1. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis Bansal, Mukesh; He, Jing; Peyton, Michael; Kustagi, Manjunath; Iyer, Archana; Comb, Michael; White, Michael; Minna, John D.; Califano, Andrea 2019 Articles AdenocarcinomaMolecular biologyLungs--Cancer--Molecular aspectsProteomics
2. Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq Zhong, Jian; Ye, Zhenqing; Clark, Chad R.; Lenz, Samuel W.; Nguyen, Justin H.; Yan, Huihuang; Robertson, Keith D.; Farrugia, Gianrico; Zhang, Zhiguo; Ordog, Tamas; Lee, Jeong-Heon 2019 Articles ChromatinEpigeneticsDiseases--Causes and theories of causationTissues
3. Live-cell single-molecule dynamics of PcG proteins imposed by the DIPG H3.3K27M mutation Tatavosian, Roubina; Duc, Huy Nguyen; Huynh, Thao Ngoc; Fang, Dong; Schmitt, Benjamin; Shi, Xiaodong; Deng, Yiming; Phiel, Christopher; Yao, Tingting; Zhang, Zhiguo; Wang, Haobin; Ren, Xiaojun 2018 Articles Brain--TumorsEpigeneticsBrain--Cancer--Molecular aspectsCancer
4. Epigenetic Alterations Affecting Transcription Factors and Signaling Pathways in Stromal Cells of Endometriosis Yotova, Iveta; Hsu, Emily; Do, Catherine; Gaba, Aulona; Sczabolcs, Matthias; Dekan, Sabine; Kenner, Lukas; Wenzl, Rene; Tycko, Benjamin 2017 Articles Medical geneticsMethylationEndometriosisGenomics
5. PAXX promotes KU accumulation at DNA breaks and is essential for end-joining in XLF-deficient mice Liu, Xiangyu; Shao, Zhengping; Jiang, Wenxia; Lee, Brian J.; Zha, Shan 2017 Articles GeneticsMice as laboratory animalsDNA damageDNA repair
6. Sensing and Processing of DNA Interstrand Crosslinks by the Mismatch Repair Pathway Kato, Niyo; Kawasoe, Yoshitaka; Williams, Hannah; Coates, Elena Lauren; Roy, Upasana; Shi, Yuqian; Beese, Lorena S.; Scharer, Orlando D.; Yan, Hong; Gottesman, Maxwell E.; Takahashi, Tatsuro S.; Gautier, Jean J. 2017 Articles Crosslinked polymersDNA repairMolecular biologyDNA
7. Epigenetic Inactivation of TRAIL Decoy Receptors at 8p12-21.3 Commonly Deleted Region Confers Sensitivity to Apo2L/TRAIL-Cisplatin Combination Therapy in Cervical Cancer Narayan, Gopeshwar; Xie, Dongxu; Ishdorj, Ganchimeg; Scotto, Luigi; Mansukhani, Mahesh M.; Pothuri, Bhavana; Wright, Jason D.; Kaufmann, Andreas; Schneider, Achim; Arias-Pulido, Hugo; Vundavalli, Murty V. 2016 Articles EpigeneticsGeneticsCervix uteri--CancerCervix uteri--Cancer--TreatmentCarcinogenesis
8. Haploinsufficiency of Bcl11b suppresses the progression of ATM-deficient T cell lymphomas Pinkney, Kerice A.; Jiang, Wenxia; Lee, Brian J.; Loredan, Denis G.; Li, Chen; Bhagat, Govind; Zha, Shan 2015 Articles Transcription factorsLeukemia--Genetic aspectsT cellsImmunologyOncology
9. Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models Mendioroz, Maite; Do, Catherine; Jiang, Xiaoling; Liu, Chunhong; Darbary, Huferesh; Lang, Charles F.; Lin, John; Thomas, Anna; Abu-Amero, Sayeda; Stanier, Philip; Temkin, Alexis; Yale, Alexander; Liu, Meng-Min; Li, Yang; Salas, Martha C.; Kerkel, Kristi; Capone, George; Silverman, Wayne; Yu, Y. Eugene; Moore, Gudrun; Wegiel, Jerzy; Tycko, Benjamin 2015 Articles EpigeneticsChromosomesDown syndromeGeneticsBiomechanics
