Prof. Aedin Culhane

Hsu L.L.;Culhane A.C. (2023) Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data. Scientific Reports

de Matos Simoes R.;Shirasaki R.;Downey-Kopyscinski S.L.;Matthews G.M.;Barwick B.G.;Gupta V.A.;Dupéré-Richer D.;Yamano S.;Hu Y.;Sheffer M.;Dhimolea E.;Dashevsky O.;Gandolfi S.;Ishiguro K.;Meyers R.M.;Bryan J.G.;Dharia N.V.;Hengeveld P.J.;Brüggenthies J.B.;Tang H.;Aguirre A.J.;Sievers Q.L.;Ebert B.L.;Glassner B.J.;Ott C.J.;Bradner J.E.;Kwiatkowski N.P.;Auclair D.;Levy J.;Keats J.J.;Groen R.W.J.;Gray N.S.;Culhane A.C.;McFarland J.M.;Dempster J.M.;Licht J.D.;Boise L.H.;Hahn W.C.;Vazquez F.;Tsherniak A.;Mitsiades C.S. (2023) Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias. Nature Cancer :754-773

Eckenrode KB;Righelli D;Ramos M;Argelaguet R;Vanderaa C;Geistlinger L;Culhane AC;Gatto L;Carey V;Morgan M;Risso D;Waldron L; (2023) Curated single cell multimodal landmark datasets for R/Bioconductor.. Plos Computational Biology

Matthew Pugh,Éanna Fennell,Ciara I Leahy,Tracey Perry,Beata Hargitai,Tamas Marton,Kelly J. Hunter,Graham Halford,Hale Onder Yilmaz,Zania Stamataki,Gary Reynolds,Harriet J. Hill,Benjamin E. Willcox,Neil Steven,Catherine A. Thornton,Stefan D. Dojcinov,Aedin Culhane,Paul G. Murray,Graham S. Taylor (2022) Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis. bioRxiv

Wang Y.;Buck A.;Grimaud M.;Culhane A.C.;Kodangattil S.;Razimbaud C.;Bonal D.M.;Nguyen Q.D.;Zhu Z.;Wei K.;O'Donnell M.L.;Huang Y.;Signoretti S.;Choueiri T.K.;Freeman G.J.;Zhu Q.;Marasco W.A. (2022) Anti-CAIX BBζ CAR4/8 T cells exhibit superior efficacy in a ccRCC mouse model. Molecular Therapy Oncolytics :385-399

Dhimolea, Eugen;Simoes, Ricardo De Matos;Kansara, Dhvanir;Vilas, Caroline;Al'Khafaji, Aziz;Bouyssou, Juliette;Culhane, Aedin;Mitsiades, Constantine S.; (2021) Treatment-induced embryonic diapause-like adaptation through suppression of Myc activity as mediator of drug persistence in cancer. Cancer Research

Lauren L. Hsu; Aedi­n C. Culhane; (2021) Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data. Biorxiv : The Preprint Server For Biology

Cao, Kim-Anh Le;Abadi, Al J.;Davis-Marcisak, Emily F.;Hsu, Lauren;Arora, Arshi;Coullomb, Alexis;Deshpande, Atul;Feng, Yuzhou;Jeganathan, Pratheepa;Loth, Melanie;Meng, Chen;Mu, Wancen;Pancaldi, Vera;Sankaran, Kris;Singh, Amrit;Sodicoff, Joshua S.;Stein-O'Brien, Genevieve L.;Subramanian, Ayshwarya;Welch, Joshua D.;You, Yue;Argelaguet, Ricard;Carey, Vincent J.;Dries, Ruben;Greene, Casey S.;Holmes, Susan;Love, Michael, I;Ritchie, Matthew E.;Yuan, Guo-Cheng;Culhane, Aedin C.;Fertig, Elana; (2021) Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology

Wang, Yufei;Buck, Alicia;Grimaud, Marion;Kodangattil, Sreekumar;Razimbaud, Cecile;Fayed, Atef;Chang, Matthew;Culhane, Aedin;Braun, David A.;Choueiri, Toni K.;Wu, Catherine J.;Wei, Kevin S.;Chan, Leo L.;Piel, Brandon P.;Ivanova, Elena V.;Paweletz, Cloud P.;Barbie, David A.;Jennings, Rebecca;Ficial, Miriam;Sticco-Ivins, Maura Aliezah;Signoretti, Sabina;Freeman, Gordon J.;Zhu, Quan K.;Marasco, Wayne A.; (2021) Development of dual-targeted fine-tuned immune restoring (DFIR) CAR T cell therapy for clear cell renal cell carcinoma (ccRCC). Cancer Research

Cao, Kim-Anh Le;Abadi, Al J.;Davis-Marcisak, Emily F.;Hsu, Lauren;Arora, Arshi;Coullomb, Alexis;Deshpande, Atul;Feng, Yuzhou;Jeganathan, Pratheepa;Loth, Melanie;Meng, Chen;Mu, Wancen;Pancaldi, Vera;Sankaran, Kris;Righelli, Dario;Singh, Amrit;Sodicoff, Joshua S.;Stein-O'Brien, Genevieve L.;Subramanian, Ayshwarya;Welch, Joshua D.;You, Yue;Argelaguet, Ricard;Carey, Vincent J.;Dries, Ruben;Greene, Casey S.;Holmes, Susan;Love, Michael I.;Ritchie, Matthew E.;Yuan, Guo-Cheng;Culhane, Aedin C.;Fertig, Elana; (2021) Community-wide hackathons to identify central themes in single-cell multi-omics (vol 22, 220, 2021). Genome Biology

Shirasaki, Ryosuke;Matthews, Geoffrey M.;Gandolfi, Sara;Simoes, Ricardo de Matos;Buckley, Dennis L.;Vora, Joseline Raja;Sievers, Quinlan L.;Bruggenthies, Johanna B.;Dashevsky, Olga;Poarch, Haley;Tang, Huihui;Bariteau, Megan A.;Sheffer, Michal;Hu, Yiguo;Downey-Kopyscinski, Sondra L.;Hengeveld, Paul J.;Glassner, Brian J.;Dhimolea, Eugen;Ott, Christopher J.;Zhang, Tinghu;Kwiatkowski, Nicholas P.;Laubach, Jacob P.;Schlossman, Robert L.;Richardson, Paul G.;Culhane, Aedin C.;Groen, Richard W. J.;Fischer, Eric S.;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William C.;Levy, Joan;Auclair, Daniel;Licht, Jonathan D.;Keats, Jonathan J.;Boise, Lawrence H.;Ebert, Benjamin L.;Bradner, James E.;Gray, Nathanael S.;Mitsiades, Constantine S.; (2021) Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins. Cell Reports

Sheffer, Michal;Lowry, Emily;Beelen, Nicky;Borah, Minasri;Naffar-Abu Amara, Suha;Mader, Chris C.;Roth, Jennifer;Tsherniak, Aviad;Dashevsky, Olga;Gandolfi, Sara;Bender, Samantha;Bryan, Jordan;Zhu, Cong;Wang, Li;Simoes, Ricardo De-Matos;Yu, Channing;Hu, Yiguo;Dufva, Olli;Giannakis, Marios;Golub, Todd;Romee, Rizwan;Mustjoki, Satu;Culhane, Aedin C.;Wieten, Lotte;Mitsiades, Constantine S.; (2021) Landscape of molecular events regulating tumor cell responses to natural killer cells. Cancer immunology research

