras Sablauer, Vishwajeeth Pagala, Anthony A. High, Xusheng Wang, Chunliang Li, Suzanne J. Baker, Junmin Peng. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nature Communications. 2019 Aug 16. 10 (1), 3718. doi.org/10.1038/s41467-019-11661-4

 

  1. Liam C Hunt, Jared Stover, Benard Haugen, Timothy I Shaw,Yuxin Li, Vishwajeeth R Pagala, David Finkelstein, Elisabeth R Barton, Yiping Fan, Myriam Labelle, Junmin Peng, Fabio Demontis. A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice. Cell Rep. 2019 Jul 30;28(5):1268-1281.e6. doi: 10.1016/j.celrep.2019.06.094.

 

  1. Bo Wang, Brian A Maxwell, Joung Hyuck Joo, Youngdae Gwon, James Messing, Ashutosh Mishra, Timothy I Shaw, Amber L Ward, Honghu Quan, Sadie Miki Sakurada, Shondra M Pruett-Miller, Tulio Bertorini, Peter Vogel, Hong Joo Kim, Junmin Peng, J Paul Taylor, Mondira Kundu. ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97. Mol Cell. 2019 Apr 3. pii: S1097-2765(19)30231-X. doi: 10.1016/j.molcel.2019.03.027

 

  1. Andre B Silveira, Lawryn H Kasper, Yiping Fan, Hongjian Jin, Gang Wu, Timothy I Shaw, Xiaoyang Zhu, Jon D Larson, John Easton, Ying Shao, Donald A Yergeau, Celeste Rosencrance, Kristy Boggs, Michael C Rusch, Liang Ding, Junyang Zhang, David Finkelstein, Rachel M Noyes, Brent L Russell, Beisi Xu, Alberto Broniscer, Cynthia Wetmore, Stanley B Pounds, David W Ellison, Jinghui Zhang, Suzanne J. Baker. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol.2019 Feb 15. doi: 10.1007/s00401-019-01975-4. 

 

  1. Jon D Larson, Lawryn H Kasper, Barbara S Paugh, Hongjian Jin, Gang Wu, Chang-Hyuk Kwon, Yiping Fan, Timothy I Shaw, André B Silveira, Chunxu Qu, Raymond Xu, Xiaoyan Zhu, Junyuan Zhang, Helen R Russell, Jennifer L Peters, David Finkelstein, Beisi Xu, Tong Lin, Christopher L Tinkle, Zoltan Patay, Arzu Onar-Thomas, Stanley B Pounds, Peter J McKinnon, David W Ellison, Jinghui Zhang, Suzanne J Baker. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell. 2018 Dec 11. pii: S1535-6108(18)30536-1. doi: 10.1016/j.ccell.2018.11.015

 

  1. Ke Xu, Liang Ding, Ti-Cheng Chang, Ying Shao, Jason Chiang, Heather Mulder, Shuoguo Wang, Tim I Shaw, Ji Wen, Laura Hover, Clay McLeod, Yong-Dong Wang, John Easton, Michael Rusch, James Dalton, James R Downing, David W Ellison#, Jinghui Zhang#, Suzanne J Baker#, Gang Wu#. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol.2018 Sep 28. doi: 10.1007/s00401-018-1912-1.

 

  1. Elizabeth Stewart*, Justina McEvoy*, Hong Wang*, Xiang Chen*, Victoria Honnell, Monica Ocarz, Brittney Gordon, Jason Dapper, Kaley Blankenship, Yanling Yang, Yuxin Li, Timothy I Shaw, Ji-Hoon Cho, Xusheng Wang, Beisi Xu, Pankaj Gupta, Yiping Fan, Yu Liu, Michael Rusch, Lyra Griffiths, Jongrye Jeon, Burgess B Freeman III, Michael R Clay, Alberto Pappo, John Easton, Sheila Shurtleff, Anang Shelat, Xin Zhou, Kristy Boggs, Heather Mulder, Donald Yergeau, Armita Bahrami, Elaine R Mardis, Richard K Wilson, Jinghui Zhang, Junmin Peng, James R Downing, Michael A Dyer. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell. 2018 Aug 23. https://doi.org/10.1016/j.ccell.2018.07.012

 

  1. Boer Xie*, Yuanyuan Wang*, Drew R. Jones*, Kaushik Kumar Dey, Xusheng Wang, Yuxin Li, Ji-Hoon Cho, Timothy I Shaw, Haiyan Tan, and Junmin Peng#. Isotope Labeling-assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling.Anal Chem. 2018 Jun 8. doi: 10.1021/acs.analchem.8b01591

 

  1. Gang Wu*, Liying Fan*, Michael N Edmondson,Timothy Shaw, Kristy Boggs, John Easton, Michael C Rusch, Thomas R Webb, Jinghui Zhang, Philip M Potter#. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA. 2018 May 29. pii: rna.065383.117. doi: 10.1261/rna.065383.117.