10. Genetics of follicular lymphoma transformation Pasqualucci, Laura; Khiabanian, Hossein; Fangazio, Marco; Vasishtha, Mansi; Messina, Monica; Holmes, Antony B.; Ouillette, Peter; Trifonov, Vladimir; Rossi, Davide; Tabbò, Fabrizio; Ponzoni, Maurilio; Chadburn, Amy; Vundavalli, Murty V.; Bhagat, Govind; Gaidano, Gianluca; Inghirami, Giorgio; Malek, Sami N.; Rabadan, Raul; Dalla-Favera, Riccardo 2014 Articles GenomicsGeneticsLymphomasCarcinogenesis
11. MYC is a critical target of FBXW7 Sato, Mai; Rodriguez-Barrueco, Ruth; Yu, Jiyang; Do, Catherine; Silva, Jose M.; Gautier, Jean 2014 Articles BiologyPathologyGeneticsOncology
12. Alterations of EGFR, p53 and PTEN that mimic changes found in basal-like breast cancer promote transformation of human mammary epithelial cells Pires, Maira M.; Hopkins, Benjamin David; Saal, Lao H.; Parsons, Ramon E. 2013 Articles OncologyCytologyGenetics
13. A Mutation in Mouse Pak1ip1 Causes Orofacial Clefting while Human PAK1IP1 Maps to 6p24 Translocation Breaking Points Associated with Orofacial Clefting Ross, Adam P.; Mansilla, M. Adela; Choe, Youngshik; Helminski, Simon; Sturm, Richard; Maute, Roy L.; May, Scott R.; Hozyasz, Kamil K.; Wójcicki, Piotr; Mostowska, Adrianna; Davidson, Beth; Adamopoulos, Iannis E.; Pleasure, Samuel J.; Murray, Jeffrey C.; Zarbalis, Konstantinos S. 2013 Articles Cleft lip--Genetic aspectsBiosynthesisMutation (Biology)Molecular biologyGeneticsOncology
14. A negative selection heuristic to predict new transcriptional targets Cerulo, Luigi; Paduano, Vincenzo; Zoppoli, Pietro; Ceccarelli, Michele 2013 Articles BioinformaticsComputer science
15. Cdc45 Is a Critical Effector of Myc-Dependent DNA Replication Stress Srinivasan, Seetha V.; Dominguez-Sola, David; Wang, Lily C.; Hyrien, Olivier; Gautier, Jean J. 2013 Articles Genetics
16. Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation Paliwal, Anupam; Temkin, Alexis M.; Kerkel, Kristi; Yale, Alexander; Yotova, Iveta; Drost, Natalia; Lax, Simon; Nhan-Chang, Chia-Ling; Powell, Charles; Borczuk, Alain; Aviv, Abraham; Wapner, Ronald J.; Chen, Xiaowei; Nagy, Peter L.; Schork, Nicholas; Do, Catherine; Torkamani, Ali; Tycko, Benjamin 2013 Articles Anatomy, ComparativeGenomic imprintingDNA--MethylationGeneticsMolecular biology
17. Ensemble of Gene Signatures Identifies Novel Biomarkers in Colorectal Cancer Activated through PPARγ and TNFα Signaling Pagnotta, Stefano Maria; Laudanna, Carmelo; Pancione, Massimo; Sabatino, Lina; Votino, Carolina; Remo, Andrea; Cerulo, Luigi; Zoppoli, Pietro; Manfrin, Erminia; Colantuoni, Vittorio; Ceccarelli, Michele 2013 Articles Biochemical markersColon (Anatomy)--CancerGene expressionMolecular biologyBioinformaticsOncology