Dhimolea, Eugen;Simoes, Ricardo De Matos;Kansara, Dhvanir;Bouyssou, Juliette;Roth, Jennifer;Sheffer, Michal;Jeselsohn, Rinath;Gray, Nathanael;Steidl, Ulrich;Bartholdy, Boris;Brown, Myles;Culhane, Aedin;Mitsiades, Constantine; (2021) Treatment persistence of residual breast tumors through an embryonic diapause-like cancer cell state with suppressed myc activity. Cancer Research

Kelly B. Eckenrode;Dario Righelli;Marcel Ramos;Ricard Argelaguet;Christophe Vanderaa;Ludwig Geistlinger;Aedin Culhane;Laurent Gatto;Vincent Carey;Martin Morgan;Davide Risso;Levi Waldron; (2021) Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor. Biorxiv : The Preprint Server For Biology

Dhimolea, Eugen;Simoes, Ricardo de Matos;Kansara, Dhvanir;Al'Khafaji, Aziz;Bouyssou, Juliette;Weng, Xiang;Sharma, Shruti;Raja, Joseline;Awate, Pallavi;Shirasaki, Ryosuke;Tang, Huihui;Glassner, Brian J.;Liu, Zhiyi;Gao, Dong;Bryan, Jordan;Bender, Samantha;Roth, Jennifer;Scheffer, Michal;Jeselsohn, Rinath;Gray, Nathanael S.;Georgakoudi, Irene;Vazquez, Francisca;Tsherniak, Aviad;Chen, Yu;Welm, Alana;Duy, Cihangir;Melnick, Ari;Bartholdy, Boris;Brown, Myles;Culhane, Aedin C.;Mitsiades, Constantine S.; (2021) An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. Cancer Cell

Wang, Y.;Buck, A.;Grimaud, M.;Kodangattil, S.;Razimbaud, C.;Fayed, A.;Chang, M. R.;Culhane, A.;Braun, D.;Choueiri, T. K.;Wu, C.;Wei, K.;Chan, L. L.;Piel, B. P.;Ivanova, E.;Paweletz, C. P.;Barbie, D.;Jenning, R.;Ficial, M.;Sticco-Ivins, M.;Signoretti, S.;Freeman, G. J.;Zhu, Q.;Marasco, W.; (2021) ACHIEVE CLEAR CELL RENAL CELL CARCINOMA (CCRCC) CURES THROUGH DUAL-TARGETED FINE-TUNED IMMUNE RESTORING (DFIR) CAR-T CELL THERAPY. Cytotherapy

Sheffer, Michal;Lowry, Emily;Beelen, Nicky;Borah, Minasri;Naffar-Abu Amara, Suha;Mader, Chris C.;Roth, Jennifer A.;Tsherniak, Aviad;Freeman, Samuel S.;Dashevsky, Olga;Gandolfi, Sara;Bender, Samantha;Bryan, Jordan G.;Zhu, Cong;Wang, Li;Tariq, Ifrah;Kamath, Govinda M.;Simoes, Ricardo De Matos;Dhimolea, Eugen;Yu, Channing;Hu, Yiguo;Dufva, Olli;Giannakis, Marios;Syrgkanis, Vasilis;Fraenkel, Ernest;Golub, Todd;Romee, Rizwan;Mustjoki, Satu;Culhane, Aedin C.;Wieten, Lotte;Mitsiades, Constantine S.; (2021) Genome-scale screens identify factors regulating tumor cell responses to natural killer cells. Nature Genetics

Burn, E.;You, S.C.;Sena, A.G.;Kostka, K.;Abedtash, H.;Abrahão, M.T.F.;Alberga, A.;Alghoul, H.;Alser, O.;Alshammari, T.M.;Aragon, M.;Areia, C.;Banda, J.M.;Cho, J.;Culhane, A.C.;Davydov, A.;DeFalco, F.J.;Duarte-Salles, T.;DuVall, S.;Falconer, T.;Fernandez-Bertolin, S.;Gao, W.;Golozar, A.;Hardin, J.;Hripcsak, G.;Huser, V.;Jeon, H.;Jing, Y.;Jung, C.Y.;Kaas-Hansen, B.S.;Kaduk, D.;Kent, S.;Kim, Y.;Kolovos, S.;Lane, J.C.E.;Lee, H.;Lynch, K.E.;Makadia, R.;Matheny, M.E.;Mehta, P.P.;Morales, D.R.;Natarajan, K.;Nyberg, F.;Ostropolets, A.;Park, R.W.;Park, J.;Posada, J.D.;Prats-Uribe, A.;Rao, G.;Reich, C.;Rho, Y.;Rijnbeek, P.;Schilling, L.M.;Schuemie, M.;Shah, N.H.;Shoaibi, A.;Song, S.;Spotnitz, M.;Suchard, M.A.;Swerdel, J.N.;Vizcaya, D.;Volpe, S.;Wen, H.;Williams, A.E.;Yimer, B.B.;Zhang, L.;Zhuk, O.;Prieto-Alhambra, D.;Ryan, P.; (2020) Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study. Nature Communications

Schwede, M.;Waldron, L.;Mok, S.C.;Wei, W.;Basunia, A.;Merritt, M.A.;Mitsiades, C.S.;Parmigiani, G.;Harrington, D.P.;Quackenbush, J.;Birrer, M.J.;Culhane, A.C.; (2020) The impact of stroma admixture on molecular subtypes and prognostic gene signatures in serous ovarian cancer. Cancer Epidemiology Biomarkers & Prevention

Hsu, L.L.;Culhane, A.C.; (2020) Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data. Frontiers In Oncology

Dashevsky, Olga;Simoes, Ricardo De Matos;Shirasaki, Ryosuke;Sheffer, Michal;Dhimolea, Eugen;Gandolfi, Sara;Tang, Huihui;Downey-Kopyscinski, Sondra L.;Bariteau, Megan;Sorrell, Jeffrey;Glassner, Brian;Doench, John;Boise, Larry H.;Licht, Jonathan D.;Culhane, Aedin;Hahn, William C.;Vazquez, Francisca;Tsherniak, Aviad;Mitsiades, Constantine S.; (2020) Use of Olfactory Receptor Genes As Controls for Genome-Scale CRISPR Functional Genomic Studies to Define Treatment Resistance Mechanisms. Blood

Simoes, Ricardo De Matos;Shirasaki, Ryosuke;Tang, Huihui;Yamano, Shizuka;Barwick, Benjamin G.;Gandolfi, Sara;Dhimolea, Eugen;Downey-Kopyscinski, Sondra L.;Dashevsky, Olga;Glassner, Brian;Sheffer, Michal;Kansara, Dhvanir;Bariteau, Megan;Sorrell, Jeffrey;Gupta, Vikas;Culhane, Aedin;Tsherniak, Aviad;Vazquez, Francisca;Boise, Larry H.;Licht, Jonathan D.;Mitsiades, Constantine S.; (2020) POU2AF1 As a Master Regulator of Oncogenic Transcription Factor Networks in Myeloma. Blood

(2020) Pleiotropic mechanisms drive endocrine resistance in the three-dimensional bone microenvironment.. Cancer Research

