Timothy Shaw, PhD

Dr. Shaw's research focuses on systems immuno-oncology, particularly in developing computational tools to study immune interactions and associated regulatory networks.  

Associations

• Biostatistics and Bioinformatics
• Immuno-Oncology Program

Education & Training

Graduate:

• University of Georgia, PhD - Bioinformatics
• University of Georgia, PhD - Bioinformatics

  Immunotherapy is emerging as a therapeutic modality, but achieving a durable response remains challenging in many instances. The problem is likely multifactorial and compounded by the complex regulatory network of the immune system. Thus, my research program aims to develop computational methodologies and tools to model these complexities. My program consists of the following three aims: 1) Building an integrative regulatory network of cancer-to-immune interactions and immune suppression. 2) Identifying targetable regulators generated from aim 1. 3) Using a proteo-genomics approach to identify cancer-specific isoforms for immunotherapy. My program will build a comprehensive systems biology resource of immune regulation of cancer, which will leverage multi-omics information derived from hidden-driver analysis, kinase activity, protein isoforms, and protein-protein interactions. Such an integrative approach presents opportunities to identify targets for immunotherapy or other therapeutic intervention.  

• Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng M. An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS Comput Biol. 2024 Feb.20(2):e1011873. Pubmedid: 38335222. Pmcid: PMC10883583.
• Peak T, Tian Y, Patel A, Shaw T, Obermayer A, Laborde J, Kim Y, Johnson J, Stewart P, Fang B, Teer JK, Koomen J, Berglund A, Marchion D, Francis N, Echevarria PR, Dhillon J, Clark N, Chang A, Sexton W, Zemp L, Chahoud J, Wang L, Manley B. Pathogenic Roles for RNASET2 in Clear Cell Renal Cell Carcinoma. Lab Invest. 2024 Feb.104(5):102041. Pubmedid: 38431116.
• Neault M, Lebert-Ghali CÉ, Fournier M, Capdevielle C, Garfinkle EAR, Obermayer A, Cotton A, Boulay K, Sawchyn C, St-Amand S, Nguyen KH, Assaf B, Mercier FE, Delisle JS, Drobetsky EA, Hulea L, Shaw TI, Zuber J, Gruber TA, Melichar HJ, Mallette FA. CBFA2T3-GLIS2-dependent pediatric acute megakaryoblastic leukemia is driven by GLIS2 and sensitive to navitoclax. Cell Rep. 2023 Sep.42(9):113084. Pubmedid: 37716355.
• Obermayer A, Chang D, Nobles G, Teng M, Tan AC, Wang X, Eschrich S, Rodriguez P, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw T. DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components. Res Sq. 2023 Mar. Pubmedid: 36993526. Pmcid: PMC10055629.
• Murphy AJ, Cheng C, Williams J, Shaw TI, Pinto EM, Dieseldorff-Jones K, Brzezinski J, Renfro LA, Tornwall B, Huff V, Hong AL, Mullen EA, Crompton B, Dome JS, Fernandez CV, Geller JI, Ehrlich PF, Mulder H, Oak N, Maciezsek J, Jablonowski C, Fleming AM, Pichavaram P, Morton CL, Easton J, Nichols KE, Clay MR, Santiago T, Zhang J, Yang J, Zambetti GP, Wang Z, Davidoff AM, Chen X. The Genetic and Epigenetic Features of Bilateral Wilms Tumor Predisposition: A Report from the Children's Oncology Group AREN18B5-Q Study. Res Sq. 2023 Mar. Pubmedid: 36993649. Pmcid: PMC10055651.
• Obermayer AN, Chang D, Nobles G, Teng M, Tan AC, Wang X, Chen YA, Eschrich S, Rodriguez PC, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw TI. PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. BMC Bioinformatics. 2023 Jun.24(1):266. Pubmedid: 37380943. Pmcid: PMC10303868.
