Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes.
Nature Communications
Lehmann, Brian D BD; Colaprico, Antonio A; Silva, Tiago C TC; Chen, Jianjiao J; An, Hanbing H; Ban, Yuguang Y; Huang, Hanchen H; Wang, Lily L; James, Jamaal L JL; Balko, Justin M JM; Gonzalez-Ericsson, Paula I PI; Sanders, Melinda E ME; Zhang, Bing B; Pietenpol, Jennifer A JA; Chen, X Steven XS
A review and comparison of breast tumor cell nuclei segmentation performances using deep convolutional neural networks.
Scientific Reports
Lagree, Andrew A; Mohebpour, Majidreza M; Meti, Nicholas N; Saednia, Khadijeh K; Lu, Fang-I FI; Slodkowska, Elzbieta E; Gandhi, Sonal S; Rakovitch, Eileen E; Shenfield, Alex A; Sadeghi-Naini, Ali A; Tran, William T WT
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform.
Plos Biology
Blatti, Charles C; Emad, Amin A; Berry, Matthew J MJ; Gatzke, Lisa L; Epstein, Milt M; Lanier, Daniel D; Rizal, Pramod P; Ge, Jing J; Liao, Xiaoxia X; Sobh, Omar O; Lambert, Mike M; Post, Corey S CS; Xiao, Jinfeng J; Groves, Peter P; Epstein, Aidan T AT; Chen, Xi X; Srinivasan, Subhashini S; Lehnert, Erik E; Kalari, Krishna R KR; Wang, Liewei L; Weinshilboum, Richard M RM; Song, Jun S JS; Jongeneel, C Victor CV; Han, Jiawei J; Ravaioli, Umberto U; Sobh, Nahil N; Bushell, Colleen B CB; Sinha, Saurabh S
NOTCH and DNA repair pathways are more frequently targeted by genomic alterations in inflammatory than in non-inflammatory breast cancers.
Molecular Oncology
Bertucci, François F; Rypens, Charlotte C; Finetti, Pascal P; Guille, Arnaud A; Adélaïde, José J; Monneur, Audrey A; Carbuccia, Nadine N; Garnier, Séverine S; Dirix, Piet P; Gonçalves, Anthony A; Vermeulen, Peter P; Debeb, Bisrat G BG; Wang, Xiaoping X; Dirix, Luc L; Ueno, Naoto T NT; Viens, Patrice P; Cristofanilli, Massimo M; Chaffanet, Max M; Birnbaum, Daniel D; Van Laere, Steven S
Integrative omics analyses broaden treatment targets in human cancer.
Genome Medicine
Sengupta, Sohini S; Sun, Sam Q SQ; Huang, Kuan-Lin KL; Oh, Clara C; Bailey, Matthew H MH; Varghese, Rajees R; Wyczalkowski, Matthew A MA; Ning, Jie J; Tripathi, Piyush P; McMichael, Joshua F JF; Johnson, Kimberly J KJ; Kandoth, Cyriac C; Welch, John J; Ma, Cynthia C; Wendl, Michael C MC; Payne, Samuel H SH; Fenyö, David D; Townsend, Reid R RR; Dipersio, John F JF; Chen, Feng F; Ding, Li L
Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.
Scientific Reports
Iorio, Francesco F; Garcia-Alonso, Luz L; Brammeld, Jonathan S JS; Martincorena, Iňigo I; Wille, David R DR; McDermott, Ultan U; Saez-Rodriguez, Julio J
Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection.
Plos One
Lehmann, Brian D BD; Jovanović, Bojana B; Chen, Xi X; Estrada, Monica V MV; Johnson, Kimberly N KN; Shyr, Yu Y; Moses, Harold L HL; Sanders, Melinda E ME; Pietenpol, Jennifer A JA
Identification by array comparative genomic hybridization of a new amplicon on chromosome 17q highly recurrent in BRCA1 mutated triple negative breast cancer.
Breast Cancer Research : Bcr
Toffoli, Sébastien S; Bar, Isabelle I; Abdel-Sater, Fadi F; Delrée, Paul P; Hilbert, Pascale P; Cavallin, Frédéric F; Moreau, Fabrice F; Van Criekinge, Wim W; Lacroix-Triki, Magali M; Campone, Mario M; Martin, Anne-Laure AL; Roché, Henri H; Machiels, Jean-Pascal JP; Carrasco, Javier J; Canon, Jean-Luc JL