Divisions of Hematology & Oncology

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Peer-reviewed Manuscripts

• Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
  Yao L, Wang JT, Jayasinghe RG, O'Neal J, Tsai CF, Rettig MP, Song Y, Liu R, Zhao Y, Ibrahim OM, Fiala MA, Fortier JM, Chen S, Gehrs L, Rodrigues FM, Wendl MC, Kohnen D, Shinkle A, Cao S, Foltz SM, Zhou DC, Storrs E, Wyczalkowski MA, Mani S, Goldsmith SR, Zhu Y, Hamilton M, Liu T, Chen F, Vij R, Ding L, DiPersio JF
  Cancer Res 2023 Apr 14;83(8):1214-1233
• Epigenetic and Transcriptomic Characterization Reveals Progression Markers and Essential Pathways in Clear Cell Renal Cell Carcinoma
  Wu Y, Terekhanova NV, Caravan W, Naser Al Deen N, Lal P, Chen S, Mo CK, Cao S, Li Y, Karpova A, Liu R, Zhao Y, Shinkle A, Strunilin I, Weimholt C, Sato K, Yao L, Serasanambati M, Yang X, Wyczalkowski M, Zhu H, Zhou DC, Jayasinghe RG, Mendez D, Wendl MC, Clark D, Newton C, Ruan Y, Reimers MA, Pachynski RK, Kinsinger C, Jewell S, Chan DW, Zhang H, Chaudhuri AA, Chheda MG, Humphreys BD, Mesri M, Rodriguez H, Hsieh JJ, Ding L, Chen F
  Nat Commun 2023 Mar 27;14(1):1681
• Histopathologic and Proteogenomic Heterogeneity Reveals Features of Clear Cell Renal Cell Carcinoma Aggressiveness
  Li Y, Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kolodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyo D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DW, Ricketts CJ, Nesvizhskii AI, Zhang H, Ding L
  Clinical Proteomic Tumor Analysis Consortium (Contributors include: Cao S)
  Cancer Cell 2023 Jan 9;41(1):139-163e17
• PDXNet Portal: Patient-Derived Xenograft Model, Data, Workflow and Tool Discovery
  Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H, Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal-Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH
  PDXNet Consortium (Contributors include: Cao S)
  NAR Cancer 2022 Apr 22;4(2):zcac014
• MITI Minimum Information Guidelines for Highly Multiplexed Tissue Images
  Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK
  Human Tumor Atlas Network (Contributors include: Cao S)
  Nat Methods 2022 Mar;19(3):262-267
• LINE-1 Expression in Cancer Correlates With p53 Mutation, Copy Number Alteration, and S Phase Checkpoint
  McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyö D
  Proc Natl Acad Sci U S A 2022 Feb 22;119(8):e2115999119
• Proteogenomic Characterization of Pancreatic Ductal Adenocarcinoma
  Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyo D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H
  Clinical Proteomic Tumor Analysis Consortium
  Cell 2021 Sep 16;184(19):5031-5052
• Comprehensive Characterization of 536 Patient-Derived Xenograft Models Prioritizes Candidates For Targeted Treatment
  Sun H*, Cao S*, Mashl RJ*, Mo CK*, Zaccaria S*, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, DiPersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L (*co-first authors)
  NCI PDXNet Consortium
  Nat Commun 2021 Aug 24;12(1):5086
• A Proteogenomic Portrait of Lung Squamous Cell Carcinoma
  Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gumus ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur O, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyo D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA
  Clinical Proteomic Tumor Analysis Consortium
  Cell 2021 Aug 5;184(16):4348-4371
• Co-Evolution of Tumor and Immune Cells During Progression of Multiple Myeloma
  Liu R, Gao Q, Foltz SM, Fowles JS, Yao L, Wang JT, Cao S, Sun H, Wendl MC, Sethuraman S, Weerasinghe A, Rettig MP, Storrs EP, Yoon CJ, Wyczalkowski MA, McMichael JF, Kohnen DR, King J, Goldsmith SR, O'Neal J, Fulton RS, Fronick CC, Ley TJ, Jayasinghe RG, Fiala MA, Oh ST, DiPersio JF, Vij R, Ding L
