Faculty
Oncology Division
Alphabetical list (active faculty):   
Song Cao

Song Cao, PhD

Instructor

Department of Medicine

Oncology Division

Computational Biology

Research Interests

  • Bioinformatics
  • Cancer virology
  • Cancer genomics
  • Cancer proteomics

Contact

  • 314-273-1207 (office)
  • 314-747-9320 (fax)
  • Division of Oncology
    Mail Stop 8076-0041-03
    Washington University
    660 South Euclid Avenue
    St. Louis, MO 63110
  • Room 3101E, Couch Biomedical Research Building (office)

Peer-reviewed Manuscripts

  • 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
  • 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