Comprensive list of publications I have co-authored
Adequacy of the linearized local electric field determination in a cubically nonlinear composite. Wyczalkowski MA. Optik 1997;105(1):41-44.
Optimization of acoustic scattering from dual-frequency driven microbubbles at the difference frequency. Wyczalkowski MA, Szeri AJ. J. Acoust. Soc. Am. 2003;113(6):3073-3079.
Characterizing the conformational ensemble of monomeric polyglutamine. Wang X, A Vitalis, Wyczalkowski MA, Pappu RV. Proteins 2006;63:297-311.
Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange. Wyczalkowski MA, Pappu RV. Phys. Rev. E 2008;77:026104.
Niche Construction through Cooperation: A Nonlinear Dynamics Contribution to Modeling Facets of the Evolutionary History in the Genus Homo. Fuentes A, Wyczalkowski MA, MacKinnon KC. Current Anthropology 2010;51(3):435-444.
New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision. Wyczalkowski MA, Vitalis A, Pappu RV. J. Phys. Chem. B 2010;114:8166-8180.
Computational Models for Mechanics of Morphogenesis. Wyczalkowski MA, Chen Z, Filas BA, Varner VD and Taber LA. Birth Defects Res C. 2012;96(2):132–152.
Computational and Experimental Study of the Mechanics of Embryonic Wound Healing. Wyczalkowski MA, Varner VD, Taber LA. J Mech Behav Biomed Mater 2013;28:125-146.
Mutational landscape and significance across 12 major cancer types. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JA, Wyczalkowski MA, Leiserson MDM, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L. Nature 2013;502:333-339.
Integrated analysis of germline and somatic variants in ovarian cancer. Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L. Nature Communications 2014;5:3156.
Simple and accurate methods for quantifying deformation, disruption, and development in biological tissues. Boyle JJ, Kume M, Wyczalkowski MA, Taber LA, Pless RB, Xia Y, Genin GM, Thomopoulos S. J R Soc Interface, 2014;11(100):20140685.
The genomic landscape of childhood and adolescent melanoma. Lu C, Zhang J, Nagahawatte P, Easton J, Lee S, Liu Z, Ding L, Wyczalkowski MA, Valentine M, Navid F, Mulder H, Tatevossian RG, Dalton J, Davenport J, Yin Z, Edmonson M, Rusch M, Wu G, Li Y, Parker M, Hedlund E, Shurtleff S, Raimondi S, Bhavin V, Donald Y, Mardis ER, Wilson RK, Evans WE, Ellison DW, Pounds S, Dyer M, Downing JR, Pappo A, Bahrami A. J Invest Dermatol 2015;135(3):816–823.
Patterns and functional implications of rare germline variants across 12 cancer types. Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, DiPersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L. Nat Commun 2015 Dec 22;6:10086.
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.
Protein-structure-guided discovery of functional mutations across 19 cancer types. Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L. Nat Genet 2016 Aug;48(8):827-37.
Integrated genomic and molecular characterization of cervical cancer. Cancer Genome Atlas Research Network (Contributors include: Ding L, Bailey M, Wyczalkowski MA. Nature 2017 Mar 16;543(7645):378-384.
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
GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Mashl RJ, Scott AS, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael B, Wendl MC, Ding L. Genome Res 2017 May 18;8:1450-1459.
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 Jun 5;33(19):3121-3122.
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cancer Genome Atlas Network (Corresponding author Ding L. Contributors include: Bailey MH, Gao Q, Wong W, Wyczalkowski MA, Yellapantula V). Cell. 2017 Nov 2;171(4):950-965
Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang W, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, The Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Cell Rep 2018 Apr 3;23(1):270-281
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Gao Q, Liang W, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao W, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, The Fusion Analysis Working Group, The Cancer Genome Atlas Research Network , Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter N, Shmulevich I, Ding L. Cell Rep 2018 Apr 3;23(1):227-238
Pathogenic Germline Variants in 10,389 Adult Cancers. Huang K, 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 L, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim T, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, The Cancer Genome Atlas Research Network , 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. Cell. 2018 Apr 5.173(2):355-370
Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang K, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich I, Lazar AJ, Wheeler DA, Getz G, The Cancer Genome Atlas Research Network. Cell. 2018 Apr 5.173(2):305-320
Integrative Omics Analyses Broaden Treatment Targets in Human Cancer. Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyo D, Townsend RR, DiPersio JF, Chen F, Ding L. Genome Med 2018 Jul 27;10(1):60
Database of Evidence for Precision Oncology Portal. Sun SQ, Mashl RJ, Sengupta S, Scott AD, Wang W, Batra P, Wang LB, Wyczalkowski MA, Ding L. Bioinformatics 2018 Dec 15;34(24):4315-4317
CharGer: Clinical Characterization of Germline Variants. Scott AD, Huang KL, Weerasinghe A, Mashl RJ, Gao Q, Martins Rodrigues F, Wyczalkowski MA, Ding L. Bioinformatics 2019 Mar 1;35(5):865-867
Dynamic host immune response in virus-associated cancers. Cao S, Wylie KM, Wyczalkowski MA, Karpova A, Ley J, Sun S, Mashl RJ, Liang W, Wang X, Johnson K, DiPersio JF, Gay H, Ratner L, Chen F, Adkins DR, Ding L. Communications Biology 2019 2, no. 1 (2019): 109.
Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data. Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Liang H, Noble MS. Genomic Data Analysis Network. Cell Syst 2019 Jul 24;9(1):24-34e10
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):964-983e31
Proteogenomic Characterization of Endometrial Carcinoma. Dou Y, Kawaler EA, Zhou DC, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai C, Wen B, Li Z, Cao S, Moon J, Shi Z, Wyczalkowski MA, …, Gao Q, …, Sethuraman S, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D, Clinical Proteomic Tumor Analysis Consortium. Cell 180, 1–20, February 20, 2020
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Gillette MA, Satpathy S, Cao S, Dhanasekaran S, Vasaikar S, Krug K, Petralia F, Li Y, Liang WW, Reva B, Hong R,…, Yao L,…, Wendl MC,…, Wyczalkowski MA,…, Ding L, Mani DR, Carr SA. Clinical Proteomic Tumor Analysis Consortium. Cell 182, 200–225, July 9, 2020
Discovery of driver non-coding splice-site-creating mutations in cancer. Cao S, Cui Zhou D, Oh C, Jayasinghe RG, Zhao Y, Yoon C, Wyczalkowski MA, Bailey MH, Tsou T, Gao Q, Malone A, Reynolds S, Shmulevich I, Wendl MC, Chen F & Ding L. Nat Commun 11, 5573 (2020)
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 L, Heiman D, Cao S, Maruvka Y, Lei J, Huang C, Kothadia R, 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 KRF, Fenyö D, Ruggles KV, Zhang B, Mani DR, Carr SA, Ellis MJ, Gillette MA. Cell 183, 1–21, November 25, 2020
Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD Clinical Tumor Analysis Consortium Cell Rep Med 2020 Apr 21;1(1)
Proteogenomic and metabolomic characterization of human glioblastoma. Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov Dˉ, Colaprico Aˉ, Rothstein JHˉ, Hong Rˉ, Stathias Vˉ, Cornwell Mˉ, Petralia Fˉ, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Zhou DC, 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, Schürer 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, Fenyö 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. Clinical Proteomic Tumor Analysis Consortium. Cancer Cell 39, 1–20 April 12, 2021
Proteogenomic Insights Into the Biology and Treatment of HPV-Negative Head and Neck Squamous Cell Carcinoma. Huang C, Chen L, Savage SR, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieslik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubinski J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW, Zhang H, Zhang B. Clinical Proteomic Tumor Analysis Consortium. Cancer Cell 2021 Jan 5;
Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Cui Zhou D, Jayasinghe RG, Herndon JM, Storrs E, Mo CK, Wu Y, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Thammavong L, Sato K, Zhu H, Sun H, Wang LB, Yize Li, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Liu R, Reeb A, Wendl MC, Oh C, Serasanambati M, Lal P, Varghese R, Mashl RJ, Ponce J, Terekhanova NV, Naser Al Deen N, Yao L, Wang F, Chen L, Schnaubelt M, Puram SV, Kim AH, Song SK, Shoghi KI, Ju T, Hawkins WG, Chen K, Chatterjee D, Zhang H, Chheda MG, Achilefu S, DeNardo DG, Oh ST, Chen F, Gillanders WE, Fields RC, Ding L https://www.biorxiv.org/content/10.1101/2021.01.13.426413v1.full
Spatially interacting phosphorylation sites and mutations in cancer. Huang KL, Scott AD, Zhou DC, Wang LB, Weerasinghe A, Elmas A, Liu R, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, Raphael B, Fenyö D, Chen K, Mills G, Ding L. Nature Communications volume 12, Article number: 2313 (2021)
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
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
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, NCI PDXNet Consortium. Nat Commun 2021 Aug 24;12(1):5086
Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cao L, Huang C, Zhou DC, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, 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, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding Lˇ, Zhang Bˇ, Zhang Hˇ Clinical Proteomic Tumor Analysis Consortium. Cell 184, 5031–5052, September 16, 2021