• Farrar JE, Smith JL, Othus M, Huang BJ, Wang YC, Ries R, Hylkema T, Pogosova-Agadjanyan EL, Challa S, Leonti A, Shaw TI, Triche TJ, Gamis AS, Aplenc R, Kolb EA, Ma X, Stirewalt DL, Alonzo TA, Meshinchi S. Long Noncoding RNA Expression Independently Predicts Outcome in Pediatric Acute Myeloid Leukemia. J Clin Oncol. 2023 Jun.41(16):2949-2962. Pubmedid: 36795987. Pmcid: PMC10414715.
• Grass GD, Ercan D, Obermayer AN, Shaw T, Stewart PA, Chahoud J, Dhillon J, Lopez A, Johnstone PAS, Rogatto SR, Spiess PE, Eschrich SA. An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery. Cancers (Basel). 2023 Jul.15(14). Pubmedid: 37509297. Pmcid: PMC10377392.
• Murphy AJ, Cheng C, Williams J, Shaw TI, Pinto EM, Dieseldorff-Jones K, Brzezinski J, Renfro LA, Tornwall B, Huff V, Hong AL, Mullen EA, Crompton B, Dome JS, Fernandez CV, Geller JI, Ehrlich PF, Mulder H, Oak N, Maciezsek J, Jablonowski CM, Fleming AM, Pichavaram P, Morton CL, Easton J, Nichols KE, Clay MR, Santiago T, Zhang J, Yang J, Zambetti GP, Wang Z, Davidoff AM, Chen X. Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children's Oncology Group AREN18B5-Q. Nat Commun. 2023 Dec.14(1):8006. Pubmedid: 38110397. Pmcid: PMC10728430.
• Helm EY, Zelenka T, Cismasiu VB, Islam S, Silvane L, Zitti B, Holmes TD, Drashansky TT, Kwiatkowski AJ, Tao C, Dean J, Obermayer AN, Chen X, Keselowsky BG, Zhang W, Huo Z, Zhou L, Sheridan BS, Conejo-Garcia JR, Shaw TI, Bryceson YT, Avram D. Bcl11b sustains multipotency and restricts effector programs of intestinal-resident memory CD8+ T cells. Sci Immunol. 2023 Apr.8(82):eabn0484. Pubmedid: 37115913. Pmcid: PMC10231135.
• Kamens JL, Dang J, Shaw TI, Gout AM, Newman S, Hagiwara K, Smith AMR, Obermayer AN, Aldridge S, Ma J, Zhang Y, Wu G, Leventaki V, Santiago T, Raimondi S, Nakitandwe J, Pappo A, Li C, Zhang J, Gruber TA. Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma. Mol Cancer Res. 2023 Apr.21(4):301-306. Pubmedid: 36637394.
• Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun. 2023 Apr.14(1):1739. Pubmedid: 37019972. Pmcid: PMC10076316.
• Huang BJ, Smith JL, Farrar JE, Wang YC, Umeda M, Ries RE, Leonti AR, Crowgey E, Furlan SN, Tarlock K, Armendariz M, Liu Y, Shaw TI, Wei L, Gerbing RB, Cooper TM, Gamis AS, Aplenc R, Kolb EA, Rubnitz J, Ma J, Klco JM, Ma X, Alonzo TA, Triche T, Meshinchi S. Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia. Nat Commun. 2022 Sep.13(1):5487. Pubmedid: 36123353. Pmcid: PMC9485122.
• Mandula JK, Chang S, Mohamed E, Jimenez R, Sierra-Mondragon RA, Chang DC, Obermayer AN, Moran-Segura CM, Das S, Vazquez-Martinez JA, Prieto K, Chen A, Smalley KSM, Czerniecki B, Forsyth P, Koya RC, Ruffell B, Cubillos-Ruiz JR, Munn DH, Shaw TI, Conejo-Garcia JR, Rodriguez PC. Ablation of the endoplasmic reticulum stress kinase PERK induces paraptosis and type I interferon to promote anti-tumor T cell responses. Cancer Cell. 2022 Oct.40(10):1145-1160.e9. Pubmedid: 36150390. Pmcid: PMC9561067.
• Chen PC, Han X, Shaw TI, Fu Y, Sun H, Niu M, Wang Z, Jiao Y, Teubner BJW, Eddins D, Beloate LN, Bai B, Mertz J, Li Y, Cho JH, Wang X, Wu Z, Liu D, Poudel S, Yuan ZF, Mancieri A, Low J, Lee HM, Patton MH, Earls LR, Stewart E, Vogel P, Hui Y, Wan S, Bennett DA, Serrano GE, Beach TG, Dyer MA, Smeyne RJ, Moldoveanu T, Chen T, Wu G, Zakharenko SS, Yu G, Peng J. Alzheimer's disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment. Nat Aging. 2022 Oct.2(10):923-940. Pubmedid: 36636325. Pmcid: PMC9833817.
• Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol. 2022 Nov.12:1051487. Pubmedid: 36505834. Pmcid: PMC9730332.
