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  • Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.

    Published in:
    Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37211-7
    By:
    • Wu, Yige;
    • Terekhanova, Nadezhda V.;
    • Caravan, Wagma;
    • Naser Al Deen, Nataly;
    • Lal, Preet;
    • Chen, Siqi;
    • Mo, Chia-Kuei;
    • Cao, Song;
    • Li, Yize;
    • Karpova, Alla;
    • Liu, Ruiyang;
    • Zhao, Yanyan;
    • Shinkle, Andrew;
    • Strunilin, Ilya;
    • Weimholt, Cody;
    • Sato, Kazuhito;
    • Yao, Lijun;
    • Serasanambati, Mamatha;
    • Yang, Xiaolu;
    • Wyczalkowski, Matthew
    Publication type:
    Article

  • Author Correction: Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.

    Published in:
    2023
    By:
    • Wu, Yige;
    • Terekhanova, Nadezhda V.;
    • Caravan, Wagma;
    • Naser Al Deen, Nataly;
    • Lal, Preet;
    • Chen, Siqi;
    • Mo, Chia-Kuei;
    • Cao, Song;
    • Li, Yize;
    • Karpova, Alla;
    • Liu, Ruiyang;
    • Zhao, Yanyan;
    • Shinkle, Andrew;
    • Strunilin, Ilya;
    • Weimholt, Cody;
    • Sato, Kazuhito;
    • Yao, Lijun;
    • Serasanambati, Mamatha;
    • Yang, Xiaolu;
    • Wyczalkowski, Matthew
    Publication type:
    Correction Notice

  • Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.

    Published in:
    Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37211-7
    By:
    • Wu, Yige;
    • Terekhanova, Nadezhda V.;
    • Caravan, Wagma;
    • Naser Al Deen, Nataly;
    • Lal, Preet;
    • Chen, Siqi;
    • Mo, Chia-Kuei;
    • Cao, Song;
    • Li, Yize;
    • Karpova, Alla;
    • Liu, Ruiyang;
    • Zhao, Yanyan;
    • Shinkle, Andrew;
    • Strunilin, Ilya;
    • Weimholt, Cody;
    • Sato, Kazuhito;
    • Yao, Lijun;
    • Serasanambati, Mamatha;
    • Yang, Xiaolu;
    • Wyczalkowski, Matthew
    Publication type:
    Article

  • Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

    Published in:
    Nature Communications, 2017, v. 8, n. 4, p. 15479, doi. 10.1038/ncomms15479
    By:
    • Huang, Kuan-lin;
    • Li, Shunqiang;
    • Mertins, Philipp;
    • Cao, Song;
    • Gunawardena, Harsha P.;
    • Ruggles, Kelly V.;
    • Mani, D. R.;
    • Clauser, Karl R.;
    • Tanioka, Maki;
    • Usary, Jerry;
    • Kavuri, Shyam M.;
    • Xie, Ling;
    • Yoon, Christopher;
    • Qiao, Jana W.;
    • Wrobel, John;
    • Wyczalkowski, Matthew A.;
    • Erdmann-Gilmore, Petra;
    • Snider, Jacqueline E.;
    • Hoog, Jeremy;
    • Singh, Purba
    Publication type:
    Article

  • Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

    Published in:
    Nature Communications, 2017, v. 8, n. 3, p. 14864, doi. 10.1038/ncomms14864
    By:
    • Huang, Kuan-lin;
    • Li, Shunqiang;
    • Mertins, Philipp;
    • Cao, Song;
    • Gunawardena, Harsha P.;
    • Ruggles, Kelly V.;
    • Mani, D. R.;
    • Clauser, Karl R.;
    • Tanioka, Maki;
    • Usary, Jerry;
    • Kavuri, Shyam M.;
    • Xie, Ling;
    • Yoon, Christopher;
    • Qiao, Jana W;
    • Wrobel, John;
    • Wyczalkowski, Matthew A.;
    • Erdmann-Gilmore, Petra;
    • Snider, Jacqueline E.;
    • Hoog, Jeremy;
    • Singh, Purba
    Publication type:
    Article

  • Patterns and functional implications of rare germline variants across 12 cancer types.