Lane, J.C.E.;Weaver, J.;Kostka, K.;Duarte-Salles, T.;Abrahao, M.T.F.;Alghoul, H.;Alser, O.;Alshammari, T.M.;Biedermann, P.;Banda, J.M.;Burn, E.;Casajust, P.;Conover, M.M.;Culhane, A.C.;Davydov, A.;DuVall, S.L.;Dymshyts, D.;Fernandez-Bertolin, S.;Fišter, K.;Hardin, J.;Hester, L.;Hripcsak, G.;Kaas-Hansen, B.S.;Kent, S.;Khosla, S.;Kolovos, S.;Lambert, C.G.;van der Lei, J.;Lynch, K.E.;Makadia, R.;Margulis, A.V.;Matheny, M.E.;Mehta, P.;Morales, D.R.;Morgan-Stewart, H.;Mosseveld, M.;Newby, D.;Nyberg, F.;Ostropolets, A.;Park, R.W.;Prats-Uribe, A.;Rao, G.A.;Reich, C.;Reps, J.;Rijnbeek, P.;Sathappan, S.M.K.;Schuemie, M.;Seager, S.;Sena, A.G.;Shoaibi, A.;Spotnitz, M.;Suchard, M.A.;Torre, C.O.;Vizcaya, D.;Wen, H.;de Wilde, M.;Xie, J.;You, S.C.;Zhang, L.;Zhuk, O.;Ryan, P.;Prieto-Alhambra, D.; (2020) Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study. The Lancet Rheumatology

Simoes, Ricardo De Matos;Shirasaki, Ryosuke;Downey-Kopyscinski, Sondra L.;Matthews, Geoffrey;Yiguo, Hu;Sheffer, Michal;Dhimolea, Eugen;Dashevsky, Olga;Gandolfi, Sara;Dempster, Joshua;Meyers, Robin M.;Bryan, Jordan;McFarland, James M.;Brueggenthies, Johanna;Tang, Huihui;Bariteau, Megan;Borah, Minasri;Sievers, Quinlan L.;Ebert, Benjamin;Glassner, Brian;Ott, Christopher J.;Kwiatkowski, Nicholas P.;Doench, John G.;Auclair, Daniel;Levy, Joan;Boise, Lawrence H.;Keats, Jonathan J.;Licht, Jonathan D.;Groen, Richard;Gray, Nathanael;Culhane, Aedin;Hahn, William C.;Vazquez, Francisca;Tsherniak, Aviad;Mitsiades, Constantine S.; (2019) Systematic Characterization of Genes Representing Preferential Molecular Vulnerabilities for Myeloma Cells Compared to Other Neoplasias - Implications for the Biology and Therapeutic Targeting of Myeloma. Blood

Thorsson, V.;Gibbs, D.L.;Brown, S.D.;Wolf, D.;Bortone, D.S.;Ou Yang, T.-H.;Porta-Pardo, E.;Gao, G.F.;Plaisier, C.L.;Eddy, J.A.;Ziv, E.;Culhane, A.C.;Paull, E.O.;Sivakumar, I.K.A.;Gentles, A.J.;Malhotra, R.;Farshidfar, F.;Colaprico, A.;Parker, J.S.;Mose, L.E.;Vo, N.S.;Liu, J.;Liu, Y.;Rader, J.;Dhankani, V.;Reynolds, S.M.;Bowlby, R.;Califano, A.;Cherniack, A.D.;Anastassiou, D.;Bedognetti, D.;Mokrab, Y.;Newman, A.M.;Rao, A.;Chen, K.;Krasnitz, A.;Hu, H.;Malta, T.M.;Noushmehr, H.;Pedamallu, C.S.;Bullman, S.;Ojesina, A.I.;Lamb, A.;Zhou, W.;Shen, H.;Choueiri, T.K.;Weinstein, J.N.;Guinney, J.;Saltz, J.;Holt, R.A.;Rabkin, C.S.;Caesar-Johnson, S.J.;Demchok, J.A.;Felau, I.;Kasapi, M.;Ferguson, M.L.;Hutter, C.M.;Sofia, H.J.;Tarnuzzer, R.;Wang, Z.;Yang, L.;Zenklusen, J.C.;Zhang, J.J.;Chudamani, S.;Liu, J.;Lolla, L.;Naresh, R.;Pihl, T.;Sun, Q.;Wan, Y.;Wu, Y.;Cho, J.;DeFreitas, T.;Frazer, S.;Gehlenborg, N.;Getz, G.;Heiman, D.I.;Kim, J.;Lawrence, M.S.;Lin, P.;Meier, S.;Noble, M.S.;Saksena, G.;Voet, D.;Zhang, H.;Bernard, B.;Chambwe, N.;Knijnenburg, T.;Kramer, R.;Leinonen, K.;Miller, M.;Reynolds, S.;Shmulevich, I.;Thorsson, V.;Zhang, W.;Akbani, R.;Broom, B.M.;Hegde, A.M.;Ju, Z.;Kanchi, R.S.;Korkut, A.;Li, J.;Liang, H.;Ling, S.;Liu, W.;Lu, Y.;Mills, G.B.;Ng, K.-S.;Ryan, M.;Wang, J.;Zhang, J.;Abeshouse, A.;Armenia, J.;Chakravarty, D.;Chatila, W.K.;de Bruijn, I.;Gao, J.;Gross, B.E.;Heins, Z.J.;Kundra, R.;La, K.;Ladanyi, M.;Luna, A.;Nissan, M.G.;Ochoa, A.;Phillips, S.M.;Reznik, E.;Sanchez-Vega, F.;Sander, C.;Schultz, N.;Sheridan, R.;Sumer, S.O.;Sun, Y.;Taylor, B.S.;Wang, J.;Zhang, H.;Anur, P.;Peto, M.;Spellman, P.;Benz, C.;Stuart, J.M.;Wong, C.K.;Yau, C.;Hayes, D.N.;Wilkerson, M.D.;Ally, A.;Balasundaram, M.;Brooks, D.;Carlsen, R.;Chuah, E.;Dhalla, N.;Holt, R.;Jones, S.J.M.;Kasaian, K.;Lee, D.;Ma, Y.;Marra, M.A.;Mayo, M.;Moore, R.A.;Mungall, A.J.;Mungall, K.;Robertson, A.G.;Sadeghi, S.;Schein, J.E.;Sipahimalani, P.;Tam, A.;Thiessen, N.;Tse, K.;Wong, T.;Berger, A.C.;Beroukhim, R.;Cibulskis, C.;Gabriel, S.B.;Ha, G.;Meyerson, M.;Schumacher, S.E.;Shih, J.;Kucherlapati, M.H.;Kucherlapati, R.S.;Baylin, S.;Cope, L.;Danilova, L.;Bootwalla, M.S.;Lai, P.H.;Maglinte, D.T.;Van Den Berg, D.J.;Weisenberger, D.J.;Auman, J.T.;Balu, S.;Bodenheimer, T.;Fan, C.;Hoadley, K.A.;Hoyle, A.P.;Jefferys, S.R.;Jones, C.D.;Meng, S.;Mieczkowski, P.A.;Perou, A.H.;Perou, C.M.;Roach, J.;Shi, Y.;Simons, J.V.;Skelly, T.;Soloway, M.G.;Tan, D.;Veluvolu, U.;Fan, H.;Hinoue, T.;Laird, P.W.;Bellair, M.;Chang, K.;Covington, K.;Creighton, C.J.;Dinh, H.;Doddapaneni, H.;Donehower, L.A.;Drummond, J.;Gibbs, R.A.;Glenn, R.;Hale, W.;Han, Y.;Hu, J.;Korchina, V.;Lee, S.;Lewis, L.;Li, W.;Liu, X.;Morgan, M.;Morton, D.;Muzny, D.;Santibanez, J.;Sheth, M.;Shinbrot, E.;Wang, L.;Wang, M.;Wheeler, D.A.;Xi, L.;Zhao, F.;Hess, J.;Appelbaum, E.L.;Bailey, M.;Cordes, M.G.;Ding, L.;Fronick, C.C.;Fulton, L.A.;Fulton, R.S.;Kandoth, C.;Mardis, E.R.;McLellan, M.D.;Miller, C.A.;Schmidt, H.K.;Wilson, R.K.;Crain, D.;Curley, E.;Gardner, J.;Lau, K.;Mallery, D.;Morris, S.;Paulauskis, J.;Penny, R.;Shelton, C.;Shelton, T.;Sherman, M.;Thompson, E.;Yena, P.;Bowen, J.;Gastier-Foster, J.M.;Gerken, M.;Leraas, K.M.;Lichtenberg, T.M.;Ramirez, N.C.;Wise, L.;Zmuda, E.;Corcoran, N.;Costello, T.;Hovens, C.;Carvalho, A.L.;de Carvalho, A.C.;Fregnani, J.H.;Longatto-Filho, A.;Reis, R.M.;Scapulatempo-Neto, C.;Silveira, H.C.S.;Vidal, D.O.;Burnette, A.;Eschbacher, J.;Hermes, B.;Noss, A.;Singh, R.;Anderson, M.L.;Castro, P.D.;Ittmann, M.;Huntsman, D.;Kohl, B.;Le, X.;Thorp, R.;Andry, C.;Duffy, E.R.;Lyadov, V.;Paklina, O.;Setdikova, G.;Shabunin, A.;Tavobilov, M.;McPherson, C.;Warnick, R.;Berkowitz, R.;Cramer, D.;Feltmate, C.;Horowitz, N.;Kibel, A.;Muto, M.;Raut, C.P.;Malykh, A.;Barnholtz-Sloan, J.S.;Barrett, W.;Devine, K.;Fulop, J.;Ostrom, Q.T.;Shimmel, K.;Wolinsky, Y.;Sloan, A.E.;De Rose, A.;Giuliante, F.;Goodman, M.;Karlan, B.Y.;Hagedorn, C.H.;Eckman, J.;Harr, J.;Myers, J.;Tucker, K.;Zach, L.A.;Deyarmin, B.;Kvecher, L.;Larson, C.;Mural, R.J.; (2019) Erratum: The Immune Landscape of Cancer (Immunity (2018) 48(4) (812â€'830.e14), (S1074761318301213), (10.1016/j.immuni.2018.03.023)). Immunity