18. p53 and DNA methylation suppress the TRAIN to cell death Tavana, Omid; Gu, Wei 2013 Articles OncologyGeneticsCytology
19. PCDH10 Promoter Hypermethylation is Frequent in most Histologic Subtypes of Mature Lymphoid Malignancies and Occurs Early in Lymphomagenesis Narayan, Gopeshwar; Xie, Dongxu; Freddy, Allen J.; Ishdorj, Ganchimeg; Do, Catherine; Satwani, Prakash; Liyanage, Hema; Clark, Lorraine N.; Kisselev, Sergey; Nandula, Subhadra; Scotto, Luigi; Alobeid, Bachir; Savage, David G.; Tycko, Benjamin; O’Connor, Owen Anthony; Bhagat, Govind; Vundavalli, Murty V. 2013 Articles LymphomasCarcinogenesisPromoters (Genetics)MethylationEpigenetics
20. Stromal Protein Ecm1 Regulates Ureteric Bud Patterning and Branching Paroly, Suneeta S.; Wang, Fengwei; Spraggon, Lee; Merregaert, Joseph; Batourina, Ekatherina; Tycko, Benjamin; Schmidt-Ott, Kai M.; Grimmond, Sean; Little, Melissa; Mendelsohn, Cathy Lee 2013 Articles Uterus--GrowthRetinoids--Physiological effectCytology
21. Functional redundancy between the XLF and DNA-PKcs DNA repair factors in V(D)J recombination and nonhomologous DNA end joining Oksenych, Valentyn; Kumar, Vipul; Liu, Xiangyu; Guo, Chunguang; Schwer, Bjoern; Zha, Shan; Alt, Frederick W. 2012 Articles MedicineGeneticsOncology
22. Combined Genetic Inactivation of b2-Microglobulin and CD58 Reveals Frequent Escape from Immune Recognition in Diffuse Large B Cell Lymphoma Challa-Malladi, Madhavi; Lieu, Yen K.; Califano, Olivia; Holmes, Antony B.; Bhagat, Govind; Vundavalli, Murty V.; Dominguez-Sola, David; Pasqualucci, Laura; Dalla-Favera, Riccardo 2011 Articles LymphomasLymphomas--Immunological aspectsCellular immunityGenetics
23. Inactivating mutations of acetyltransferase genes in B-cell lymphoma Pasqualucci, Laura; Dominguez-Sola, David; Chiarenza, Annalisa; Fabbri, Giulia; Grunn, Adina; Trifonov, Vladimir; Kasper, Lawryn H.; Lerach, Stephanie; Tang, Hongyan; Ma, Jing; Rossi, Davide; Chadburn, Amy; Vundavalli, Murty V.; Mullighan, Charles G.; Gaidano, Gianluca; Rabadan, Raul; Brindle, Paul K.; Dalla-Favera, Riccardo 2011 Articles LymphomasB cellsAcetylationCarcinogenesisCytogenetics
24. Promoter Methylation-Mediated Inactivation of PCDH10 in Acute Lymphoblastic Leukemia Contributes to Chemotherapy Resistance Narayan, Gopeshwar; Freddy, Allen J.; Xie, Dongxu; Liyanage, Hema; Clark, Lorraine N.; Kisselev, Sergey; Kang, Ji Un; Nandula, Subhadra; McGuinn, Catherine; Subramaniyam, Shivakumar; Alobeid, Bachir; Satwani, Prakash; Savage, David G.; Vundavalli, Murty V. 2011 Articles EpigeneticsLymphoblastic leukemiaPromoters (Genetics)MethylationDrug resistance in cancer cells
25. Altered DNA Methylation in Leukocytes with Trisomy 21 Kerkel, Kristi; Schupf, Nicole; Hatta, Kota; Pang, Deborah I.; Salas, Martha; Kratz, Alexander; Minden, Mark; Vundavalli, Murty V.; Zigman, Warren; Mayeux, Richard Paul; Jenkins, Edmund C.; Torkamani, Ali; Schork, Nicholas J.; Silverman, Wayne; Croy, B. Anne; Tycko, Benjamin 2010 Articles DNA--MethylationT cellsDown syndromeAutoimmune diseasesGenetics