 

  1. Xusheng Wang*, Drew R Jones*, Timothy I Shaw, Ji-Hoon Cho, Yuanyuan Wang, Haiyan Tan, Boer Xie, Suiping Zhou, Yuxin Li, Junmin Peng#. Target-decoy Based False Discovery Rate Estimation for Large-scale Metabolite Identification. Journal of proteome research.2018 May 23. 10.1021/acs.jproteome.8b00019.

 

  1. Elena Kozina, Shankar Sadasivan, Yun Jiao, Yuchen Dou, Zhijun Ma, Haiyan Tan, Kiran Kodali, Timothy Shaw, Junmin Peng, Richard J Smeyne#. Mutant LRRK2 mediates peripheral and central immune responses leading to neurodegeneration in vivo. Brain. 2018, Mar 21. awy077, https://doi.org/10.1093/brain/awy077

 

  1. Gustavo Palacios, Timothy I. Shaw,Yongjin Li. Ravi K Singh, Marc Valentine, John T. Sandlund, Megan S.Lim, Charles G. Mullighan, Vasiliki Leventaki#. A new variant of Anaplastic Lymphoma Kinase(ALK) fusion in a case of Anaplastic Large Cell Lymphoma involving EEF1G, a subunit of the elongation factor-1 complex. Leukemia. 2016 Nov 14. doi: 10.1038/leu.2016.331.

 

  1. Kyung-Ha Lee*, Peipei Zhang*, Hong Joo Kim*, Mohona Sarkar, Diana Mitrea, Brian Freibaum, Jaclyn Cika, MauraCoughlin, James Messing, Amandine Molliex, Brian Maxwell, Nam Chul Kim, Jamshid Temirov,Jennifer Moore, Timothy I. Shaw, Bing Bai, Junmin Peng, Richard Kriwacki, Paul J.Taylor#. C9orf72 dipeptide repeats impair the assembly, dynamics and function of membrane-lessorganelles. Cell. 2016 Oct 20;167(3):774-788.e17. doi: 10.1016/j.cell.2016.10.002

 

  1. Yuxin Li, Xusheng Wang, Zhiping Wu, Bing Bai, Ji-Hoon Cho, Timothy I. Shaw, Hong Wang, Suiping Zhou, Thomas Beach, Gang Wu, Jinghui Zhang, Junmin Peng#. JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. J Proteome Res.2016 Jul 1;15(7):2309-20. doi: 10.1021/acs.jproteome.6b00344.

 

  1. Joung Hyuck Joo*, Bo Wang*, Elisa Frankel, Liang Ge, Lu Xu, Rekha Iyengar, XiuJie Li-Harms, Christopher Wright, Timothy I. Shaw,Tullia Lindsten, Douglas R. Green, Junmin Peng, Linda M. Hendershot, Fusun Kilic, Ji Ying Sze, Anjon Audhya, Mondira Kundu#. The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis. Mol Cell.2016 May 19;62(4):491-506. doi: 10.1016/j.molcel.2016.04.020.

 

  1. Joseph Leo Mertz, Haiyan Tan, Vishwajeeth Pagala, Bing Bai, Ping-Chung Chen, Yuxin Li, Ji-Hoon Cho, Timothy I. Shaw, Xusheng Wang, Junmin Peng#. Sequential elution interactome analysis of the Mind bomb 1 ubiquitin ligase reveals a novel role in dendritic spine outgrowth.  Mol Cell Proteomics.2015 Jul;14(7):1898-910. doi: 10.1074/mcp.M114.045898. Epub 2015 Apr 30.

 

  1. Bradnam, K.R., … Timothy I. Shaw… and 89 other co-authors, and Korf, I.K#., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience.2013 Jul 22;2(1):10.

 

  1. Tony Schountz#, Timothy I. Shaw, Travis Glenn, Heinz Feldmann and Joseph Prescott.  Expression Profiling of Lymph Node Cells from Deer Mice Infected with Andes Virus.  BMC Immunol. 2013 Apr 9;14(1):18.

 

  1. Amir Manzour#, Yingfeng Wang, Timothy I. Shaw, Russel L. Malmberg.  (2012) Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA.  J Theor Biol. 2012 Nov 14. pii: S0022-5193(12)00562-0. doi: 10.1016/j.jtbi.2012.10.023.

 

  1. Anuj Srivastava*, Kevin Winker*, Timothy I. Shaw, Kenneth L. Jones, and Travis C. Glenn# (2012) Transcriptome analysis of a North American songbird, Melospiza melodia, DNA Research2012;19(4):325-33

 

  1. Dent Earl, Keith Bradnam, ....., Timothy I. Shaw,....., Ian Korf, Benedict Paten#, (2011), Assemblathon 1: A competitive assessment of de novo short read assembly methods, Genome Research. 21, 2224-2241.

 

  1. Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Yingwai Li., Russell Malmberg, and Liming Cai#. (2011) Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds, (Invited) BMC Bioinformatics.2012 Apr 12;13 Suppl 5:S1. 

 

  1. Russell L. Malmberg, Timothy I. Shaw, Liming Cai#. RNApasta: a tool for analysis of RNA structural alignments. Int J Bioinform Res Appl. 2010;6(6):571-83.