Simoes, Ricardo de Matos;Shirasaki, Ryosuke;Tang, Huihui;Sheffer, Michal;Dashevsky, Olga;Downey-Kopyscinski, Sondra;Dhimolea, Eugen;Bariteau, Megan;Licht, Jonathan;Glassner, Brian J.;Levy, Joan;Auclair, Daniel;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William;Culhane, Aedin;Mitsiades, Constantine; (2019) CRISPR-based functional genomics landscape of genes recurrently mutated in MM. Clinical Lymphoma Myeloma And Leukemia

Shirasaki, Ryosuke;Simoes, Ricardo de Matos;Gandolfi, Sara;Matthews, Geoffrey;Buckley, Dennis;Raja, Joseline;Sievers, Quinlan;Bruggenthies, Johanna;Dashevsky, Olga;Poarch, Haley;Tang, Huihui;Bariteau, Megan;Sheffer, Michal;Hu, Yiguo;Downey-Kopyscinski, Sondra;Hengeveld, Paul;Glassner, Brian J.;Dhimolea, Eugen;Ott, Christopher;Zhang, Tinghu;Kwiatkowski, Nicholas;Laubach, Jacob;Schlossman, Robert;Culhane, Aedin;Richardson, Paul G.;Groen, Richard;Fischer, Eric;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William;Levy, Joan;Auclair, Daniel;Licht, Jonathan;Keats, Jonathan;Boise, Lawrence;Ebert, Benjamin;Bradner, James;Gray, Nathanael;Mitsiades, Constantine; (2019) Molecular markers of myeloma cell sensitivity vs. resistance to heterobifunctional degraders of oncoproteins: therapeutic implications. Clinical Lymphoma Myeloma And Leukemia

Shirasaki, Ryosuke;Simoes, Ricardo de Matos;Downey-Kopyscinski, Sondra;Matthews, Geoffrey;Hu, Yiguo;Sheffer, Michal;Dhimolea, Eugen;Dashevsky, Olga;Gandolfi, Sara;Hengeveld, Paul;Dempster, Joshua;Meyers, Robin;Bryan, Jordan;Dharia, Neekesh;McFarland, James;Sarkar, Subhashis;Bruggenthies, Johanna;Tang, Huihui;Bariteau, Megan;Aguirre, Andrew;Borah, Minasri;Sievers, Quinlan;Ebert, Benjamin;Raja, Joseline;Glassner, Brian J.;Ott, Christopher;Bradner, James;Kwiatkowski, Nicholas;Auclair, Daniel;Levy, Joan;Poarch, Haley;Zhang, Tinghu;Laubach, Jacob;Buckley, Dennis;Schlossman, Robert;Groen, Richard;Fischer, Eric;Richardson, Paul G.;Keats, Jonathan;Boise, Lawrence;Licht, Jonathan;Culhane, Aedin;Gray, Nathanael;Hahn, William;Vazquez, Francisca;Tsherniak, Aviad;Mitsiades, Constantine; (2019) CRISPR studies identify genes preferentially essential for myeloma cells vs. other neoplasias: implications for future therapies selective against MM. Clinical Lymphoma Myeloma And Leukemia

Shirasaki, Ryosuke;Gandolfi, Sara;Simoes, Ricardo De Matos;Matthews, Geoffrey M.;Buckley, Dennis;Raja, Joseline;Sievers, Quinlan L.;Dashevsky, Olga;Poarch, Haley;Tang, Huihui;Bariteau, Megan;Sheffer, Michal;Downey-Kopyscinski, Sondra L.;Hengeveld, Paul;Glassner, Brian;Dhimolea, Eugen;Ott, Christopher J.;Zhang, Tinghu;Kwiatkowski, Nicholas P.;Laubach, Jacob P.;Schlossman, Robert L.;Richardson, Paul G.;Culhane, Aedin;Groen, Richard W. J.;Fischer, Eric;Ebert, Benjamin L.;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William C.;Levy, Joan;Auclair, Daniel;Licht, Jonathan D.;Keats, Jonathan J.;Boise, Lawrence H.;Bradner, James;Gray, Nathanael;Mitsiades, Constantine S.; (2019) Functional Characterization of E3 Ligases and Their Regulators: Therapeutic Implications for Development of New Proteolysis-Targeting Chimeric Degraders of Oncoproteins. Blood

Simoes, Ricardo De Matos;Shirasaki, Ryosuke;Tang, Huihui;Sheffer, Michal;Dashevsky, Olga;Gandolfi, Sara;Dhimolea, Eugen;Bariteau, Megan;Licht, Jonathan D.;Glassner, Brian;Groen, Richard W. J.;Levy, Joan;Auclair, Daniel;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William C.;Culhane, Aedin;Mitsiades, Constantine S.; (2018) Functional Genomic Landscape of Genes with Recurrent Mutations in Multiple Myeloma. Blood

