2024

  1. Mandula JK, Sierra-Mondragon RA, Jimenez RV, Chang D, Mohamed E, Chang S, Vazquez-Martinez JA, Cao Y, Anadon CM, Lee SB, Das S, Rocha-Munguba L, Pham VM, Li R, Tarhini AA, Furqan M, Dalton W, Churchman M, Moran-Segura CM, Nguyen J, Perez B, Kojetin DJ, Obermayer A, Yu X, Chen A, Shaw TI, Conejo-Garcia JR, Rodriguez PC. Jagged2 targeting in lung cancer activates anti-tumor immunity via Notch-induced functional reprogramming of tumor-associated macrophages. Immunity. 2024 May 14;57(5):1124-1140.e9. doi: 10.1016/j.immuni.2024.03.020. Epub 2024 Apr 17. PubMed PMID: 38636522; PubMed Central PMCID: PMC11096038.
  2. Shaw TI, Wagner J, Tian L, Wickman E, Poudel S, Wang J, Paul R, Koo SC, Lu M, Sheppard H, Fan Y, O'Neill FH, Lau CC, Zhou X, Zhang J, Gottschalk S. Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression. Nat Commun. 2024 May 3;15(1):3732. doi: 10.1038/s41467-024-47649-y. PubMed PMID: 38702309; PubMed Central PMCID: PMC11068777.
  3. 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 May;104(5):102041. doi: 10.1016/j.labinv.2024.102041. Epub 2024 Feb 29. PubMed PMID: 38431116.
  4. Shaw TI, Pounds S, Cao X, Ma J, Palacios G, Mason J, Perkins S, Wu G, Fan Y, Wang J, Zhou X, Obermayer A, Kinney MC, Kraveka J, Gross T, Sandlund J, Zhang J, Mullighan C, Lim MS, Leventaki V. Comprehensive genomic analysis reveals molecular heterogeneity in pediatric ALK-positive anaplastic large cell lymphoma. Res Sq. 2024 Mar 28;. doi: 10.21203/rs.3.rs-4145750/v1. PubMed PMID: 38585847; PubMed Central PMCID: PMC10996813.
  5. 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. doi: 10.1371/journal.pcbi.1011873. eCollection 2024 Feb. PubMed PMID: 38335222; PubMed Central PMCID: PMC10883583.

2023

  1. 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 18;14(1):8006. doi: 10.1038/s41467-023-43730-0. PubMed PMID: 38110397; PubMed Central PMCID: PMC10728430.
  2. 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 26;42(9):113084. doi: 10.1016/j.celrep.2023.113084. Epub 2023 Sep 15. PubMed PMID: 37716355
  3. Bertrums EJM, Smith JL, Harmon L, Ries RE, Wang YJ, Alonzo TA, Menssen AJ, Chisholm KM, Leonti AR, Tarlock K, Ostronoff F, Pogosova-Agadjanyan EL, Kaspers GJL, Hasle H, Dworzak M, Walter C, Muhlegger N, Morerio C, Pardo L, Hirsch B, Raimondi S, Cooper TM, Aplenc R, Gamis AS, Kolb EA, Farrar JE, Stirewalt D, Ma X, Shaw TI, Furlan SN, Brodersen LE, Loken MR, Van den Heuvel-Eibrink MM, Zwaan CM, Triche TJ, Goemans BF, Meshinchi S. Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica.2023 Aug 1;108(8):2044-2058. doi: 10.3324/haematol.2022.281653. PubMed PMID: 36815378; PubMed Central PMCID: PMC10388277.
  4. 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;15(14). doi: 10.3390/cancers15143636. PubMed PMID: 37509297; PubMed Central PMCID: PMC10377392.
  5. 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 28;24(1):266. doi: 10.1186/s12859-023-05393-y. PubMed PMID: 37380943; PubMed Central PMCID: PMC10303868.
  6. 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 Jr, 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 1;41(16):2949-2962. doi: 10.1200/JCO.22.01114. Epub 2023 Feb 16. PubMed PMID: 36795987; PubMed Central PMCID: PMC10414715.
  7. 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 28;8(82):eabn0484. doi: 10.1126/sciimmunol.abn0484. Epub 2023 Apr 28. PubMed PMID: 37115913; PubMed Central PMCID: PMC10231135.
  8. 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 5;14(1):1739. doi: 10.1038/s41467-023-37438-4. PubMed PMID: 37019972; PubMed Central PMCID: PMC10076316. 
  9. 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 1;21(4):301-306. doi: 10.1158/1541-7786.MCR-22-0544. PubMed PMID: 36637394.