Moving pan-cancer studies from basic research toward the clinic. Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L. Nature Cancer, 2021 Sep 16
Pollock: Fishing for Cell States. Storrs EP, Zhou DC, Wendl MC, Wyczalkowski MA, Karpova A, Wang LB, Li Y, Southard-Smith A, Jayasinghe RG, Yao L, Liu R, Wu Y, Terekhanova NV, Zhu H, Herndon JM, Puram S, Chen F, Gillanders WE, Fields RC, Ding L. Bioinform Adv 2022 May 13;2(1):vbac028
Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Cui Zhou D, Jayasinghe RG, Chen S, Herndon JM, Storrs E, Mo CK, Wu Y, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Thammavong L, Sato K, Zhu H, Sun H, Wang LB, Li Y, Zuo C, McMichael JF, Davies SR, Appelbaum EL, Robbins KJ, Chasnoff SE, Yang X, Liu R, Reeb A, Wendl MC, Oh C, Serasanambati M, Lal P, Varghese R, Mashl RJ, Ponce J, Terekhanova NV, Naser Al Deen N, Yao L, Wang F, Chen L, Schnaubelt M, Puram SV, Kim AH, Song SK, Shoghi KI, Ju T, Hawkins WG, Chen K, Chatterjee D, Zhang H, Achilefu S, Chheda MG, Oh ST, Gillanders WE, Chen F, DeNardo DG, Fields RC, Ding L. Nature genetics, 2022 Aug 22
Ghobadi, A and JF DiPersio. Gene and Cellular Immunotherapy for Cancer. Illustrations by Wyczalkowski MA et al. Humana Press, 2022.
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. SenNet Consortium (Contributors include: Ding L, Wendl MC, Wyczalkowski MA). Nature Aging; 20 December 2022
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 DWˇ, Ricketts CJˇ, Nesvizhskii AIˇ, Zhang Hˇ, Ding Lˇ. Clinical Proteomic Tumor Analysis Consortium Cancer Cell 2022 Dec 20:S1535-6108(22)00565-7;
Single-Cell Discovery and Multi-Omic 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, Martins Rodrigues F, 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 Feb 13:CAN-22-1769
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 MA, 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
Proteogenomic Insights Suggest Druggable Pathways in Endometrial Carcinoma. Dou Y, Katsnelson L, Gritsenko MA, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJ, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekanski A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jedryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B, Liu T, Fenyo D Clinical Proteomic Tumor Analysis Consortium. Cancer Cell 2023 Aug 2:S1535-6108(23)00247-7
Proteogenomic data and resources for pan-cancer analysis. Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH. Clinical Proteomic Tumor Analysis Consortium. Cancer Cell 41 (8), 1397-1406
Pan-cancer proteogenomics connects oncogenic drivers to functional states Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias Vˉ , Geffen Yˉ , Imbach KJˉ , Cao Sˉ , Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, Wendl MC, Zhang W, Sibai M, Ruiz-Serra V, Liang WW, Terekhanova NV, Rodrigues FM, Clauser KR, Heiman DI, Zhang Q, Aguet F, Calinawan AP, Dhanasekaran SM, Birger C, Satpathy S, Zhou DC, Wang LB, Baral J, Johnson JL, Huntsman EM, Pugliese P, Colaprico A, Iavarone A, Chheda MG, Ricketts CJ, Fenyö D, Payne SH, Rodriguez H, Robles AI, Gillette MA, Kumar-Sinha C, Lazar AJ, Cantley LC, Getz G, Ding L. Clinical Proteomic Tumor Analysis Consortium. Cell 2023; DOI: 10.1016/j.cell.2023.07.014
Epigenetic regulation during cancer transitions across 11 tumour types. Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, X L, Wyczalkowski MA, Lu RJ, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo C, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L. Nature (2023)
Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma Wu Y, Chen S, Yang X, Sato K, Lal P, Wang Y, Shinkle A, Wendl M, Primeau T, Zhao Y, Gould A, Sun H, Mudd J, Hoog J, Mashl RJ, Wyczalkowski M, Mo C, Liu R, Herndon J, Davies R, Liu D, Ding X, Evrard Y, Welm B, Lum D, Koh M, Welm A, Chuang J, Moscow J, Meric-Bernstam F, Govindan R, Li S, Hsieh J, Fields RC, Lim K, Ma C, Zhang H, Ding L, Chen F. Cancer Res (2023)
T-cell redirecting therapies for B-cell non-Hodgkin lymphoma: recent progress and future directions. Russler-Germain DA, Ghobadi A. Frontiers in Oncology, Volume 13 (2023). Figures by Wyczalkowski MA.