26. Protocadherin PCDH10, Involved in Tumor Progression, Is a Frequent and Early Target of Promoter Hypermethylation in Cervical Cancer Narayan, Gopeshwar; Scotto, Luigi; Neelakantan, Vijayalakshmi; Kottoor, Sherine H.; Wong, Ada Ho Yan; Loke, Shee‐Loong; Mansukhani, Mahesh M.; Pothuri, Bhavana; Wright, Jason D.; Kaufmann, Andreas; Schneider, Achim; Arias-Pulido, Hugo; Tao, Qian; Vundavalli, Murty V. 2009 Articles GeneticsCervix uteri--CancerCervix uteri--Cancer--TreatmentPromoters (Genetics)Methylation
27. WT1 mutations in T-ALL Tosello, Valeria; Mansour, Marc R.; Barnes, Kelly; Paganin, Maddalena; Sulis, Maria-Luisa; Jenkinson, Sarah; Allen, Christopher G.; Gale, Rosemary E.; Linch, David C.; Palomero, Teresa; Real, Pedro; Vundavalli, Murty V.; Yao, Xiaopan; Richards, Susan M.; Goldstone, Anthony; Rowe, Jacob; Basso, Giuseppe; Wiernik, Peter H.; Paietta, Elisabeth; Pieters, Rob; Horstmann, Martin; Meijerink, Jules P. P.; Ferrando, Adolfo A. 2009 Articles LymphomasAdult T-cell leukemiaT cellsMutation (Biology)Pathology
28. Genetic and phenotypic analysis of B-cell post-transplant lymphoproliferative disorders provides insights into disease biology Vakiani, Efsevia; Basso, Katia; Klein, Ulf; Mansukhani, Mahesh M.; Narayan, Gopeshwar; Smith, Paula M.; Vundavalli, Murty V.; Dalla-Favera, Riccardo; Pasqualucci, Laura; Bhagat, Govind 2008 Articles Lymphoproliferative disordersPhenotypeGene expressionGenetics
29. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation Kerkel, Kristi; Spadola, Alexandra; Yuan, Eric; Kosek, Jolanta; Jiang, Le; Hod, Eldad Arie; Li, Kerry; Vundavalli, Murty V.; Schupf, Nicole; Vilain, Eric; Morris, Mitzi; Haghighi, Fatemeh; Tycko, Benjamin 2008 Articles DNA--MethylationGeneticsGenomicsHuman genome
30. Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair Saal, Lao H.; Gruvberger-Saal, Sofia K.; Persson, Camilla; Lövgren, Kristina; Jumppanen, Mervi; Staaf, Johan; Jönsson, Göran; Pires, Maira M.; Maurer, Mathew; Holm, Karolina; Koujack, Susan; Subramaniyam, Shivakumar; Vallon-Christersson, Johan; Olsson, Håkan; Su, Tao; Memeo, Lorenzo; Ludwig, Thomas; Ethier, Stephen P.; Krogh, Morton; Szabolcs, Matthias; Vundavalli, Murty V.; Isola, Jorma; Hibshoosh, Hanina; Parsons, Ramon E.; Borg, Åke 2008 Articles Breast--Cancer--Genetic aspectsBRCA genesOncogenesGenomicsCytogenetics
31. The CD44+/CD24- phenotype is enriched in basal-like breast tumors Honeth, Gabriella; Bendahl, Pär-Ola; Ringnér, Markus; Saal, Lao H.; Gruvberger-Saal, Sofia K.; Lövgren, Kristina; Grabau, Dorthe; Fernö, Mårten; Borg, Åke; Hegardt, Cecilia 2008 Articles OncologyGeneticsBreast--CancerBreast--Cancer--Genetic aspectsBreast--Tumors
32. Diagnosis of Burkitt's lymphoma in due time: a practical approach Cogliatti, S. B.; Novak, U.; Henz, S.; Schmid, U.; Möller, P.; Barth, T. F. E. 2007 Articles Lymphomas--DiagnosisBurkitt's lymphomaOncology