  Nat Commun 2021 May 7;12(1):2559
• Proteogenomic and Metabolomic Characterization of Human Glioblastoma
  Wang LB*, Karpova A*, Gritsenko MA*, Kyle JE*, Cao S*, Li Y*, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Cui Zhou D, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schurer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyo D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD, Liu T, Ding L (*co-first authors)
  Clinical Proteomic Tumor Analysis Consortium
  Cancer Cell 2021 Apr 12;39(4):509-528
• Conservation of Copy Number Profiles During Engraftment and Passaging of Patient-Derived Cancer Xenografts
  Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA 2nd, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH
  PDXNet Consortium (Contributors include: Cao S)
  Nat Genet 2021 Jan;53(1):86-99
• Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy
  Krug K, Jaehnig EJ, Satpathy S, Blumenberg L, Karpova A, Anurag M, Miles G, Mertins P, Geffen Y, Tang LC, Heiman DI, Cao S, Maruvka YE, Lei JT, Huang C, Kothadia RB, Colaprico A, Birger C, Wang J, Dou Y, Wen B, Shi Z, Liao Y, Wiznerowicz M, Wyczalkowski MA, Chen XS, Kennedy JJ, Paulovich AG, Thiagarajan M, Kinsinger CR, Hiltke T, Boja ES, Mesri M, Robles AI, Rodriguez H, Westbrook TF, Ding L, Getz G, Clauser KR, Fenyo D, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA
  Clinical Proteomic Tumor Analysis Consortium
  Cell 2020 Nov 25;183(5):1436-1456
• Discovery of Driver Non-Coding Splice-Site-Creating Mutations in Cancer
  Cao S, Zhou DC, Oh C, Jayasinghe RG, Zhao Y, Yoon CJ, Wyczalkowski MA, Bailey MH, Tsou T, Gao Q, Malone A, Reynolds S, Shmulevich I, Wendl MC, Chen F, Ding L
  Nat Commun 2020 Nov 4;11(1):5573
• Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
  Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gumus ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyo D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA
  Clinical Proteomic Tumor Analysis Consortium
  Cell 2020 Jul 9;182(1):200-225
• Evolution and Structure of Clinically Relevant Gene Fusions in Multiple Myeloma
  Foltz SM, Gao Q, Yoon CJ, Sun H, Yao L, Li Y, Jayasinghe RG, Cao S, King J, Kohnen DR, Fiala MA, Ding L, Vij R
  Nat Commun 2020 May 29;11(1):2666
• Proteogenomic Characterization of Endometrial Carcinoma
  Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekanski A, Jedryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyo D
  Clinical Proteomic Tumor Analysis Consortium
  Cell 2020 Feb 20;180(4):729-748
• Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
  Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gumus ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyo D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H
  Clinical Proteomic Tumor Analysis Consortium
  Cell 2019 Oct 31;179(4):964-983
• Regulated Phosphosignaling Associated With Breast Cancer Subtypes and Druggability
  Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held JM, Payne SH, Davies S, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyo D, Li S, Liu T, Carr SA, Ding L
  Mol Cell Proteomics 2019 Aug;18(8):1630-1650
• Dynamic Host Immune Response in Virus-Associated Cancers
  Cao S, Wylie KM, Wyczalkowski MA, Karpova A, Ley J, Sun S, Mashl RJ, Liang WW, Wang X, Johnson K, DiPersio JF, Gay H, Ratner L, Chen F, Adkins DR, Ding L
  Commun Biol 2019 Mar 22;2(1):109
• Systematic Analysis of Splice-Site-Creating Mutations in Cancer
  Jayasinghe RG*, Cao S*, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-Gonzalez H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyo D, Miner JH, Walter MJ, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L (*co-first author)
  Cancer Genome Atlas Research Network
