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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Author / Creator:Mounir, Mohamed ; Lucchetta, Marta ; Silva, Tiago C. ; Olsen, Catharina ; Bontempi, Gianluca ; Chen, Xi ; Noushmehr, Houtan ; Colaprico, Antonio ; Papaleo, Elena
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2019-03, Vol.15 (3), p.e1006701-e1006701
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TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]
Author / Creator:Silva, Tiago C ; Colaprico, Antonio ; Olsen, Catharina ; D'Angelo, Fulvio ; Bontempi, Gianluca ; Ceccarelli, Michele ; Noushmehr, Houtan
Publisher:England: Faculty of 1000 Ltd
Journal title:F1000 research, 2016, Vol.5, p.1542-1542
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Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Author / Creator:Golebiewska, Anna ; Hau, Ann-Christin ; Oudin, Anaïs ; Stieber, Daniel ; Yabo, Yahaya A. ; Baus, Virginie ; Barthelemy, Vanessa ; Klein, Eliane ; Bougnaud, Sébastien ; Keunen, Olivier ; Wantz, May ; Michelucci, Alessandro ; Neirinckx, Virginie ; Muller, Arnaud ; Kaoma, Tony ; Nazarov, Petr V. ; Azuaje, Francisco ; De Falco, Alfonso ; Flies, Ben ; Richart, Lorraine ; Poovathingal, Suresh ; Arns, Thais ; Grzyb, Kamil ; Mock, Andreas ; Herold-Mende, Christel ; Steino, Anne ; Brown, Dennis ; May, Patrick ; Miletic, Hrvoje ; Malta, Tathiane M. ; Noushmehr, Houtan ; Kwon, Yong-Jun ; Jahn, Winnie ; Klink, Barbara ; Tanner, Georgette ; Stead, Lucy F. ; Mittelbronn, Michel ; Skupin, Alexander ; Hertel, Frank ; Bjerkvig, Rolf ; Niclou, Simone P.
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:Acta neuropathologica, 2020-12, Vol.140 (6), p.919-949
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Interpreting pathways to discover cancer driver genes with Moonlight
Author / Creator:Colaprico, Antonio ; Olsen, Catharina ; Bailey, Matthew H. ; Odom, Gabriel J. ; Terkelsen, Thilde ; Silva, Tiago C. ; Olsen, André V. ; Cantini, Laura ; Zinovyev, Andrei ; Barillot, Emmanuel ; Noushmehr, Houtan ; Bertoli, Gloria ; Castiglioni, Isabella ; Cava, Claudia ; Bontempi, Gianluca ; Chen, Xi Steven ; Papaleo, Elena
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-01, Vol.11 (1), p.69-17, Article 69
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A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants
Author / Creator:Gusev, Alexander ; Lawrenson, Kate ; Lin, Xianzhi ; Lyra, Paulo C. ; Kar, Siddhartha ; Vavra, Kevin C. ; Segato, Felipe ; Fonseca, Marcos A. S. ; Lee, Janet M. ; Pejovic, Tanya ; Liu, Gang ; Karlan, Beth Y. ; Freedman, Matthew L. ; Noushmehr, Houtan ; Monteiro, Alvaro N. ; Pharoah, Paul D. P. ; Pasaniuc, Bogdan ; Gayther, Simon A.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2019-05, Vol.51 (5), p.815-823
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Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens
Author / Creator:Prendergast, Emily N. ; de Souza Fonseca, Marcos Abraão ; Dezem, Felipe Segato ; Lester, Jenny ; Karlan, Beth Y. ; Noushmehr, Houtan ; Lin, Xianzhi ; Lawrenson, Kate
Publisher:United States: Public Library of Science
Journal title:PloS one, 2018-05, Vol.13 (5), p.e0196913
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Molecular landscape of IDH-mutant primary astrocytoma Grade IV/glioblastomas
Author / Creator:Wong, Queenie Hoi-Wing ; Li, Kay Ka-Wai ; Wang, Wei-Wei ; Malta, Tathiane M. ; Noushmehr, Houtan ; Grabovska, Yura ; Jones, Chris ; Chan, Aden Ka-Yin ; Kwan, Johnny Sheung-Him ; Huang, Queenie Jun-Qi ; Wong, Gabriel Chun-Hei ; Li, Wen-Cai ; Liu, Xian-Zhi ; Chen, Hong ; Chan, Danny Tat-Ming ; Mao, Ying ; Zhang, Zhen-Yu ; Shi, Zhi-Feng ; Ng, Ho-Keung
Publisher:New York: Elsevier Inc
Journal title:Modern pathology, 2021-07, Vol.34 (7), p.1245-1260
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Expression and regulatory roles of lncRNAs in G-CIMP-low vs G-CIMP-high Glioma: an in-silico analysis
Author / Creator:Datta, Indrani ; Noushmehr, Houtan ; Brodie, Chaya ; Poisson, Laila M.