33. Faithful tissue-specific expression of the human chromosome 21-linked COL6A1 gene in BAC-transgenic mice Xing, Luzhou; Salas, Martha; Lin, Chyuan-Sheng; Zigman, Warren; Silverman, Wayne; Subramaniyam, Shivakumar; Vundavalli, Murty V.; Tycko, Benjamin 2007 Articles Gene expressionDown syndromeEndocardial cushion defectsBacterial artificial chromosomes
34. Gene Dosage Alterations Revealed by cDNA Microarray Analysis in Cervical Cancer: Identification of Candidate Amplified and Overexpressed Genes Narayan, Gopeshwar; Bourdon, Veronique; Chaganti, Seeta; Arias-Pulido, Hugo; Nandula, Subhadra; Rao, Pulivarthi; Gissmann, Lutz; Dürst, Matthias; Schneider, Achim; Pothuri, Bhavana; Mansukhani, Mahesh M.; Basso, Katia; Chaganti, R.S.K.; Vundavalli, Murty V. 2007 Articles GeneticsGenomicsCervix uteri--CancerOverexpression (Genetics)Gene amplification
35. Structural Requirements for the BARD1 Tumor Suppressor in Chromosomal Stability and Homology-directed DNA Repair Laufer, Marsha; Nandula, Subhadra; Modi, Ami P.; Wang, Shuang; Jasin, Maria; Vundavalli, Murty V.; Ludwig, Thomas; Baer, Richard J. 2007 Articles BRCA genesTumor suppressor proteinsDNA repairGenetics
36. CUTLL1, a novel human T-cell lymphoma cell line with t(7;9) rearrangement, aberrant NOTCH1 activation and high sensitivity to c-secretase inhibitors Palomero, Teresa; Barnes, K. C.; Real, P. J.; Glade Bender, Julia L.; Sulis, Maria-Luisa; Vundavalli, Murty V.; Colovai, Adriana I.; Balbin, M.; Ferrando, Adolfo A. 2006 Articles Lymphoblastic leukemiaT cells--ResearchGeneticsCancer--TreatmentPathology
37. Dominant negative retinoic acid receptor initiates tumor formation in mice Kupumbati, Tara; Cattoretti, Giorgio; Marzan, Christine; Farias, Eduardo; Taneja, Reshma; Mira-y-Lopez, Rafael 2006 Articles Transgenic miceTumors--GrowthCancer--Molecular aspectsTretinoin--ReceptorsOncologyCytology
38. Promoter hypermethylation-mediated inactivation of multiple Slit-Robo pathway genes in cervical cancer progression Narayan, Gopeshwar; Goparaju, Chandra; Arias-Pulido, Hugo; Kaufmann, Andreas; Schneider, Achim; Dürst, Matthias; Mansukhani, Mahesh M.; Pothuri, Bhavana; Vundavalli, Murty V. 2006 Articles EpigeneticsPrecancerous conditionsCervix uteri--CancerOncologyBiology
39. Deregulated BCL6 expression recapitulates the pathogenesis of human diffuse large B cell lymphomas in mice Cattoretti, Giorgio; Pasqualucci, Laura; Ballon, Gianna; Tam, Wayne; Nandula, Subhadra; Shen, Qiong; Mo, Tongwei; Vundavalli, Murty V.; Dalla-Favera, Riccardo 2005 Articles LymphomasCarcinogenesisB cellsGenetics
40. Genomic Profiling Maps Loss of Heterozygosity and Defines the Timing and Stage Dependence of Epigenetic and Genetic Events in Wilms’ Tumors Yuan, Eric; Li, Chi-Ming; Yamashiro, Darrell J.; Kandel, Jessica J.; Thaker, Harshwardhan; Vundavalli, Murty V.; Tycko, Benjamin 2005 Articles GenomicsGeneticsEpigeneticsNephroblastoma
