1. Gabriel NN, Balaji K, Jayachandran K, Inkman M, Zhang J, Dahiya S, Goldstein M. Loss of H3K27 trimethylation promotes radiotherapy resistance in medulloblastoma and induces an actionable vulnerability to BET inhibition. Cancer Res. 2022 Mar 22; PubMed PMID: 35315927.
  2. Zhang J, Eteleeb AM, Rozycki EB, Inkman MJ, Ly A, Scharf RE, Jayachandran K, Krasnick BA, Mazur T, White NM, Fields RC, Maher CA. DANSR: A Tool for the Detection of Annotated and Novel Small RNAs. Noncoding RNA. 2022. 13;8(1):9. PMID: 35076605.
  3. Wang S, Luke CJ, Pak SC, Shi V, Chen L, Moore J, Andress AP, Jayachandran K, Zhang J, Huang Y, Platik M, Apicelli AA, Schwarz JK, Grigsby PW, Silverman GA, Markovina S. SERPINB3 (SCCA1) inhibits cathepsin L and lysoptosis, protecting cervical cancer cells from chemoradiation. Communications Biology. 2022. 12;5(1):46. PMID: 35022555. PMCID: PMC8755728.
  4. Ruiz FJ, Sundaresan A, Zhang J, Pedamallu CS, Halle MK, Srinivasasainagendra V, Zhang JQ, Muhammad N, Stanley J, Markovina S, Tiwari HK, Grigsby PW, Krakstad C, Schwarz JK, Ojesina AI. Genomic Characterization and Therapeutic Targeting of HPV Undetected Cervical Carcinomas. Cancers. 2021. 13(18):4551. PMID: 34572780. PMCID: PMC8467954
  5. Ruiz FJ, Inkman M, Rashmi R, Muhammad N, Gabriel N, Miller CA, McLellan MD, Goldstein M, Markovina S, Grigsby PW, Zhang J, Schwarz JK. HPV transcript expression affects cervical cancer response to chemoradiation. JCI Insight. 2021 Jul 13:138734. doi: 10.1172/jci.insight.138734. Epub ahead of print. PMID: 34255749.
  6. Creason A, Haan D, Dang K, Chiotti KE, Inkman M, Lamb A, Yu T, Hu Y, Norman TC, Buchanan A, van Baren J, Spangler R, Rollins MR, Spellman PT, Rozanov D, Zhang J, Maher CA, Caloian C, Watson JD, Uhrig S, Haas BJ, Jain M, Akeson M, Ahsen ME; SMC-RNA Challenge Participants, Stolovitzky G, Guinney J, Boutros PC, Stuart JM, Ellrott K. A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Cell Systems. 2021 Jun 16:S2405-4712(21)00207-6. doi: 10.1016/j.cels.2021.05.021. Epub ahead of print. PMID: 34146471.
  7. Floberg J.M., Zhang J., Muhammad N., DeWees T.A., Inkman M., Chen K., Lin A.J., Rashmi R., Jayachandran K., Edelson B.T., Siegel B.A., Dehdashti F., Grigsby P.W., Markovina S., Schwarz J.K., “Standardized Uptake Value for 18F-Fluorodeoxyglucose is a Marker of Inflammatory State and Immune Infiltrate in Cervical Cancer“. Clinical Cancer Research. 2021 Apr 5:clincanres.4450.2020. doi: 10.1158/1078-0432.CCR-20-4450. Epub ahead of print. PMID: 33820781.
  8. Zhang J., Rashmi R., Inkman M., Jayachandran K., Ruiz F., Waters M.R., Grigsby P.W., Markovina S., and Schwarz J.K., “Integrating imaging and RNA-seq improves outcome prediction in cervical cancer”. Journal of Clinical Investigation. 2021 Mar 1;131(5):139232. doi: 10.1172/JCI139232. PMID: 33645544.