  Cell Rep 2018 Apr 3;23(1):270-281
• Pathogenic Germline Variants in 10,389 Adult Cancers
  Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L
  Cancer Genome Atlas Research Network
  Cell 2018 Apr 5;173(2):355-370
• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
  Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L
  Fusion Analysis Working Group; Cancer Genome Atlas Research Network
  Cell Rep 2018 Apr 3;23(1):227-238
• Comprehensive Characterization of Cancer Driver Genes and Mutations
  Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortes-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L
  MC3 Working Group; Cancer Genome Atlas Research Network
  Cell 2018 Apr 5;173(2):371-385e18
• BreakPoint Surveyor: A Pipeline for Structural Variant Visualization
  Wyczalkowski MA, Wylie KM, Cao S, McLellan MD, Flynn J, Huang M, Ye K, Fan X, Chen K, Wendl MC, Ding L
  Bioinformatics 2017 Oct 1;33(19):3121-3122
• Proteogenomic Integration Reveals Therapeutic Targets in Breast Cancer Xenografts
  Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyo D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L
  Nat Commun 2017 Mar 28;8:14864
• Divergent Viral Presentation Among Human Tumors and Adjacent Normal Tissues
  Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L
  Sci Rep 2016 Jun 24;6:28294
• Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer
  Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyo D, Ellis MJ, Carr SA
  NCI CPTAC
  Nature 2016 Jun 2;534(7605):55-62
• An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer
  Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyo D
  Mol Cell Proteomics 2016 Mar;15(3):1060-71
• Systematic Discovery of Complex Insertions and Deletions in Human Cancers
  Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, Huang KL, Scott A, Foltz S, Niu B, Johnson KJ, Moed M, Slagboom PE, Chen F, Wendl MC, Ding L
  Nat Med 2016 Jan;22(1):97-104
• Gut DNA Viromes of Malawian Twins Discordant for Severe Acute Malnutrition
  Reyes A, Blanton LV, Cao S, Zhao G, Manary M, Trehan I, Smith MI, Wang D, Virgin HW, Rohwer F, Gordon JI
  Proc Natl Acad Sci U S A 2015 Sep 22;112(38):11941-6
• Species-Specific Transmission of Novel Picornaviruses in Lemurs
  Lim ES, Deem SL, Porton IJ, Cao S, Wang D
  J Virol 2015 Apr;89(7):4002-10
• An Outbreak of Acute Febrile Illness Caused by Sandfly Fever Sicilian Virus in the Afar Region of Ethiopia, 2011
  Woyessa AB, Omballa V, Wang D, Lambert A, Waiboci L, Ayele W, Ahmed A, Abera NA, Cao S, Ochieng M, Montgomery JM, Jima D, Fields B
  Am J Trop Med Hyg 2014 Dec;91(6):1250-3
• Geographic Variation in the Eukaryotic Virome of Human Diarrhea
  Holtz LR, Cao S, Zhao G, Bauer IK, Denno DM, Klein EJ, Antonio M, Stine OC, Snelling TL, Kirkwood CD, Wang D
  Virology 2014 Nov;468-470:556-564
• Predicting Structure and Stability for RNA Complexes With Intermolecular Loop-Loop Base-Pairing
  Cao S, Xu X, Chen SJ
  RNA 2014 Jun;20(6):835-45
• Discovery of Rosavirus 2, a Novel Variant of a Rodent-Associated Picornavirus, in Children From the Gambia
  Lim ES, Cao S, Holtz LR, Antonio M, Stine OC, Wang D
  Virology 2014 Apr;454-455:25-33
• Identification of Novel Viruses Using VirusHunter--An Automated Data Analysis Pipeline
  Zhao G, Krishnamurthy S, Cai Z, Popov VL, Travassos da Rosa AP, Guzman H, Cao S, Virgin HW, Tesh RB, Wang D
  PLoS One 2013 Oct 22;8(10):e78470
• Predicting Kissing Interactions in MicroRNA-Target Complex and Assessment of MicroRNA Activity
  Cao S, Chen SJ
  Nucleic Acids Res 2012 May;40(10):4681-90
• RNA-Puzzles: A CASP-Like Evaluation of RNA Three-Dimensional Structure Prediction
  Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E
  RNA 2012 Apr;18(4):610-25