Stein-O'Brien, G.L.;Arora, R.;Culhane, A.C.;Favorov, A.V.;Garmire, L.X.;Greene, C.S.;Goff, L.A.;Li, Y.;Ngom, A.;Ochs, M.F.;Xu, Y.;Fertig, E.J.; (2018) Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends In Genetics

Li, A.G.;Murphy, E.C.;Culhane, A.C.;Powell, E.;Wang, H.;Bronson, R.T.;Von, T.;Giobbie-Hurder, A.;Gelman, R.S.;Briggs, K.J.;Piwnica-Worms, H.;Zhao, J.J.;Kung, A.L.;Kaelin, W.G.;Livingston, D.M.; (2018) BRCA1-IRIS promotes human tumor progression through PTEN blockade and HIF-1α activation. Proceedings of the National Academy of Sciences of the United States of America

Thorsson V;Gibbs DL;Brown SD;Wolf D;Bortone DS;Ou Yang TH;Porta-Pardo E;Gao GF;Plaisier CL;Eddy JA;Ziv E;Culhane AC;Paull EO;Shmulevich L; (2018) The Immune Landscape of Cancer.. Immunity

Shirasaki, Ryosuke;Gandolfi, Sara;Simoes, Ricardo De Matos;Matthews, Geoffrey;Buckley, Dennis;Dashevsky, Olga;Downey-Kopyscinski, Sondra L.;Tang, Huihui;Sheffer, Michal;Dhimolea, Eugen;Glassner, Brian;Bariteau, Megan;Sorrell, Jeffrey;Bruggenthies, Johanna B.;Sievers, Quinlan;Poarch, Haley;Kwiatkowski, Nicholas P.;Zhang, Tinghu;Laubach, Jacob;Schlossman, Robert L.;Richardson, Paul;Culhane, Aedin;Groen, Richard W. J.;Fischer, Eric S.;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William C.;Levy, Joan;Auclair, Daniel;Licht, Jonathan D.;Keats, Jonathan J.;Boise, Lawrence H.;Ebert, Benjamin L.;Bradner, James;Gray, Nathanae;Mitsiades, Constantine S.; (2018) CRISPR-Based Functional Genomics Studies Reveal Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins: Implications for Novel Therapeutics across Diverse Neoplasias. Blood

Simoes, Ricardo De Matos;Matthews, Geoffrey;Shirasaki, Ryosuke;Hu Yiguo;Sheffer, Michal;Dashevsky, Olga;Gandolfi, Sara;Hengeveld, Paul;Bruggenthies, Johanna;Dhimolea, Eugen;Tang, Huihui;Bariteau, Megan;Aguirre, Andrew;Sievers, Quinlan;Ebert, Benjamin L.;Glassner, Brian;Ott, Christopher J.;Buckley, Dennis;Kwiatkowski, Nicholas P.;Licht, Jonathan D.;Gray, Nathanael;Dempster, Joshua;Groen, Richard W. J.;Vazquez, Francisca;Tsherniak, Aviad;Hahn, William C.;Culhane, Aedin;Mitsiades, Constantine S.; (2017) Integration of Functional Dependencies and Molecular Alterations of Myeloma Cells. Blood

Simoes, Ricardo De Matos;Matthews, Geoffrey;Richer, Daphne Dupere;Shirasaki, Ryosuke;Sheffer, Michal;Dashevsky, Olga;Gandolfi, Sara;Dhimolea, Eugen;Glassner, Brian;Groen, Richard W. J.;Vazquez, Franciska;Dempster, Joshua;Tsherniak, Aviad;Hahn, William C.;Culhane, Aedin;Licht, Jonathan D.;Mitsiades, Constantine S.; (2017) Functional Genomic Landscape of Epigenetic Dependencies in Myeloma. Blood

Dhimolea, E.;Simoes, R. De Matos;Awate, P.;Tang, H.;Culhane, A.;Mitsiades, C.; (2017) High-throughput pharmacogenomic platform to functionally probe breast cancer vulnerabilities in the context of the 3-dimensional tumor microenvironment. Cancer Research

Ramos M;Schiffer L;Re A;Azhar R;Basunia A;Rodriguez C;Chan T;Chapman P;Davis SR;Gomez-Cabrero D;Culhane AC;Haibe-Kains B;Hansen KD;Waldron L; (2017) Software for the Integration of Multiomics Experiments in Bioconductor.. Cancer Research

de Velasco G;Culhane AC;Fay AP;Hakimi AA;Voss MH;Tannir NM;Tamboli P;Appleman LJ;Bellmunt J;Kimryn Rathmell W;Albiges L;Hsieh JJ;Heng DY;Choueiri TK; (2017) Molecular Subtypes Improve Prognostic Value of International Metastatic Renal Cell Carcinoma Database Consortium Prognostic Model.. Oncologist

de Velasco G;Culhane AC;Heng DYC;Signoretti S;Choueiri TK; (2017) In Reply.. Oncologist

Matthews, Geoffrey M.;Simoes, Ricardo de Matos;Hu, Yiguo;Sheffer, Michal;Dashevsky, Olga;Dhimolea, Eugen;Hengeveld, Paul J.;Glassner, Brian J.;Gandolfi, Sara;Bariteau, Megan A.;Sievers, Quinlan;Ebert, Benjamin L.;Vazquez, Franciska;Culhane, Aedin;Mitsiades, Constantine S.; (2017) Characterization of lineage vs. context-dependent essential genes in multiple myeloma using CRISPR-Cas9 genome editing. Cancer Research

Genevieve L. Stein-O’Brien;Raman Arora;Aedin C. Culhane;Alexander V. Favorov;Lana X. Garmire;Casey S. Greene;Loyal A. Goff;Yifeng Li;Aloune Ngom;Michael F. Ochs;Yanxun Xu;Elana J. Fertig; (2017) Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations.

Jacene, H. A.;Overmoyer, B.;Schlosnagle, E. J.;Abbott, A.;Yeh, E.;Paolino, J.;Goel, S.;Culhane, A.;Bellon, J. R.;Nakhlis, F.;Hirshfield-Bartek, J.;Van den Abbeele, A.; (2017) Pilot study of zirconium-89 bevacizumab positron emission tomography for imaging angiogenesis in patients with inflammatory breast carcinoma receiving preoperative chemotherapy. Cancer Research

Dhimolea, Eugen;Simoes, Ricardo De Matos;DeRose, Yoko;Awate, Pallavi;Weng, Xiang;Tang, Huihui;Culhane, Aedin;Welm, Alana;Mitsiades, Constantine; (2017) High-throughput patient-derived 3-dimensional organoid cultures as personalized models to assess drug response and post-treatment residual disease. Cancer Research

Shirasaki, Ryosuke;Tamas, Csikos;Matthews, Geoffrey;Simoes, Ricardo De Matos;Sarkar, Subhashis;Dashevsky, Olga;Hu Yiguo;Sorrell, Jeffrey;Sheffer, Michal;Dhimolea, Eugen;Bariteau, Megan;Glassner, Brian;Culhane, Aedin;Groen, Richard W. J.;Mitsiades, Constantine S.; (2017) In Vivo Validation of Essential Genes for Myeloma Cells By CRISPR/Cas9 Studies in a Scaffold-Based System Engineered to Establish a "Humanized" Bone Marrow-like Microenvironment. Blood