    Featured at QuadShot (http://www.quadshotnews.com/2021/03/a-hot-mes.html)
  9. Potluri, H.K., Ng, T., Newton, M.A., Zhang, J., Maher, C.A., Nelson, P. S., McNeel, D. G., “Antibody Profiling of Prostate Cancer Patients Reveals Differences in Antibody Signatures Among Disease Stages and Following Treatment.” Journal for ImmunoTherapy of Cancer. 2020 Dec;8(2):e001510. PMID: 33335027.
  10. Rashmi R., Jayachandran K., Zhang J., Menon V., Muhammad N., Zahner M., Ruiz F., Zhang S., Cho K., Wang Y., Huang X., Huang Y., McCormick M.L., Rogers B.E., Spitz D.R., Patti G.J., Schwarz J.K., “Glutaminase inhibitors induce thiol-mediated oxidative stress and radio-sensitization in treatment resistant cervical cancers”. Molecular Cancer Therapeutics. 2020: molcanther.0271.2020. Epub 2020 Oct 21. PMID: 33087507.
  11. Inkman M.J., Jayachandran K., Ellis T.M., Ruiz F., McLellan M.D., Miller C.A., Wu Y., Ojesina A.I., Schwarz J.K., Zhang J., “HPV-EM: an accurate HPV detection and genotyping EM algorithm”. Scientific Reports. 2020; 10(1): 14340. PMID: 32868873.
  12. Dang H.X., Krasnick B.A., White B.S., Grossman J.G., Strand M.S., Zhang J., Cabanski C.R., Miller C.A., Fulton R.S., Goedegebuure S.P., Fronick C.C., Griffith M., Larson D.E., Goetz B.D., Walker J.R., Hawkins W.G., Strasberg S.M., Linehan D.C., Lim K.H., Lockhart A.C., Mardis E.R., Wilson R.K., Ley T.J., Maher C.A., Fields R.C., “The clonal evolution of metastatic colorectal cancer”. Science Advances. 2020; 6(24): eaay9691. PMID: 32577507.
  13. Zhang J., and Maher C.A., “Gene Fusion Discovery with INTEGRATE”, Volume of “Chimeric RNA”, series of “Methods in Molecular Biology”, Springer, 2020. PMID: 31728961.
  14. Wisdom A.J., Hong C.S., Lin A.J., Xiang Y., Cooper D.E., Zhang J., Xu E.S., Kuo H.C., Mowery Y.M., Carpenter D.J., Kadakia K.T., Himes J.E., Luo L., Ma Y., Williams N., Cardona D.M., Haldar M., Diao Y., Markovina S., Schwarz J.K., and Kirsch D.G., “Neutrophils Promote Tumor Resistance to Radiation Therapy”, Proceedings of the National Academy of Sciences of the United States of America (PNAS). 2019; 116 (37): 18584-18589.  PMID: 31462499; PMCID: PMC6744874.
  15. Lei J.T.*, Shao J.*, Zhang J.*, Iglesia M.*, Chan D.W., Cao J., Anurag M., Singh P., He X., Kosaka Y., Matsunuma R., Crowder R., Hoog J., Phommaly C., Goncalves R., Ramalho S., Peres R.M.R., Punturi N., Schmidt C., Bartram A., Jou E., Devarakonda V., Holloway K.R., Lai W.V., Hampton O., Rogers A., Tobias E., Parikh P.A., Davies S.R., Li S., Ma C.X., Suman V.J., Hunt K.K., Watson M.A., Hoadley K.A., Thompson E.A., Chen X., Kavuri S.M., Creighton C.J., Maher C.A., Perou C.M., Haricharan S., and Ellis M.J., “Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer”, Cell reports. 2018; 24(6):1434-1444.e7.  PMID: 30089255; PPMCID: PMC6171747. *co-first authors.