 

2022

  1. 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. Frontiers in Oncology. 2022 Dec; 12. doi: 10.3389/fonc.2022.1051487.
  2. 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 8;11(2):260. doi: 10.3390/biology11020260. PMID: 35205126 PMCID: PMC8869715
  3. Chen, PC., Han, X., Shaw, TI., Jiao, Y., Teubner, BJW., Eddins, D., Niu, M., Bai, B., Mertz, J., Li, Y., Cho, JH., Wang, X., Wu, Z., Mancieri, A., Earls, LR., Stewart, E., Vogel, P., Beach, TG., Dyer, MA., Smeyne, RJ., Zakharneko, SS., Yu, G., Peng, J. Neuronal expression of Alzheimer’s disease-associated U1-70K cleavage product causes splicing dysfunction and cognitive impairment in mice. Nature Aging. 2022. 2, 923–940 https://doi.org/10.1038/s43587-022-00290-0
  4. 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 10;40(10):1145-1160.e9. doi: 10.1016/j.ccell.2022.08.016. Epub 2022 Sep 22. PMID: 36150390; PMCID: PMC9561067.
  5. 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 Jr, Meshinchi S. Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia. Nat Commun. 2022 Sep 19;13(1):5487. doi: 10.1038/s41467-022-33244-6. PMID: 36123353; PMCID: PMC9485122.
  6. Liu X, Zhao B, Shaw TI, Brooke F, Derek D, Tan AC, Teng M. Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. Nucleic Acids Res. 2022 Apr 8;50(6):3115-3127. doi: 10.1093/nar/gkac141. PMID: 35234924 PMCID: PMC8989535
  7. 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 3;82(9):1724-1735. doi: 10.1158/0008-5472.CAN-21-3113. PMID: 35176128; PMCID: PMC9064917.

2021 

  1. 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 4;11(1):5154. doi: 10.1038/s41598-021-84647-2. PMID: 33664368; PMCID: PMC7933146.
  2. 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 19;(176). doi: 10.3791/62796. PMID: 34747401.
  3. Wen J, Rusch M, Brady SW, Shao Y, Edmonson MN, Shaw TI (BB), 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- PMID: 34789196. PMCID: PMC8597231
  4. 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 Sep 21:bloodadvances.2021004965. doi: 10.1182/bloodadvances.2021004965. PMID: 34547772
  5. 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 15;109(24):3962-3979.e6. doi: 10.1016/j.neuron.2021.09.040. Epub 2021 Oct 15. PMID: 34655526; PMCID: PMC8686690.
  6. 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 17;7(51):eabg6363. doi: 10.1126/sciadv.abg6363. Epub 2021 Dec 15. PMID: 34910524.
  7. 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 13;16(7):e0253852. doi: 10.1371/journal.pone.0253852. PMID: 34255797; PMCID: PMC8277073.
  8. 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. doi: 10.1158/2326-6066.CIR-20-0280. Epub 2020 Dec 22. PMID: 33355188; PMCID: PMC7925432.
  9. 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. Neuro Oncol. 2021 Jun 1;23(6):999-1011. doi: 10.1093/neuonc/noaa278. PMID: 33320196; PMCID: PMC8168826.