(2016) moGSA: integrative single sample gene-set analysis of multiple omics data. Biorxiv

Matthews, Geoffrey M.;Simoes, Ricardo De Matos;Hu, Yiguo;Sheffer, Michal;Dhimolea, Eugen;Hengeveld, Paul J.;Bariteau, Megan A.;Glassner, Brian;Sievers, Quinlan;Ebert, Benjamin L.;Gandolfi, Sara;Awate, Pallavi;Tang, Huihui;Vazquez, Franciska;Culhane, Aedin;Mitsiades, Constantine S.; (2016) Characterization of Lineage Vs. Context-Dependent Essential Genes in Multiple Myeloma Using Crispr/Cas9 Genome Editing. Blood

Pathania, Shailja;Reed, Rachel;Duan, Haohui;Culhane, Aedin;Garber, Judy; (2016) BRCA2, and not BRCA1, dependent crosstalk between replication stress suppression and nucleotide excision repair - Clinical implications. Cancer Research

(2016) Dimension reduction techniques for the integrative analysis of multi-omics data. Briefings In Bioinformatics

Neupane, M.;Clark, A.P.;Landini, S.;Birkbak, N.J.;Eklund, A.C.;Lim, E.;Culhane, A.C.;Barry, W.T.;Schumacher, S.E.;Beroukhim, R.;Szallasi, Z.;Vidal, M.;Hill, D.E.;Silver, D.P.; (2016) MECP2 is a frequently amplified oncogene with a novel epigenetic mechanism that mimics the role of activated RAS in malignancy. Cancer Discovery

de Velasco, Guillermo;Fay, Andre Poisl;Culhane, Aedin;Hakimi, A. Ari;Voss, Martin Henner;Tannir, Nizar M.;Tamboli, Pheroze;Appleman, Leonard Joseph;Bellmunt, Joaquim;Rathmell, Kimryn;Albiges, Laurence K.;Hsieh, James;Heng, Daniel Yick Chin;Signoretti, Sabina;Choueiri, Toni K.; (2015) Prognostic value of genomic signatures in metastatic Clear Cell Renal Cell Carcinoma (mRCC) using The Cancer Genome Atlas (TCGA) data. Clinical Oncology

Kochupurakkal, B.S.;Wang, Z.C.;Hua, T.;Culhane, A.C.;Rodig, S.J.;Rajkovic-Molek, K.;Lazaro, J.-B.;Richardson, A.L.;Biswas, D.K.;Iglehart, J.D.; (2015) RelA-induced interferon response negatively regulates proliferation. Plos One

Eugen Dhimolea;Richard Groen;Culhane Aedin;Mitsiades Nicholas;Polyak Kornelia;Mitsiades Constantine; (2015) Abstract B54: Non-malignant cells from metastatic niches induce estrogen receptor-positive breast cancer cell resistance to therapy. Cell Interactions In The Tumor Microenvironment

(2015) Public data and open source tools for multi-assay genomic investigation of disease. Briefings In Bioinformatics

Waldron, L.;Haibe-Kains, B.;Culhane, A.C.;Riester, M.;Ding, J.;Wang, X.V.;Ahmadifar, M.;Tyekucheva, S.;Bernau, C.;Risch, T.;Ganzfried, B.F.;Huttenhower, C.;Birrer, M.;Parmigiani, G.; (2014) Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.. Journal Of The National Cancer Institute

Riester, Markus;Wei, Wei;Culhane, Aedin C.;Trippa, Lorenzo;Michor, Franziska;Huttenhower, Curtis;Parmigiani, Giovanni;Birrer, Michael; (2014) Risk prediction for late-stage ovarian cancer by meta-analysis of 1,525 patient samples. Cancer Research

Riester, M.;Wei, W.;Waldron, L.;Culhane, A.C.;Trippa, L.;Oliva, E.;Kim, S.H.;Michor, F.;Huttenhower, C.;Parmigiani, G.;Birrer, M.J.; (2014) Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.. Journal Of The National Cancer Institute

Birrer, Michael J.;Riester, Markus;Wei, Wei;Waldron, Levi;Culhane, Aedin;Trippa, Lorenzo;Oliva, Esther;Kim, Sunghoon;Michor, Franziska;Huttenhower, Curtis;Parmigiani, Giovanni; (2014) Meta-analysis of public microarray databases for prognostic and predictive gene signatures of late-stage ovarian cancer. Clinical Oncology

Meng, C.;Kuster, B.;Culhane, A.C.;Gholami, A.M.; (2014) A multivariate approach to the integration of multi-omics datasets. Bmc Bioinformatics

Santagata, S.;Thakkar, A.;Ergonul, A.;Wang, B.;Woo, T.;Hu, R.;Harrell, J.C.;McNamara, G.;Schwede, M.;Culhane, A.C.;Kindelberger, D.;Rodig, S.;Richardson, A.;Schnitt, S.J.;Tamimi, R.M.;Ince, T.A.; (2014) Taxonomy of breast cancer based on normal cell phenotype predicts outcome. Journal Of Clinical Investigation

Beck, A.H.;Knoblauch, N.W.;Hefti, M.M.;Kaplan, J.;Schnitt, S.J.;Culhane, A.C.;Schroeder, M.S.;Risch, T.;Quackenbush, J.;Haibe-Kains, B.; (2013) Significance Analysis of Prognostic Signatures. Plos Computational Biology

Thakkar, Ankita;Santagata, Sandro;Ergonul, Ayse;Wang, Bin;Woo, Terri;Hu, Rong;Harrell, J. Chuck;McNamara, George;Schwede, Matthew;Culhane, Aedin C.;Kindelberger, David;Rodig, Scott;Richardson, Andrea;Schnitt, Stuart J.;Tamimi, Rulla M.;Ince, Tan A.; (2013) Taxonomy of breast cancer based on normal cell phenotype and ontology. Molecular Cancer Research

Schwede, M.;Spentzos, D.;Bentink, S.;Hofmann, O.;Haibe-Kains, B.;Harrington, D.;Quackenbush, J.;Culhane, A.C.; (2013) Stem Cell-Like Gene Expression in Ovarian Cancer Predicts Type II Subtype and Prognosis. Plos One

Schröder, M.S.;Gusenleitner, D.;Quackenbush, J.;Culhane, A.C.;Haibe-Kains, B.; (2013) RamiGO: An R/Bioconductor package providing an AmiGO Visualize interface. Bioinformatics

Kelly, A.D.;Haibe-Kains, B.;Janeway, K.A.;Hill, K.E.;Howe, E.;Goldsmith, J.;Kurek, K.;Perez-Atayde, A.R.;Francoeur, N.;Fan, J.-B.;April, C.;Schneider, H.;Gebhardt, M.C.;Culhane, A.;Quackenbush, J.;Spentzos, D.; (2013) MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32. Genome Medicine

Bowman-Colin, C.;Xia, B.;Bunting, S.;Klijn, C.;Drost, R.;Bouwman, P.;Fineman, L.;Chen, X.;Culhane, A.C.;Cai, H.;Rodig, S.J.;Bronson, R.T.;Jonkers, J.;Nussenzweig, A.;Kanellopoulou, C.;Livingston, D.M.; (2013) Palb2 synergizes with Trp53 to suppress mammary tumor formation in a model of inherited breast cancer. Proceedings of the National Academy of Sciences of the United States of America