  16. Quigley D.A., Dang H.X., Zhao S.G., Lloyd P., Aggarwal R., Alumkal J.J., Foye A., Kothari V., Perry M.D., Bailey A.M., Playdle D., Barnard T.J., Zhang L., Zhang J., Youngren J.F., Cieslik M.P., Parolia A., Beer T.M., Thomas G., Chi K.N., Gleave M., Lack N.A., Zoubeidi A., Reiter R.E., Rettig M.B., Witte O., Ryan C.J., Fong L., Kim W., Friedlander T., Chou J., Li H., Das R., Li H., Moussavi-Baygi R., Goodarzi H., Gilbert L.A., Lara P.N. Jr, Evans C.P., Goldstein T.C., Stuart J.M., Tomlins S.A., Spratt D.E., Cheetham R.K., Cheng D.T., Farh K., Gehring J.S., Hakenberg J., Liao A., Febbo P.G., Shon J., Sickler B., Batzoglou S., Knudsen K.E., He H.H., Huang J., Wyatt A.W., Dehm S.M., Ashworth A., Chinnaiyan A.M., Maher C.A., Small E.J., and Feng F.Y., “Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer”, Cell. 2018; 174(3):758-769.e9.  PMID: 30033370; PMCID:  PMC6425931.
  17. Zhang J., Gao T., and Maher C.A., “INTEGRATE-Vis: A Tool for Comprehensive Gene Fusion Visualization”, Scientific reports. 2017; 7(1):17808.  PMID: 29259323; PMCID: PMC5736641.
  18. Zhang J., Griffith M., Miller C.A., Griffith O.L., Spencer D.H., Walker J.R., Magrini V., McGrath S.D., Ly A., Helton N.M., Trissal M., Link D.C., Dang H.X., Larson D.E., Kulkarni S., Cordes M.G., Fronick C.C., Fulton R.S., Klco J.M., Mardis E.R., Ley T.J., Wilson R.K., and Maher C.A., “Comprehensive Discovery of Non-coding RNAs in Acute Myeloid Leukemia Cell Transcriptomes”, Experimental Hematology. 2017; 55:19-33. PMID: 28760689; PMCID: PMC5772960.
    Featured in lncRNA blog (http://www.lncrnablog.com/comprehensive-discovery-of-non-coding-rnas-in-acute-myeloid-leukemia-cell-transcriptomes)
  19. Zhang J., Mardis E.R., and Maher C.A., “INTEGRATE-Neo: A Pipeline for Personalized Gene Fusion Neoantigen Discovery”, Bioinformatics. 2017; 33(4):555-557. PMID: 27797777; PMCID: PMC5408800.
  20. White N.M.*, Zhao S.G.*, Zhang J., Rozycki E., Dang H.X., McFadden S.D., Eteleeb A., Alshalalfa M., Vergara  I.A., Erho  N., Arbeit J.M., Karnes R.J.,  Den R.B., Davicioni E., and Maher C.A., “Multi-institutional Analysis Shows that Low PCAT-14 Expression Associates with Poor Outcomes in Prostate Cancer”, European Urology. 2017; 71(2):257-266. PMID: 27460352. *co-first authors.
    Highlighted in The Source (https://source.wustl.edu/2016/08/study-finds-marker-aggressive-prostate-cancer)
  21. Griffith M., Griffith O.L., Krysiak K., Skidmore Z.L., Christopher M.J., Klco J.M., Ramu A., Lamprecht T.L., Wagner A.H., Campbell K.M., Lesurf R., Hundal J., Zhang J., Spies N.C., Ainscough B.J., Larson D.E., Heath S.E., Fronick C., O’Laughlin S., Fulton R., Magrini V., McGrath S., Smith S.M., Miller C.A., Maher C.A., Payton J.E., Walker J.R., Eldred J., Walter M.J., Daniel C., Link D.C., Graubert T.A., Westervelt P., Kulkarni S., DiPersio J.F., Mardis E.R., Wilson R.K., and Ley T.J., “Comprehensive Genomic Analysis Reveals FLT3 Activation and a Therapeutic Strategy for a Patient with Relapsed Adult B-lymphoblastic Leukemia”, Experimental Hematology. 2016; 44(7):603-13.  PMID: 27181063; PMCID: PMC4914477.