    Published in:
    Nature Communications, 2015, v. 6, n. 12, p. 10086, doi. 10.1038/ncomms10086
    By:
    • Lu, Charles;
    • Xie, Mingchao;
    • Wendl, Michael C.;
    • Wang, Jiayin;
    • McLellan, Michael D.;
    • Leiserson, Mark D. M.;
    • Huang, Kuan-lin;
    • Wyczalkowski, Matthew A.;
    • Jayasinghe, Reyka;
    • Banerjee, Tapahsama;
    • Ning, Jie;
    • Tripathi, Piyush;
    • Zhang, Qunyuan;
    • Niu, Beifang;
    • Ye, Kai;
    • Schmidt, Heather K.;
    • Fulton, Robert S.;
    • McMichael, Joshua F.;
    • Batra, Prag;
    • Kandoth, Cyriac
    Publication type:
    Article

  • Integrated analysis of germline and somatic variants in ovarian cancer.

    Published in:
    Nature Communications, 2014, v. 5, n. 1, p. 3156, doi. 10.1038/ncomms4156
    By:
    • Kanchi, Krishna L.;
    • Johnson, Kimberly J.;
    • Lu, Charles;
    • McLellan, Michael D.;
    • Leiserson, Mark D. M.;
    • Wendl, Michael C.;
    • Zhang, Qunyuan;
    • Koboldt, Daniel C.;
    • Xie, Mingchao;
    • Kandoth, Cyriac;
    • McMichael, Joshua F.;
    • Wyczalkowski, Matthew A.;
    • Larson, David E.;
    • Schmidt, Heather K.;
    • Miller, Christopher A.;
    • Fulton, Robert S.;
    • Spellman, Paul T.;
    • Mardis, Elaine R.;
    • Druley, Todd E.;
    • Graubert, Timothy A.
    Publication type:
    Article

  • CharGer: clinical Characterization of Germline variants.

    Published in:
    Bioinformatics, 2019, v. 35, n. 5, p. 865, doi. 10.1093/bioinformatics/bty649
    By:
    • Scott, Adam D;
    • Huang, Kuan-Lin;
    • Weerasinghe, Amila;
    • Mashl, R Jay;
    • Gao, Qingsong;
    • Rodrigues, Fernanda Martins;
    • Wyczalkowski, Matthew A;
    • Ding, Li
    Publication type:
    Article

  • Database of evidence for precision oncology portal.

    Published in:
    Bioinformatics, 2018, v. 34, n. 24, p. 4315, doi. 10.1093/bioinformatics/bty531
    By:
    • Sun, Sam Q;
    • Mashl, R Jay;
    • Sengupta, Sohini;
    • Scott, Adam D;
    • Wang, Weihua;
    • Wang, Liang-Bo;
    • Wyczalkowski, Matthew A;
    • Batra, Prag;
    • Ding, Li
    Publication type:
    Article

  • Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.

    Published in:
    Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25177-3
    By:
    • Sun, Hua;
    • Cao, Song;
    • Mashl, R. Jay;
    • Mo, Chia-Kuei;
    • Zaccaria, Simone;
    • Wendl, Michael C.;
    • Davies, Sherri R.;
    • Bailey, Matthew H.;
    • Primeau, Tina M.;
    • Hoog, Jeremy;
    • Mudd, Jacqueline L.;
    • Dean II, Dennis A.;
    • Patidar, Rajesh;
    • Chen, Li;
    • Wyczalkowski, Matthew A.;
    • Jayasinghe, Reyka G.;
    • Rodrigues, Fernanda Martins;
    • Terekhanova, Nadezhda V.;
    • Li, Yize;
    • Lim, Kian-Huat
    Publication type:
    Article

  • Co-evolution of tumor and immune cells during progression of multiple myeloma.