• A Domain-Based Model for Predicting Large and Complex Pseudoknotted Structures
  Cao S, Chen SJ
  RNA Biol 2012 Feb;9(2):200-11
• Structure and Stability of RNA/RNA Kissing Complex: With Application to HIV Dimerization Initiation Signal
  Cao S, Chen SJ
  RNA 2011 Dec;17(12):2130-43
• Rational Truncation of an RNA Aptamer to Prostate-Specific Membrane Antigen Using Computational Structural Modeling
  Rockey WM, Hernandez FJ, Huang SY, Cao S, Howell CA, Thomas GS, Liu XY, Lapteva N, Spencer DM, McNamara JO, Zou X, Chen SJ, Giangrande PH
  Nucleic Acid Ther 2011 Oct;21(5):299-314
• A Conserved RNA Pseudoknot in a Putative Molecular Switch Domain of the 3'-Untranslated Region of Coronaviruses Is Only Marginally Stable
  Stammler SN, Cao S, Chen SJ, Giedroc DP
  RNA 2011 Sep;17(9):1747-59
• Physics-Based De Novo Prediction of RNA 3D Structures
  Cao S, Chen SJ
  J Phys Chem B 2011 Apr 14;115(14):4216-26
• Folding Kinetics for the Conformational Switch Between Alternative RNA Structures
  Cao S, Furtig B, Schwalbe H, Chen SJ
  J Phys Chem B 2010 Oct 28;114(42):13609-15
• Predicting Loop-Helix Tertiary Structural Contacts in RNA Pseudoknots
  Cao S, Giedroc DP, Chen SJ
  RNA 2010 Mar;16(3):538-52
• A New Computational Approach for Mechanical Folding Kinetics of RNA Hairpins
  Cao S, Chen SJ
  Biophys J 2009 May 20;96(10):4024-34
• Predicting Structures and Stabilities for H-Type Pseudoknots With Interhelix Loops
  Cao S, Chen SJ
  RNA 2009 Apr;15(4):696-706
• Predicting Ribosomal Frameshifting Efficiency
  Cao S, Chen SJ
  Phys Biol 2008 Mar 11;5(1):016002
• Biphasic Folding Kinetics of RNA Pseudoknots and Telomerase RNA Activity
  Cao S, Chen SJ
  J Mol Biol 2007 Mar 30;367(3):909-24
• Free Energy Landscapes of RNA/RNA Complexes: With Applications to SnRNA Complexes in Spliceosomes
  Cao S, Chen SJ
  J Mol Biol 2006 Mar 17;357(1):292-312
• Predicting RNA Pseudoknot Folding Thermodynamics
  Cao S, Chen SJ
  Nucleic Acids Res 2006 May 18;34(9):2634-52
• Predicting RNA Folding Thermodynamics With a Reduced Chain Representation Model
  Cao S, Chen SJ
  RNA 2005 Dec;11(12):1884-97
• Multiple-Scattering Approaches to Near-Edge X-Ray Absorption Fine Structure of N2O/Cu(100)
  Wu TQ, Tang JC, Shen SL, Cao S, Li HY
  Chinese Physics Letters 2004;21: 1586-1589
• New Insight on C-H Resonances in the Simple Hydrocarbons
  Zhu P, Tang JC, Cao S
  Journal of Electron Spectroscopy and Related Phenomena 2003;129:27-33
• Multiple-Scattering and DV-Xα Analyses of a Cl-Passivated Ge(111) Surface
  Cao S, Tang JC, Shen SL
  Journal of Physics: Condensed Matter 2003;15:5261-5268
• Multiple-Scattering of Near-Edge X-Ray Absorption Fine Structure of Sulphur-Passivated InP(100) Surface
  Cao S, Tang JC, Shen SL, Chen G, Ma D
  Chinese Physics Letters 2003;20:1151-1154
• Multiple-Scattering and DV-Xα Theoretical Analyses for Near-Edge X-Ray Absorption Fine Structure of SO3 /Cu(111)
  Cao S, Tang JC, Zhu P, Wang L, Shen SL
  Physical Review B 2002;66:045403 (9 pages)
• Multiple-Scattering Studies of the Near Edge X-Ray Absorption Fine Structure of the Cl-Passivated Ge(111) Surface
  Cao S, Tang JC, Wang L, Zhu P, Shen SL
  Surface Science 2002;505:289-294
• Multiple-Scattering and DV-Xα Theoretical Determination of the Local Structure of SO2 /Pd(111)
  Cao S, Tang JC, Wang L, Zhu P, Shen SL
  Journal of Physics: Condensed Matter 2002;4:3099-3113
• The Determination of the Local Adsorption Structure of SO2 /Ni(111): Multiple-Scattering Cluster Studies
  Cao S, Tang JC, Zhu P, Wang L
  Journal of Physics: Condensed Matter 2001;13:5865-5874

Invited Publications

• Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction
  Cao S, Chen SJ
  In: RNA 3D Structure Analysis and Prediction (Neocles Leontis N, Westhof E, eds), Chapter 10, pp 185-212, Springer, 2012