  22. Zhang J., Chu C., and Wu. Y., “Computational Approaches for Finding Long Insertions and Deletions with Next Generation Sequencing Data”, in I. Mandoiu, editor, Computational Methods for Next Generation Sequencing Data Analysis, Wiley Book Series on Bioinformatics, 2016.
  23. Griffith O.L., Griffith M., Krysiak K., Magrini V., Ramu A., Skidmore Z.L., Kunisaki J.H., Austin R., McGrath S., Zhang J., Demeter R., Graves T., Eldred J., Walker J., Larson D., Maher C.A., Lin Y., Chapman W., Mahadevan A., Miksad R., Nasser I., Hanto D.W., and Mardis E.R., “A Genomic Case Study of Mixed Fibrolamellar Hepatocellular Carcinoma”, Annals of Oncology. 2016; 27(6):1148-54. PMC4880064 PMID: 27029710; PMCID: PMC4880064.
  24. Zhang J., White N.M., Schmidt H.K., Fulton R.S., Tomlinson C., Warren W.C., Wilson R.K., and Maher C.A., “INTEGRATE: Gene Fusion Discovery Using Whole Genome and Transcriptome Data”, Genome Research. 2016; 26(1):108-18.  PMID: 26556708; PMCID: PMC4691743.
    Selected and featured in the 2017 International Medical Informatics Association (IMIA) Yearbook of Medical Informatics as one of the four best articles in the Bioinformatics and Translational Informatics subfield of medical informatics literature published in 2016.
  25. Cabanski C.R., Magrini V., Griffith M., Griffith O.L., McGrath S., Zhang J., Walker J., Ly A., Demeter R., Fulton R.S., Pong W.W., Gutmann D.H., Govindan R., Mardis E.R., and Maher C.A., “cDNA Hybrid Capture Improves Transcriptome Analysis on Low-input and Archived Samples”, Journal of Molecular Diagnostics. 2014; 16(4):440-51. PMID: 24814956; PMCID: PMC4078367.
  26. Chu C., Zhang J., and Wu Y., “GINDEL: Accurate Genotype Calling of Insertions and Deletions from Low Coverage Population Sequence Reads”, PLOS One. 2014; 25;9(11):e113324. PMID: 25423315; PMCID: PMC4244156.
  27. Li S., Shen D., Shao J., Crowder R., Liu W., Prat A., He X., Liu S., Hoog J., Lu C., Ding L., Griffith O.L., Miller C., Larson D., Fulton R.S., Harrison M., Mooney T., McMichael J.F., Luo J., Tao Y., Goncalves R., Schlosberg C., Hiken J.F., Saied L., Sanchez C., Giuntoli T., Bumb C., Cooper C., Kitchens R.T., Lin A., Phommaly C., Davies S.R., Zhang J., Kavuri M.S., McEachern D., Dong Y.Y., Ma C., Pluard T., Naughton M., Bose R., Suresh R., McDowell R., Michel L., Aft R., Gillanders W., DeSchryver K., Wilson R.K., Wang S., Mills G.B., Gonzalez-Angulo A., Edwards J.R., Maher C.A., Perou C.M., Mardis E.R., and Ellis M.J., “Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts”, Cell Reports. 2013; 26;4(6):1116-30. PMID: 24055055; PMCID: PMC3881975.
    Cover story of the issue.
  28. Wang J., Zhang X., Liu Y., Zhang J., and Wu Y., “A Synchronization Detection Approach for Identifying Rare Mutations Underlying Common Disease”, in 5th International Conference on Bioinformatics and Computational Biology (BICoB 2013).
  29. Wang J., Zhao Z., Cao Z., Yang A. and Zhang J., “A Probabilistic Method for Identifying Rare Variants Underlying Complex Traits”, BMC Genomics2013; 14(Suppl 1):S11. PMID: 23369113; PMCID: PMC3549819.