    Published in:
    Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22804-x
    By:
    • Liu, Ruiyang;
    • Gao, Qingsong;
    • Foltz, Steven M.;
    • Fowles, Jared S.;
    • Yao, Lijun;
    • Wang, Julia Tianjiao;
    • Cao, Song;
    • Sun, Hua;
    • Wendl, Michael C.;
    • Sethuraman, Sunantha;
    • Weerasinghe, Amila;
    • Rettig, Michael P.;
    • Storrs, Erik P.;
    • Yoon, Christopher J.;
    • Wyczalkowski, Matthew A.;
    • McMichael, Joshua F.;
    • Kohnen, Daniel R.;
    • King, Justin;
    • Goldsmith, Scott R.;
    • O'Neal, Julie
    Publication type:
    Article

  • Spatially interacting phosphorylation sites and mutations in cancer.

    Published in:
    Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22481-w
    By:
    • Huang, Kuan-lin;
    • Scott, Adam D.;
    • Zhou, Daniel Cui;
    • Wang, Liang-Bo;
    • Weerasinghe, Amila;
    • Elmas, Abdulkadir;
    • Liu, Ruiyang;
    • Wu, Yige;
    • Wendl, Michael C.;
    • Wyczalkowski, Matthew A.;
    • Baral, Jessika;
    • Sengupta, Sohini;
    • Lai, Chin-Wen;
    • Ruggles, Kelly;
    • Payne, Samuel H.;
    • Raphael, Benjamin;
    • Fenyö, David;
    • Chen, Ken;
    • Mills, Gordon;
    • Ding, Li
    Publication type:
    Article

  • Discovery of driver non-coding splice-site-creating mutations in cancer.

    Published in:
    Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19307-6
    By:
    • Cao, Song;
    • Zhou, Daniel Cui;
    • Oh, Clara;
    • Jayasinghe, Reyka G.;
    • Zhao, Yanyan;
    • Yoon, Christopher J.;
    • Wyczalkowski, Matthew A.;
    • Bailey, Matthew H.;
    • Tsou, Terrence;
    • Gao, Qingsong;
    • Malone, Andrew;
    • Reynolds, Sheila;
    • Shmulevich, Ilya;
    • Wendl, Michael C.;
    • Chen, Feng;
    • Ding, Li
    Publication type:
    Article

  • Mutational landscape and significance across 12 major cancer types.

    Published in:
    Nature, 2013, v. 502, n. 7471, p. 333, doi. 10.1038/nature12634
    By:
    • Kandoth, Cyriac;
    • McLellan, Michael D.;
    • Vandin, Fabio;
    • Ye, Kai;
    • Niu, Beifang;
    • Lu, Charles;
    • Xie, Mingchao;
    • Zhang, Qunyuan;
    • McMichael, Joshua F.;
    • Wyczalkowski, Matthew A.;
    • Leiserson, Mark D. M.;
    • Miller, Christopher A.;
    • Welch, John S.;
    • Walter, Matthew J.;
    • Wendl, Michael C.;
    • Ley, Timothy J.;
    • Wilson, Richard K.;
    • Raphael, Benjamin J.;
    • Ding, Li
    Publication type:
    Article

  • Pollock: fishing for cell states.

    Published in:
    Bioinformatics Advances, 2022, v. 2, n. 1, p. 1, doi. 10.1093/bioadv/vbac028
    By:
    • Storrs, Erik P;
    • Zhou, Daniel Cui;
    • Wendl, Michael C;
    • Wyczalkowski, Matthew A;
    • Karpova, Alla;
    • Wang, Liang-Bo;
    • Li, Yize;
    • Southard-Smith, Austin;
    • Jayasinghe, Reyka G;
    • Yao, Lijun;
    • Liu, Ruiyang;
    • Wu, Yige;
    • Terekhanova, Nadezhda V;
    • Zhu, Houxiang;
    • Herndon, John M;
    • Puram, Sid;
    • Chen, Feng;
    • Gillanders, William E;
    • Fields, Ryan C;
    • Ding, Li
    Publication type:
    Article

  • Divergent viral presentation among human tumors and adjacent normal tissues.