• Yu X, Cen L, Chen YA, Markowitz J, Shaw TI, Tsai KY, Conejo-Garcia JR, Wang X. Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures. Cancer Res. 2022 May.82(9):1724-1735. Pubmedid: 35176128. Pmcid: PMC9064917.
• Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw TI. DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. Biology (Basel). 2022 Feb.11(2). Pubmedid: 35205126. Pmcid: PMC8869715.
• Liu X, Zhao B, Shaw TI, Fridley BL, Duckett DR, Tan AC, Teng M. Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. Nucleic Acids Res. 2022 Apr.50(6):3115-3127. Pubmedid: 35234924. Pmcid: PMC8989535.
• Vanderwall D, Suresh P, Fu Y, Cho JH, Shaw TI, Mishra A, High AA, Peng J, Li Y. JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics. J Vis Exp. 2021 Oct.(176). Pubmedid: 34747401. Pmcid: PMC9185798.
• Wen J, Rusch M, Brady SW, Shao Y, Edmonson MN, Shaw TI, Powers BB, Tian L, Easton J, Mullighan CG, Gruber T, Ellison D, Zhang J. The landscape of coding RNA editing events in pediatric cancer. BMC Cancer. 2021 Nov.21(1):1233. Pubmedid: 34789196. Pmcid: PMC8597231.
• Shaw TI, Dong L, Tian L, Qian C, Liu Y, Ju B, High A, Kavdia K, Pagala VR, Shaner B, Pei D, Easton J, Janke LJ, Porter SN, Ma X, Cheng C, Pruett-Miller SM, Choi J, Yu J, Peng J, Gu W, Look AT, Downing JR, Zhang J. Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL). Sci Rep. 2021 Mar.11(1):5154. Pubmedid: 33664368. Pmcid: PMC7933146.
• Wagner J, Wickman E, Shaw TI, Anido AA, Langfitt D, Zhang J, Porter SN, Pruett-Miller SM, Tillman H, Krenciute G, Gottschalk S. Antitumor Effects of CAR T Cells Redirected to the EDB Splice Variant of Fibronectin. Cancer Immunol Res. 2021 Mar.9(3):279-290. Pubmedid: 33355188. Pmcid: PMC7925432.
• Haydar D, Houke H, Chiang J, Yi Z, Odé Z, Caldwell K, Zhu X, Mercer KS, Stripay JL, Shaw TI, Vogel P, DeRenzo C, Baker SJ, Roussel MF, Gottschalk S, Krenciute G. 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. Neurooncol. 2021 Jun.23(6):999-1011. Pubmedid: 33320196. Pmcid: PMC8168826.
• Ganguly S, Finkelstein D, Shaw TI, Michalek RD, Zorn KM, Ekins S, Yasuda K, Fukuda Y, Schuetz JD, Mukherjee K, Schuetz EG. Metabolomic and transcriptomic analysis reveals endogenous substrates and metabolic adaptation in rats lacking Abcg2 and Abcb1a transporters. PLoS One. 2021 Jul.16(7):e0253852. Pubmedid: 34255797. Pmcid: PMC8277073.
• Kwak YD, Shaw TI, Downing SM, Tewari A, Jin H, Li Y, Dumitrache LC, Katyal S, Khodakhah K, Russell HR, McKinnon PJ. Chromatin architecture at susceptible gene loci in cerebellar Purkinje cells characterizes DNA damage-induced neurodegeneration. Sci Adv. 2021 Dec.7(51):eabg6363. Pubmedid: 34910524.
• Huang BJ, Smith J, Wang J, Taghizadeh K, Leonti AR, Ries RE, Liu Y, Kolekar P, Tarlock K, Gerbing RB, Crowgey E, Furlan SN, Shaw TI, Hagiwara K, Wei L, Cooper T, Gamis AS, Aplenc R, Kolb EA, Farrar JE, Triche TJ, Alonzo T, Ma X, Meshinchi S. CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Adv. 2021 Dec.5(23):4963-4968. Pubmedid: 34547772. Pmcid: PMC9153007.
• Aditi, Downing SM, Schreiner PA, Kwak YD, Li Y, Shaw TI, Russell HR, McKinnon PJ. Genome instability independent of type I interferon signaling drives neuropathology caused by impaired ribonucleotide excision repair. Neuron. 2021 Dec.109(24):3962-3979.e6. Pubmedid: 34655526. Pmcid: PMC8686690.
• Wang X, Cho JH, Poudel S, Li Y, Jones DR, Shaw TI, Tan H, Xie B, Peng J. JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics. Metabolites. 2020 May.10(5). Pubmedid: 32408578. Pmcid: PMC7281133.