Before 2021

  1. Jia M*, Shaw T*, Zhang X, Liu D, Shen Y, Ezeamama AE, Yang C, Zhang M. Decoding noises in HIV computational genotyping. Virology. 2017 Nov;511:249-255. doi: 10.1016/j.virol.2017.08.031. Epub 2017 Sep 14. PMID: 28918303; PMCID: PMC6443101.
  2. 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 21;46(3):488-503. doi: 10.1016/j.immuni.2017.02.010. Epub 2017 Mar 9. PMID: 28285833; PMCID: PMC5466820.
  3. 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 13;7:500. doi: 10.3389/fmicb.2016.00500. PMID: 27148189; PMCID: PMC4830129.
  4. Shaw TI, Zhang M. HIV N-linked glycosylation site analyzer and its further usage in anchored alignment. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W454-8. doi: 10.1093/nar/gkt472. Epub 2013 Jun 8. PMID: 23748959; PMCID: PMC3692120.
  5. Shaw TI, Ruan Z, Glenn TC, Liu L. STRAW: Species TRee Analysis Web server. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W238-41. doi: 10.1093/nar/gkt377. Epub 2013 May 9. PMID: 23661681; PMCID: PMC3692081.
  6. 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. 2012;7(11):e48472. doi: 10.1371/journal.pone.0048472. Epub 2012 Nov 15. PMID: 23166587; PMCID: PMC3499531.
  7. 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):283-98. doi: 10.1142/s0219720011005495. PMID: 21523933.
  8. Brewer CT, Kodali K, Wu J, Shaw TI, Peng J, Chen T. Toxicoproteomic Profiling of hPXRTransgenic Mice Treated with Rifampicin and Isoniazid. Cells. 2020 Jul 9;9(7):1654. doi: 10.3390/cells9071654. PMID: 32660103; PMCID: PMC7407182.
  9. 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 12;10(5):190. doi: 10.3390/metabo10050190. PMID: 32408578; PMCID: PMC7281133.
  10. Bai B, Wang X, Li Y, Chen PC, Yu K, Dey KK, Yarbro JM, Han X, Lutz BM, Rao S, Jiao Y, Sifford JM, Han J, Wang M, Tan H, Shaw TI, Cho JH, Zhou S, Wang H, Niu M, Mancieri A, Messler KA, Sun X, Wu Z, Pagala V, High AA, Bi W, Zhang H, Chi H, Haroutunian V, Zhang B, Beach TG, Yu G, Peng J. Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression. Neuron. 2020 Mar 18;105(6):975-991.e7. doi: 10.1016/j.neuron.2019.12.015. Epub 2020 Jan 8. Erratum in: Neuron. 2020 May 20;106(4):700. PMID: 31926610; PMCID: PMC7318843.
  11. 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 Jr, 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 11;7:e7786. doi: 10.7717/peerj.7786. PMID: 31616589; PMCID: PMC6791344.
  12. 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 16;10(1):3718. doi: 10.1038/s41467-019-11661-4. PMID: 31420543; PMCID: PMC6697699.
  13. 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 30;28(5):1268-1281.e6. doi: 10.1016/j.celrep.2019.06.094. PMID: 31365869; PMCID: PMC6697171.
  14. 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 16;74(4):742-757.e8. doi: 10.1016/j.molcel.2019.03.027. Epub 2019 Apr 9. PMID: 30979586; PMCID: PMC6859904.
  15. 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. doi: 10.1007/s00401-019-02006-y. Epub 2019 Apr 11. Erratum for: Acta Neuropathol. 2019 Apr;137(4):637-655. PMID: 30976974; PMCID: PMC6999025.
  16. 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 Jan 14;35(1):140-155.e7. doi: 10.1016/j.ccell.2018.11.015. Epub 2018 Dec 27. PMID: 30595505; PMCID: PMC6570409.
  17. 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. doi: 10.1007/s00401-018-1912-1. Epub 2018 Sep 28. PMID: 30267146; PMCID: PMC6338707.