  30. Zhang J., Wang J., and Wu Y., “An Improved Approach for Accurate and Efficient Calling of Structural Variations with Low-coverage Sequence Data”, BMC Bioinformatics. 2012; 13(Suppl 6):S6.  PMID: 22537045; PMCID: PMC3358659.
  31. Zhang J. and Wu Y., “SVseq: An Approach for Detecting Exact Breakpoints of Deletions with Low-coverage Sequence Data”, Bioinformatics. 2011; 27(23), 3228-3234.  PMID: 21994222.
  32. Wang J, Zhang J., and Wu Y, “Identifying Interacting SNPs with Parallel Fish-Agent based Logic Regression”, in Proceedings of 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2011).  PMID: 23984382; PMCID: PMC3747618
  33. Zhang J. and Wu Y., “Haplotype Inference from Short Sequence Reads Using a Population Genealogical History Model”, in proceedings of Pacific Symposium on Biocomputing (PSB 2011), 288-299.  PMID: 21121056.

Abstracts

  1. BET Inhibition Targets Radiotherapy Resistance in H3K27ME3-deficient Group 3 Medulloblastoma”, Neuro-Oncology, 2021. Neuro-Oncology, Volume 23, Issue Supplement_1, June 2021
  2. SERPINB3 promotes myeloid cell chemotaxis and associated chemokine production in cervical cancer”, Cancer Research, 2021. Cancer Research 81 (13 Supplement), 2680-2680
  3. Genetic characterization of metastasis and prognosis in high-grade serous ovarian cancer”, Cancer Research, 2021. Cancer Research 81 (13 Supplement), 2202-2202
  4. Association of circulating myeloid derived suppressor cells with systemic lymphopenia following chemoradiotherapy in glioblastoma”, Cancer Research, 2021. Cancer Research 81 (13 Supplement), 507-507
  5. Characterization of Primary-Metastasis Pairs in High-Grade Serous Ovarian Cancer with Short- and Long-Term Survival”, Society of Gynecologic Oncology (SGO), 2020. Clinical Cancer Research 26 (S13)
  6. Pre-Treatment [F-18]FDG-PET SUVmax as a Prognostic and Radiogenomic Marker in Cervical Cancer”, American Society for Radiation Oncology (ASTRO), Oct. 2018. International Journal of Radiation Oncology• Biology• Physics, 102(3), S82-S83.
  7. Characterization of the Novel LncRNA, PCAT14, Clinically Associated with Metastatic Prostate Cancer”, in Cancer Research 76 (14 Supplement), Apr. 2016. American Association for Cancer Research
  8. ESR1 Gene Fusions Implicated in Endocrine Therapy Resistance of ER+ Breast Cancer”, in Cancer Research 75 (9 Supplement), May 2015. American Association for Cancer Research
  9. An Improved Approach for Accurate and Efficient Calling of Structural Variations with Low-coverage Sequence Data”, presented at Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq), Apr. 2012. BMC Bioinformatics
  10. Calling Structural Variation with Low-coverage Sequencing Data by Mapping to Focal Region”, presented at the Second IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Feb. 2012. IEEE Xplore
  11. Finding Deletions with Exact Break Points from Noisy Low Coverage Paired-end Short Sequence Reads”, presented at First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq), Mar. 2011. BMC Bioinformatics
  12.  “Finding Deletions with Exact Break Points from Noisy Low Coverage Paired-end Short Sequence Reads”, presented at 7th International Symposium on Bioinformatics Research and Applications (ISBRA), May. 2011. BMC Bioinformatics
  13. “Poster: Scaffolding Draft Genomes Using Paired Sequencing Data”, in the First IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Feb. 2011. IEEE Xplore
  14. Haplotype Inference from Short Sequence Reads Using a Population Genealogical History Model”, presented at Pacific Symposium on Biocomputing (PSB), Jan. 2011. World Scientific