• Brewer CT, Kodali K, Wu J, Shaw TI, Peng J, Chen T. Toxicoproteomic Profiling of hPXR Transgenic Mice Treated with Rifampicin and Isoniazid. Cells. 2020 Jul.9(7). Pubmedid: 32660103. Pmcid: PMC7407182.
• Glenn TC, Pierson TW, Bayona-Vásquez NJ, Kieran TJ, Hoffberg SL, Thomas Iv JC, Lefever DE, Finger JW, Gao B, Bian X, Louha S, Kolli RT, Bentley KE, Rushmore J, Wong K, Shaw TI, Rothrock MJ, McKee AM, Guo TL, Mauricio R, Molina M, Cummings BS, Lash LH, Lu K, Gilbert GS, Hubbell SP, Faircloth BC. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ. 2019 Oct.7:e7786. Pubmedid: 31616589. Pmcid: PMC6791344.
• Wang B, Maxwell BA, Joo JH, Gwon Y, Messing J, Mishra A, Shaw TI, Ward AL, Quan H, Sakurada SM, Pruett-Miller SM, Bertorini T, Vogel P, Kim HJ, Peng J, Taylor JP, Kundu M. ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97. Mol Cell. 2019 May.74(4):742-757.e8. Pubmedid: 30979586. Pmcid: PMC6859904.
• Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, Zhang J, Finkelstein D, Noyes RM, Russell BL, Xu B, Broniscer A, Wetmore C, Pounds SB, Ellison DW, Zhang J, Baker SJ. Correction to: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol. 2019 Jun.137(6):1021. Pubmedid: 30976974. Pmcid: PMC6999025.
• Hunt LC, Stover J, Haugen B, Shaw TI, Li Y, Pagala VR, Finkelstein D, Barton ER, Fan Y, Labelle M, Peng J, Demontis F. A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice. Cell Rep. 2019 Jul.28(5):1268-1281.e6. Pubmedid: 31365869. Pmcid: PMC6697171.
• Xu K, Ding L, Chang TC, Shao Y, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol. 2019 Jan.137(1):123-137. Pubmedid: 30267146. Pmcid: PMC6338707.
• Wang H, Diaz AK, Shaw TI, Li Y, Niu M, Cho JH, Paugh BS, Zhang Y, Sifford J, Bai B, Wu Z, Tan H, Zhou S, Hover LD, Tillman HS, Shirinifard A, Thiagarajan S, Sablauer A, Pagala V, High AA, Wang X, Li C, Baker SJ, Peng J. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nat Commun. 2019 Aug.10(1):3718. Pubmedid: 31420543. Pmcid: PMC6697699.
• Silveira AB, Kasper LH, Fan Y, Jin H, Wu G, Shaw TI, Zhu X, Larson JD, Easton J, Shao Y, Yergeau DA, Rosencrance C, Boggs K, Rusch MC, Ding L, Zhang J, Finkelstein D, Noyes RM, Russell BL, Xu B, Broniscer A, Wetmore C, Pounds SB, Ellison DW, Zhang J, Baker SJ. H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. Acta Neuropathol. 2019 Apr.137(4):637-655. Pubmedid: 30770999. Pmcid: PMC6546611.
• Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, Finkelstein D, Xu B, Lin T, Tinkle CL, Patay Z, Onar-Thomas A, Pounds SB, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell. 2019 01.35(1):140-155.e7. Pubmedid: 30595505. Pmcid: PMC6570409.
• Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman BB, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, Dyer MA. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell. 2018 Sep.34(3):411-426.e19. Pubmedid: 30146332. Pmcid: PMC6158019.
• Xie B, Wang Y, Jones DR, Dey KK, Wang X, Li Y, Cho JH, Shaw TI, Tan H, Peng J. Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling. Anal Chem. 2018 Jul.90(14):8538-8545. Pubmedid: 29883117. Pmcid: PMC6324930.
• Wang X, Jones DR, Shaw TI, Cho JH, Wang Y, Tan H, Xie B, Zhou S, Li Y, Peng J. Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification. J Proteome Res. 2018 Jul.17(7):2328-2334. Pubmedid: 29790753. Pmcid: PMC6252074.
• Tan H, Yang K, Li Y, Shaw TI, Wang Y, Blanco DB, Wang X, Cho JH, Wang H, Rankin S, Guy C, Peng J, Chi H. Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation. Immunity. 2017 Mar.46(3):488-503. Pubmedid: 28285833. Pmcid: PMC5466820.