Prencipe, M.;Madden, S.F.;O'Neill, A.;O'Hurley, G.;Culhane, A.;O'Connor, D.;Klocker, H.;Kay, E.W.;Gallagher, W.M.;Watson, W.R.; (2013) Identification of transcription factors associated with castration-resistance: Is the serum responsive factor a potential therapeutic target?. Prostate

Gusenleitner, D.;Howe, E.A.;Bentink, S.;Quackenbush, J.;Culhane, A.C.; (2012) iBBiG: Iterative binary bi-clustering of gene sets. Bioinformatics

Culhane, A.C.;Schröder, M.S.;Sultana, R.;Picard, S.C.;Martinelli, E.N.;Kelly, C.;Haibe-Kains, B.;Kapushesky, M.;St Pierre, A.-A.;Flahive, W.;Picard, K.C.;Gusenleitner, D.;Papenhausen, G.;O'Connor, N.;Correll, M.;Quackenbush, J.; (2012) GeneSigDB: A manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Research

Wang, Z.C.;Birkbak, N.J.;Culhane, A.C.;Drapkin, R.;Fatima, A.;Tian, R.;Schwede, M.;Alsop, K.;Daniels, K.E.;Piao, H.;Liu, J.;Etemadmoghadam, D.;Miron, A.;Salvesen, H.B.;Mitchell, G.;DeFazio, A.;Quackenbush, J.;Berkowitz, R.S.;Iglehart, J.D.;Bowtell, D.D.L.;Matulonis, U.A.; (2012) Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clinical Cancer Research

Haibe-Kains, B.;Desmedt, C.;Loi, S.;Culhane, A.C.;Bontempi, G.;Quackenbush, J.;Sotiriou, C.; (2012) A three-gene model to robustly identify breast cancer molecular subtypes. Journal Of The National Cancer Institute

Kapushesky, M.;Adamusiak, T.;Burdett, T.;Culhane, A.;Farne, A.;Filippov, A.;Holloway, E.;Klebanov, A.;Kryvych, N.;Kurbatova, N.;Kurnosov, P.;Malone, J.;Melnichuk, O.;Petryszak, R.;Pultsin, N.;Rustici, G.;Tikhonov, A.;Travillian, R.S.;Williams, E.;Zorin, A.;Parkinson, H.;Brazma, A.; (2012) Gene Expression Atlas update - Value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Research

Bentink, S.;Haibe-Kains, B.;Risch, T.;Fan, J.-B.;Hirsch, M.S.;Holton, K.;Rubio, R.;April, C.;Chen, J.;Wickham-Garcia, E.;Liu, J.;Culhane, A.;Drapkin, R.;Quackenbush, J.;Matulonis, U.A.; (2012) Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. Plos One

Brennan, D.J.;O'connor, D.P.;Laursen, H.;Mcgee, S.F.;Mccarthy, S.;Zagozdzon, R.;Rexhepaj, E.;Culhane, A.C.;Martin, F.M.;Duffy, M.J.;Landberg, G.;Ryden, L.;Hewitt, S.M.;Kuhar, M.J.;Bernards, R.;Millikan, R.C.;Crown, J.P.;Jirström, K.;Gallagher, W.M.; (2012) The cocaine-and amphetamine-regulated transcript mediates ligand-independent activation of ERα, and is an independent prognostic factor in node-negative breast cancer. Oncogene

Prencipe, Maria;Madden, Stephen;O'Neill, Amanda;Culhane, Aedin;O'Connor, Darran;Klocker, Helmut;Gallagher, William M.;Watson, William; (2011) Transcriptomic profiling of castrate resistant prostate cancer cells: identification of transcription factors associated with androgen resistance. Cancer Research

Schröder, M.S.;Culhane, A.C.;Quackenbush, J.;Haibe-Kains, B.; (2011) survcomp: An R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics

(2011) The prognostic value of the cocaine and amphetamine-regulated transcript (CART) in breast cancer (BC).. Clinical Oncology

(2011) The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Research

Konstantinopoulos, P.A.;Cannistra, S.A.;Fountzilas, H.;Culhane, A.;Pillay, K.;Rueda, B.;Cramer, D.;Seiden, M.;Birrer, M.;Coukos, G.;Zhang, L.;Quackenbush, J.;Spentzos, D.; (2011) Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer. Plos One

(2010) Robustness of breast cancer molecular subtypes identification. Ann Oncol

Chen, D.-T.;Nasir, A.;Culhane, A.;Venkataramu, C.;Fulp, W.;Rubio, R.;Wang, T.;Agrawal, D.;McCarthy, S.M.;Gruidl, M.;Bloom, G.;Anderson, T.;White, J.;Quackenbush, J.;Yeatman, T.; (2010) Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. Breast Cancer Research And Treatment

Wang, Zhigang C.;Culhane, Aedin;Drapkin, Ronny;Fatima, Aquila;Tian, Ruiyang;Daniels, Kathryn E.;Kantoff, Emily;Liu, Joyce;Quackenbush, John;Richardson, Andrea L.;Berkowitz, Ross S.;Iglehart, J. Dirk;Matulonis, Ursula A.; (2010) Genetic relationships between ovarian and breast cancers. Cancer Research

Chittenden, T.W.;Pak, J.;Rubio, R.;Cheng, H.;Holton, K.;Prendergast, N.;Glinskii, V.;Cai, Y.;Culhane, A.;Bentink, S.;Schwede, M.;Mar, J.C.;Howe, E.A.;Aryee, M.;Sultana, R.;Lanahan, A.A.;Taylor, J.M.;Holmes, C.;Hahn, W.C.;Zhao, J.J.;Iglehart, J.D.;Quackenbush, J.; (2010) Therapeutic implications of GIPC1 silencing in cancer. Plos One

Speers, C.;Tsimelzon, A.;Sexton, K.;Herrick, A.M.;Gutierrez, C.;Culhane, A.;Quackenbush, J.;Hilsenbeck, S.;Chang, J.;Brown, P.; (2009) Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clinical Cancer Research

Nasir, A.;Chen, D. T.;Culhane, A. C.;Gruidl, M.;McCarthy, S. M.;Venkataramu, C.;Quackenbush, J.;Yeatman, T. J.; (2009) Immunohistochemical Validation of Topoisomerase 2 alpha and BubR1 as Novel Breast Cancer Risk Genes in Benign Breast Tissue. Modern Pathology

Ioannidis, J.P.A.;Allison, D.B.;Ball, C.A.;Coulibaly, I.;Cui, X.;Culhane, A.C.;Falchi, M.;Furlanello, C.;Game, L.;Jurman, G.;Mangion, J.;Mehta, T.;Nitzberg, M.;Page, G.P.;Petretto, E.;Van Noort, V.; (2009) Repeatability of published microarray gene expression analyses. Nature Genetics

Culhane, A. C.;Nasir, A.;Chen, D. T.;Venkataramu, C.;White, J.;Andersson, T.;Gruidl, M.;Bloom, G.;Rubio, R.;Centeno, B. A.;Quackenbush, J.;Yeatman, T. J.; (2009) A 19-Gene Classifier Distinguishes Invasive Ductal and Classic Lobular Breast Carcinomas: Amplification of Chromosome 8q Characterizes Ductal While Estrogen-Related EGR-1 Characterizes Lobular Cancers. Laboratory Investigation