    Published in:
    Scientific Reports, 2016, p. 28294, doi. 10.1038/srep28294
    By:
    • Cao, Song;
    • Wendl, Michael C.;
    • Wyczalkowski, Matthew A.;
    • Wylie, Kristine;
    • Ye, Kai;
    • Jayasinghe, Reyka;
    • Xie, Mingchao;
    • Wu, Song;
    • Niu, Beifang;
    • Grubb, Robert;
    • Johnson, Kimberly J.;
    • Gay, Hiram;
    • Chen, Ken;
    • Rader, Janet S.;
    • Dipersio, John F.;
    • Chen, Feng;
    • Ding, Li
    Publication type:
    Article

  • Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment.

    Published in:
    2022
    By:
    • Sun, Hua;
    • Cao, Song;
    • Mashl, R. Jay;
    • Mo, Chia-Kuei;
    • Zaccaria, Simone;
    • Wendl, Michael C.;
    • Davies, Sherri R.;
    • Bailey, Matthew H.;
    • Primeau, Tina M.;
    • Hoog, Jeremy;
    • Mudd, Jacqueline L.;
    • Dean II, Dennis A.;
    • Patidar, Rajesh;
    • Chen, Li;
    • Wyczalkowski, Matthew A.;
    • Jayasinghe, Reyka G.;
    • Rodrigues, Fernanda Martins;
    • Terekhanova, Nadezhda V.;
    • Li, Yize;
    • Lim, Kian-Huat
    Publication type:
    Correction Notice

  • Characterizing the conformational ensemble of monomeric polyglutamine.

    Published in:
    Proteins, 2006, v. 63, n. 2, p. 297, doi. 10.1002/prot.20761
    By:
    • Wang, Xiaoling;
    • Vitalis, Andreas;
    • Wyczalkowski, Matthew A.;
    • Pappu, Rohit V.
    Publication type:
    Article

  • Integrative omics analyses broaden treatment targets in human cancer.

    Published in:
    Genome Medicine, 2018, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13073-018-0564-z
    By:
    • Sengupta, Sohini;
    • Sun, Sam Q.;
    • Huang, Kuan-lin;
    • Oh, Clara;
    • Bailey, Matthew H.;
    • Varghese, Rajees;
    • Wyczalkowski, Matthew A.;
    • Ning, Jie;
    • Tripathi, Piyush;
    • McMichael, Joshua F.;
    • Johnson, Kimberly J.;
    • Kandoth, Cyriac;
    • Welch, John;
    • Ma, Cynthia;
    • Wendl, Michael C.;
    • Payne, Samuel H.;
    • Fenyö, David;
    • Townsend, Reid R.;
    • Dipersio, John F.;
    • Chen, Feng
    Publication type:
    Article

  • Breakpoint Surveyor: a pipeline for structural variant visualization.

    Published in:
    Bioinformatics, 2017, v. 33, n. 19, p. 3121, doi. 10.1093/bioinformatics/btx362
    By:
    • Wyczalkowski, Matthew A.;
    • Wylie, Kristine M.;
    • Song Cao;
    • McLellan, Michael D.;
    • Flynn, Jennifer;
    • Mo Huang;
    • Kai Ye;
    • Xian Fan;
    • Ken Chen;
    • Wendl, Michael C.;
    • Li Ding
    Publication type:
    Article

  • The Genomic Landscape of Childhood and Adolescent Melanoma.

    Published in:
    Journal of Investigative Dermatology, 2015, v. 135, n. 3, p. 816, doi. 10.1038/jid.2014.425
    By:
    • Lu, Charles;
    • Zhang, Jinghui;
    • Nagahawatte, Panduka;
    • Easton, John;
    • Lee, Seungjae;
    • Liu, Zhifa;
    • Ding, Li;
    • Wyczalkowski, Matthew A;
    • Valentine, Marcus;
    • Navid, Fariba;
    • Mulder, Heather;
    • Tatevossian, Ruth G;
    • Dalton, James;
    • Davenport, James;
    • Yin, Zhirong;
    • Edmonson, Michael;
    • Rusch, Michael;
    • Wu, Gang;
    • Li, Yongjin;
    • Parker, Matthew
    Publication type:
    Article