41. Lack of PTEN sequesters CHK1 and initiates genetic instability Puc, Janusz; Keniry, Megan; Li, Hong Shen; Pandita, Tej K.; Choudhury, Atish D.; Memeo, Lorenzo; Mansukhani, Mahesh M.; Vundavalli, Murty V.; Gaciong, Zbigniew; Meek, Sarah E.M.; Piwnica-Worms, Helen; Hibshoosh, Hanina; Parsons, Ramon E. 2005 Articles CytogeneticsGenomicsCarcinogenesisPhosphorylation
42. Two Somatic Biallelic Lesions Within and Near SMAD4 in a Human Breast Cancer Cell Line Jakob, John; Nagase, Satoru; Gazdar, Adi; Chien, Minchen; Morozova, Irina; Russo, James J.; Nandula, Subhadra; Vundavalli, Murty V.; Li, Chi-Ming; Tycko, Benjamin; Parsons, Ramon E. 2005 Articles Breast--CancerCell linesCytogenetics
43. Promoter Hypermethylation of FANCF: Disruption of Fanconi Anemia-BRCA Pathway in Cervical Cancer Narayan, Gopeshwar; Arias-Pulido, Hugo; Nandula, Subhadra; Basso, Katia; Sugirtharaj, Dorcas D.; Vargas, Hernan; Mansukhani, Mahesh M.; Villella, Jeannine; Meyer, Larissa; Schneider, Achim; Gissmann, Lutz; Dürst, Matthias; Pothuri, Bhavana; Vundavalli, Murty V. 2004 Articles EpigeneticsGenomicsCervix uteri--CancerFanconi's anemiaBRCA genes
44. Biallelic expression of HRAS and MUCDHL in human and mouse Goldberg, Michael E.; Wei, Michelle L.; Yuan, Luwa; Vundavalli, Murty V.; Tycko, Benjamin 2003 Articles GeneticsGenomicsGenomic imprinting
45. Comprehensive Molecular Cytogenetic Characterization of Cervical Cancer Cell Lines Harris, Charles P.; Lu, Xin-Yan; Narayan, Gopeshwar; Singh, Bhuvanesh; Vundavalli, Murty V.; Rao, Pulivarthi 2003 Articles Cervix uteri--CancerCell linesComparative genomic hybridizationFluorescence in situ hybridizationCytogenetics
46. Genetic analysis identifies putative tumor suppressor sites at 2q35–q36.1 and 2q36.3–q37.1 involved in cervical cancer progression Narayan, Gopeshwar; Arias-Pulido, Hugo; Koul, Sanjay; Lu, Xin-Yan; Harris, Charles P.; Yeh, Y. Albert; Vargas, Hernan; Posso, Hector; Terry, Mary Beth; Gissmann, Lutz; Schneider, Achim; Mansukhani, Mahesh M.; Rao, Pulivarthi; Vundavalli, Murty V. 2003 Articles GeneticsEpigeneticsCervix uteri--CancerHuman chromosome 2Comparative genomic hybridizationGene amplification
47. The Tnfrh1 (Tnfrsf23) gene is weakly imprinted in several organs and expressed at the trophoblast-decidua interface Clark, Lorraine N.; Wei, Michelle L.; Cattoretti, Giorgio; Mendelsohn, Cathy Lee; Tycko, Benjamin 2002 Articles Cancer--Genetic aspectsTrophoblastic tumorsTrophoblastPlacenta--DiseasesTumors--Genetic aspectsGenerative organs, Female--TumorsTumor necrosis factor--ReceptorsOncologyGenetics
48. Deficiency of Pten accelerates mammary oncogenesis in MMTV-Wnt-1 transgenic mice Li, Yi; Podsypanina, Katrina; Liu, Xiufan; Crane, Allison; Tan, Lee; Parsons, Ramon; Varmus, Harold 2001 Articles AntioncogenesBreast--CancerBreast--Cancer--Genetic aspectsBreast--TumorsBreast--Cancer--EtiologyCarcinogenesisMedicineOncology