Multi-scale signaling and tumor evolution in high-grade gliomas. Liu J, Cao S, Imbach KJ , Gritsenko MA , Lih TM , Kyle JEˉ, Yaron-Barir TMˉ, Binder ZAˉ, Li Yˉ, Strunilin Iˉ, Wang YTˉ, Tsai CFˉ, Ma Wˉ, Chen Lˉ, Clark NM, Shinkle A, Naser Al Deen N, Caravan W, Houston A, Simin FA, Wyczalkowski MA, Wang LB, Storrs E, Chen S, Illindala R, Li YD, Jayasinghe RG, Rykunov D, Cottingham SL, Chu RK, Weitz KK, Moore RJ, Sagendorf T, Petyuk VA, Nestor M, Bramer LM, Stratton KG, Schepmoes AA, Couvillion SP, Eder J, Kim YM, Gao Y, Fillmore TL, Zhao R, Monroe ME, Southard-Smith AN, Li YE, Lu RJ, Johnson JL, Wiznerowicz M, Hostetter G, Newton CJ, Ketchum KA, Thangudu RR, Barnholtz-Sloan JS, Wang P, Fenyö D, An E, Thiagarajan M, Robles AI, Mani DR, Smith RD, Porta-Pardo E, Cantley LC, Iavarone A, Chen F, Mesri M, Nasrallah MP, Zhang H, Resnick AC, Chheda MG, Rodland KD, Liu T , Ding L. Philadelphia Coalition for a Cure, Clinical Proteomic Tumor Analysis Consortium. Cancer Cell (2024): 1217-1238
Differential Chromatin Accessibility and Transcriptional Dynamics Define Breast Cancer Subtypes and Their Lineages. Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Naser Al Deen N, Shinkle AT, Lu RJH, Caravan W, Houston A, Zhao Y, Sato K, Lal P, Street C, Rodrigues FM, Southard-Smith AN, Targino da Costa ALN, Zhu H, Mo CK, Crowson L, Fulton RS, Wyczalkowski MA, Fronick CC, Fulton LA, Sun H, Davies SR, Appelbaum EL, Chasnoff SE, Carmody M, Brooks C, Liu R, Wendl MC, Oh C, Bender D, Cruchaga C, Harari O, Bredemeyer A, Lavine K, Bose R, Margenthaler J, Held JM, Achilefu S, Ademuyiwa F, Aft R, Ma C, Colditz GA, Ju T, Oh ST, Fitzpatrick J, Hwang ES, Shoghi KI, Chheda MG, Veis DJ, Chen F, Fields RC, Gillanders WE, Ding L. Nature Cancer. Oct. 30, 2024
Pan-cancer proteogenomics characterization of tumor immunity. Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MGR, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma’ayan A, Lazar AJ, Ceccarelli M, Wang P. Clinical Proteomic Tumor Analysis Consortium (Contributors include: Ding L, Cao S, Zhou DC, RodriguesFM, Song Y, Storrs EP, Wang LB, Terekhanova NV, Wu Y, Wyczalkowski MA, Yao L). Cell (2024)
Cellular senescence in human liver under normal aging and cancer. Karpova A, Li X, Peng CW , Gallant KL , Rapp DR , Alligood DM, Houston AJ, Park A, Targino da Costa ALN, Chou WH, Iglesia MD, Herndon JM, Byrnes K, Naser Al Deen N, Lal P, Fang X, Jayasinghe RG, Blatnik JA, Hawkins WG, Sanford DE, Eagon JC, Leigh N, Doyle MBM, Brunt LM, Chapman WC, Panni RZ, Cullinan DR, Davies SR, Guo J, Wyczalkowski MA, Wendl MC, Zhang H, Martin CA, Warner BW, Chheda MG, Stewart SA, Chen F, Fields RC, Ding L. Cell Genomics (2026)
Last update: Feb. 2026