• Lee KH, Zhang P, Kim HJ, Mitrea DM, Sarkar M, Freibaum BD, Cika J, Coughlin M, Messing J, Molliex A, Maxwell BA, Kim NC, Temirov J, Moore J, Kolaitis RM, Shaw TI, Bai B, Peng J, Kriwacki RW, Taylor JP. C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles. Cell. 2016 Oct.167(3):774-788.e17. Pubmedid: 27768896. Pmcid: PMC5079111.
• Joo JH, Wang B, Frankel E, Ge L, Xu L, Iyengar R, Li-Harms X, Wright C, Shaw TI, Lindsten T, Green DR, Peng J, Hendershot LM, Kilic F, Sze JY, Audhya A, Kundu M. The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis. Mol Cell. 2016 May.62(4):491-506. Pubmedid: 27203176. Pmcid: PMC4993601.
• Joo JH, Wang B, Frankel E, Ge L, Xu L, Iyengar R, Li-Harms X, Wright C, Shaw TI, Lindsten T, Green DR, Peng J, Hendershot LM, Kilic F, Sze JY, Audhya A, Kundu M. The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis. Mol Cell. 2016 Jun.62(6):982. Pubmedid: 27315557.
• Li Y, Wang X, Cho JH, Shaw TI, Wu Z, Bai B, Wang H, Zhou S, Beach TG, Wu G, Zhang J, Peng J. JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. J Proteome Res. 2016 Jul.15(7):2309-2320. Pubmedid: 27225868. Pmcid: PMC5033046.
• Wong K, Shaw TI, Oladeinde A, Glenn TC, Oakley B, Molina M. Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions. Front Microbiol. 2016 Apr.7:500. Pubmedid: 27148189. Pmcid: PMC4830129.
• Shaw TI, Srivastava A, Chou WC, Liu L, Hawkinson A, Glenn TC, Adams R, Schountz T. Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PLoS One. 2013 May.7(11):e48472. Pubmedid: 23166587. Pmcid: PMC3499531.
• Shaw TI, Zhang M. HIV N-linked glycosylation site analyzer and its further usage in anchored alignment. Nucleic Acids Res. 2013 Jul.41(Web):W454-W458. Pubmedid: 23748959. Pmcid: PMC3692120.
• Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul.2(1):10. Pubmedid: 23870653. Pmcid: PMC3844414.
• Shaw TI, Ruan Z, Glenn TC, Liu L. STRAW: Species TRee Analysis Web server. Nucleic Acids Res. 2013 Jul.41(Web):W238-W241. Pubmedid: 23661681. Pmcid: PMC3692081.
• Manzourolajdad A, Wang Y, Shaw TI, Malmberg RL. Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA. J Theor Biol. 2013 Feb.318:140-163. Pubmedid: 23160142. Pmcid: PMC3538908.
• Schountz T, Shaw TI, Glenn TC, Feldmann H, Prescott J. Expression profiling of lymph node cells from deer mice infected with Andes virus. BMC Immunol. 2013 Apr.14:18. Pubmedid: 23570545. Pmcid: PMC3637227.
• Srivastava A, Winker K, Shaw TI, Jones KL, Glenn TC. Transcriptome analysis of a North American songbird, Melospiza melodia. DNA Res. 2012 Nov.19(4):325-333. Pubmedid: 22645122. Pmcid: PMC3415294.
• Wang Y, Manzour A, Shareghi P, Shaw TI, Li YW, Malmberg RL, Cai L. Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds. BMC Bioinformatics. 2012 Apr.13 Suppl 5:S1. Pubmedid: 22537005. Pmcid: PMC3358654.
• Shaw TI, Manzour A, Wang Y, Malmberg RL, Cai L. Analyzing modular RNA structure reveals low global structural entropy in microRNA sequence. J Bioinform Comput Biol. 2011 Apr.9(2):283-298. Pubmedid: 21523933.
• Malmberg RL, Shaw TI, Cai L. RNApasta: a tool for analysis of RNA structural alignments. Int J Bioinform Res Appl. 2010 Dec.6(6):571-583. Pubmedid: 21354963.

• Title: Targeting ER Stress in Pediatric Acute Myeloid Leukemia
  Sponsor: Florida Biomedical Research Program (FBRP)
  PI: Shaw, T.
• Title: Integrated transcriptome-based prognostic and disease monitoring strategies in childhood AML
  Sponsor: Amer Cancer Society
  PI: Shaw, T.