Smith, M.J.;Culhane, A.C.;Donovan, M.;Coffey, J.C.;Barry, B.D.;Kelly, M.A.;Higgins, D.G.;Wang, J.H.;Kirwan, W.O.;Cotter, T.G.;Redmond, H.P.; (2009) Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification. British Journal Of Cancer

Culhane, A. C.;Nastr, A.;Chen, D. T.;Venkataramu, C.;White, J.;Anderson, T.;Gruidl, M.;Bloom, G.;Rubio, R.;Centeno, B. A.;Quackenbush, J.;Yeatman, T. J.; (2009) A 19-Gene Classifier Distinguishes Invasive Ductal and Classic Lobular Breast Carcinomas: Amplification of Chromosome 8q Characterizes Ductal While Estrogen-Related EGR-1 Characterizes Lobular Cancers. Modern Pathology

Culhane, A.C.;Quackenbush, J.; (2009) Confounding effects in "a six-gene signature predicting breast cancer lung metastasis". Cancer Research

Quackenbush, John;Fan, Jian-Bing;Hirsch, Michelle;Mar, Jessica;Howe, Eleanor;Holton, Kristina;Rubio, Renee;April, Craig;Chen, Jing;Wickham-Garcia, Eliza;Liu, Joyce;Culhane, Aedin;Drapkin, Ronny;Matulonis, Ursula; (2009) Molecular classification of serous ovarian cancer subtypes. Cancer Research

Culhane, A.C.;Schwarzl, T.;Sultana, R.;Picard, K.C.;Picard, S.C.;Lu, T.H.;Franklin, K.R.;French, S.J.;Papenhausen, G.;Correll, M.;Quackenbush, J.; (2009) GeneSigDB-A curated database of gene expression signatures. Nucleic Acids Research

Nasir, A.;Chen, D. T.;Culhane, A. C.;Gruidl, M.;McCarthy, S. M.;Venkataramu, C.;Quackenbush, J.;Yeatman, T. J.; (2009) Immunohistochemical Validation of Topoisomerase 2 alpha and BubR1 as Novel Breast Cancer Risk Genes in Benign Breast Tissue. Laboratory Investigation

(2008) Systematic validation of novel breast cancer progression-associated biomarkers via high-throughput antibody generation and application of tissue microarray technology: an initial report. Clinical Oncology

Chittenden, T.W.;Howe, E.A.;Culhane, A.C.;Sultana, R.;Taylor, J.M.;Holmes, C.;Quackenbush, J.; (2008) Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics

Smith, M.J.;Culhane, A.C.;Killeen, S.;Kelly, M.A.;Wang, J.H.;Cotter, T.G.;Redmond, H.P.; (2008) Mechanisms driving local breast cancer recurrence in a model of breast-conserving surgery. Annals Of Surgical Oncology

Brennan, D.J.;Rexhepaj, E.;O'Brien, S.L.;McSherry, E.;O'Connor, D.P.;Fagan, A.I.;Culhane, A.C.;Higgins, D.G.;Jirstrom, K.;Millikan, R.C.;Landberg, G.;Duffy, M.J.;Hewitt, S.M.;Gallagher, W.M.; (2008) Altered cytoplasmic-to-nuclear ratio of survivin is a prognostic indicator in breast cancer. Clinical Cancer Research

Cheng, A.S.L.;Culhane, A.C.;Chan, M.W.Y.;Venkataramu, C.R.;Ehrich, M.;Nasir, A.;Rodriguez, B.A.T.;Liu, J.;Yan, P.S.;Quackenbush, J.;Nephew, K.P.;Yeatman, T.J.;Huang, T.H.-M.; (2008) Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Research

Penny, S. A.;Kelly, C. M.;Brennan, D. J.;Culhane, A. C.;Higgins, D. G.;Dervan, P. A.;Jirstrom, K.;Ponten, F.;Uhlen, M.;Gallagher, W. M.; (2008) Systematic validation of novel breast cancer progression-associated biomarkers via high-throughput antibody generation and application of tissue microarray technology. European Journal Of Cancer, Supplement

Sobhian, B.;Shao, G.;Lilli, D.R.;Culhane, A.C.;Moreau, L.A.;Xia, B.;Livingston, D.M.;Greenberg, R.A.; (2007) RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science

Jeffery, I.B.;Madden, S.F.;McGettigan, P.A.;Perrière, G.;Culhane, A.C.;Higgins, D.G.; (2007) Integrating transcription factor binding site information with gene expression datasets. Bioinformatics

Rafferty, Mairin;Donoghue, Stephen;Faller, William J.;Nolan, Ilse-Maria;Culhane, Aedin C.;Moss, Catherine;McCormick, Janet;Easty, David J.;Dervan, Peter A.;Gallagher, William M.; (2007) Gene expression profiling of malignant melanoma: Application of TaqMan technology for high-throughput downstream validation of transcriptomic studies. Anticancer Research

O'Brien, S.L.;Fagan, A.;Fox, E.J.P.;Millikan, R.C.;Culhane, A.C.;Brennan, D.J.;McCann, A.H.;Hegarty, S.;Moyna, S.;Duffy, M.J.;Higgins, D.G.;Jirström, K.;Landberg, G.;Gallagher, W.M.; (2007) CENP-F expression is associated with poor prognosis and chromosomal instability in patients with primary breast cancer. International Journal Of Cancer

Fagan, A.;Culhane, A.C.;Higgins, D.G.; (2007) A multivariate analysis approach to the integration of proteomic and gene expression data. Journal Of Proteomics

Culhane, A.C.;Howlin, J.; (2007) Molecular profiling of breast cancer: Transcriptomic studies and beyond. Cellular And Molecular Life Sciences

(2006) Differential Gene Expression of Clinically Resected Colorectal Cancer and Flow Cytometrically Sorted Tumour Cells. Endoscopy

Jeffery, I.B.;Higgins, D.G.;Culhane, A.C.; (2006) Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. Bmc Bioinformatics

(2006) A Multivariate Approach to Integrating Datasets using made4 and ade4. The Newsletter Of The R Project Volume 6/5, December 2006

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Smith, MJ;Shilling, DA;Kelly, MA;England, KE;Culhane, A;Wang, JH;O'Mahony, L;Cotter, TG;Redmond, HP; (2005) Administration of a perioperative multiple heat shock protein dendritic cell vaccine significantly attenuates recurrent breast cancer growth in vivo. Annals Of Surgical Oncology

Brennan, D.J.;O'Brien, S.L.;Fagan, A.;Culhane, A.C.;Higgins, D.G.;Duffy, M.J.;Gallagher, W.M.; (2005) Application of DNA microarray technology in determining breast cancer prognosis and therapeutic response. Expert Opinion On Biological Therapy

Culhane, A.C.;Thioulouse, J.;Perrière, G.;Higgins, D.G.; (2005) MADE4: An R package for multivariate analysis of gene expression data. Bioinformatics

Duffy, M.J.;Kelly, Z.D.;Culhane, A.C.;O'Brien, S.L.;Gallagher, W.M.; (2005) DNA microarray-based gene expression profiling in cancer: Aiding cancer diagnosis, assessing prognosis and predicting response to therapy. Current Pharmacogenomics

Baty, F.;Bihl, M.P.;Perrière, G.;Culhane, A.C.;Brutsche, M.H.; (2005) Optimized between-group classification: A new jackknife-based gene selection procedure for genome-wide expression data. Bmc Bioinformatics

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