  18. 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 3rd, 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; St. Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell. 2018 Sep 10;34(3):411-426.e19. doi: 10.1016/j.ccell.2018.07.012. Epub 2018 Aug 23. PMID: 30146332; PMCID: PMC6158019.
  19. 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 17;90(14):8538-8545. doi: 10.1021/acs.analchem.8b01591. Epub 2018 Jun 25. PMID: 29883117; PMCID: PMC6324930.
  20. Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, Rusch MC, Webb TR, Zhang J, Potter PM. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA. 2018 Aug;24(8):1056-1066. doi: 10.1261/rna.065383.117. Epub 2018 May 29. Erratum in: RNA. 2018 Dec;24(12):1886. PMID: 29844105; PMCID: PMC6049506.
  21. 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 6;17(7):2328-2334. doi: 10.1021/acs.jproteome.8b00019. Epub 2018 May 29. PMID: 29790753; PMCID: PMC6252074.
  22. Kozina E, Sadasivan S, Jiao Y, Dou Y, Ma Z, Tan H, Kodali K, Shaw T, Peng J, Smeyne RJ. Mutant LRRK2 mediates peripheral and central immune responses leading to neurodegeneration in vivo. Brain. 2018 Jun 1;141(6):1753-1769. doi: 10.1093/brain/awy077. PMID: 29800472; PMCID: PMC7190032.
  23. Palacios G, Shaw TI, Li Y, Singh RK, Valentine M, Sandlund JT, Lim MS, Mullighan CG, Leventaki V. Novel ALK fusion in anaplastic large cell lymphoma involving EEF1G, a subunit of the eukaryotic elongation factor-1 complex. Leukemia. 2017 Mar;31(3):743-747. doi: 10.1038/leu.2016.331. Epub 2016 Nov 14. PMID: 27840423; PMCID: PMC5639880.
  24. 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 20;167(3):774-788.e17. doi: 10.1016/j.cell.2016.10.002. PMID: 27768896; PMCID: PMC5079111.
  25. 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 1;15(7):2309-20. doi: 10.1021/acs.jproteome.6b00344. Epub 2016 Jun 13. PMID: 27225868; PMCID: PMC5033046.
  26. 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 19;62(4):491-506. doi: 10.1016/j.molcel.2016.04.020. Erratum in: Mol Cell. 2016 Jun 16;62(6):982. PMID: 27203176; PMCID: PMC4993601.
  27. Mertz J, Tan H, Pagala V, Bai B, Chen PC, Li Y, Cho JH, Shaw T, Wang X, Peng J. 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. PMID: 25931508; PMCID: PMC4587327.
  28. 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 22;2(1):10. doi: 10.1186/2047-217X-2-10. PMID: 23870653; PMCID: PMC3844414.
  29. 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 9;14:18. doi: 10.1186/1471-2172-14-18. PMID: 23570545; PMCID: PMC3637227.
  30. 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 7;318:140-63. doi: 10.1016/j.jtbi.2012.10.023. Epub 2012 Nov 14. PMID: 23160142; PMCID: PMC3538908.
  31. Srivastava A, Winker K, Shaw TI, Jones KL, Glenn TC. Transcriptome analysis of a North American songbird, Melospiza melodia. DNA Res. 2012;19(4):325-33. doi: 10.1093/dnares/dss015. Epub 2012 May 29. PMID: 22645122; PMCID: PMC3415294.
  32. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. PMID: 21926179; PMCID: PMC3227110.
  33. 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 12;13 Suppl 5(Suppl 5):S1. doi: 10.1186/1471-2105-13-S5-S1. PMID: 22537005; PMCID: PMC3358654.
  34. Malmberg RL, Shaw TI, Cai L. RNApasta: a tool for analysis of RNA structural alignments. Int J Bioinform Res Appl. 2010;6(6):571-83. doi: 10.1504/IJBRA.2010.038738. PMID: 21354963.