Publisher:England: BioMed Central
Journal title:Journal of translational medicine, 2021-04, Vol.19 (1), p.182-182, Article 182
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Impact of developmental state, p53 status, and interferon signaling on glioblastoma cell response to radiation and temozolomide treatment
Author / Creator:Berezovsky, Artem ; Nuga, Oluwademilade ; Datta, Indrani ; Bergman, Kimberly ; Sabedot, Thais ; Gurdziel, Katherine ; Irtenkauf, Susan ; Hasselbach, Laura ; Meng, Yuling ; Mueller, Claudius ; Petricoin, 3rd, Emanuel F ; Brown, Stephen ; Purandare, Neeraja ; Aras, Sidhesh ; Mikkelsen, Tom ; Poisson, Laila ; Noushmehr, Houtan ; Ruden, Douglas ; deCarvalho, Ana C
Publisher:United States: Public Library of Science
Journal title:PloS one, 2025-02, Vol.20 (2), p.e0315171
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Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions
Author / Creator:Yang, Xiaojing ; Noushmehr, Houtan ; Han, Han ; Andreu-Vieyra, Claudia ; Liang, Gangning ; Jones, Peter A.
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2012-03, Vol.8 (3), p.e1002604
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Correction to: Molecular landscape of IDH-mutant primary astrocytoma Grade IV/Glioblastomas
Author / Creator:Wong, Queenie Hoi-Wing ; Li, Kay Ka-Wai ; Wang, Wei-Wei ; Malta, Tathiane M. ; Noushmehr, Houtan ; Grabovska, Yura ; Jones, Chris ; Chan, Aden Ka-Yin ; Kwan, Johnny Sheung-Him ; Huang, Queenie Jun-Qi ; Wong, Gabriel Chun-Hei ; Li, Wen-Cai ; Liu, Xian-Zhi ; Chen, Hong ; Chan, Danny Tat-Ming ; Mao, Ying ; Zhang, Zhen-Yu ; Shi, Zhi-Feng ; Ng, Ho-Keung
Publisher:New York: Elsevier Inc
Journal title:Modern pathology, 2021-06, Vol.34 (6), p.1231-1231
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ArticlesPeer ReviewedFull Text
Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
Author / Creator:Rhie, Suhn Kyong ; Hazelett, Dennis J ; Coetzee, Simon G ; Yan, Chunli ; Noushmehr, Houtan ; Coetzee, Gerhard A
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2014-05, Vol.15 (1), p.331-331, Article 331
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Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci
Author / Creator:Rhie, Suhn Kyong ; Coetzee, Simon G. ; Noushmehr, Houtan ; Yan, Chunli ; Kim, Jae Mun ; Haiman, Christopher A. ; Coetzee, Gerhard A.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-05, Vol.8 (5), p.e63925
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Transcriptional profiling of endogenous germ layer precursor cells identifies dusp4 as an essential gene in zebrafish endoderm specification
Author / Creator:Brown, Jamie L ; Snir, Mirit ; Noushmehr, Houtan ; Kirby, Martha ; Hong, Sung-Kook ; Elkahloun, Abdel G ; Feldman, Benjamin
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2008-08, Vol.105 (34), p.12337-12342
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Fatty Acid Translocase (FAT/CD36) Is Localized on Insulin-Containing Granules in Human Pancreatic β-Cells and Mediates Fatty Acid Effects on Insulin Secretion
Author / Creator:Noushmehr, Houtan ; D’Amico, Eugenio ; Farilla, Loredana ; Hui, Hongxiang ; Wawrowsky, Kolja A. ; Mlynarski, Wojciech ; Doria, Alessandro ; Abumrad, Nada A. ; Perfetti, Riccardo
Publisher:Alexandria, VA: American Diabetes Association
Journal title:Diabetes (New York, N.Y.), 2005-02, Vol.54 (2), p.472-481
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
Author / Creator:Chng, Kern Rei ; Li, Chenhao ; Bertrand, Denis ; Ng, Amanda Hui Qi ; Kwah, Junmei Samantha ; Low, Hwee Meng ; Tong, Chengxuan ; Natrajan, Maanasa ; Zhang, Michael Hongjie ; Xu, Licheng ; Ko, Karrie Kwan Ki ; Ho, Eliza Xin Pei ; Av-Shalom, Tamar V. ; Teo, Jeanette Woon Pei ; Khor, Chiea Chuen ; Chen, Swaine L. ; Mason, Christopher E. ; Ng, Oon Tek ; Marimuthu, Kalisvar ; Ang, Brenda ; Nagarajan, Niranjan
Publisher:New York: Nature Publishing Group US
Journal title:Nature Medicine, 2020-06, Vol.26 (6), p.941-951
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Exploring the cancer methylome
Author / Creator:Berman, Benjamin P ; Weisenberger, Daniel J ; Hinoue, Toshinori ; Noushmehr, Houtan ; Liu, Yaping ; Aman, Joseph F ; Shen, Hui ; Malik, Simeen ; Mahurkar, Swapna ; Triche, Timothy ; Ramjan, Zachary ; Nicolet, Charles M ; Van Den Berg, David ; Cope, Leslie ; Herman, James G ; Baylin, Stephen B ; Laird, Peter W
Publisher:London: BioMed Central
Journal title:BMC proceedings, 2012-10, Vol.6 (S6), p.O24-O24, Article O24
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Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains
Author / Creator:Berman, Benjamin P ; Weisenberger, Daniel J ; Aman, Joseph F ; Hinoue, Toshinori ; Ramjan, Zachary ; Liu, Yaping ; Noushmehr, Houtan ; Lange, Christopher P E ; van Dijk, Cornelis M ; Tollenaar, Rob A E M ; Van Den Berg, David ; Laird, Peter W
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2012-01, Vol.44 (1), p.40-46
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ArticlesPeer ReviewedFull Text
SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data
Author / Creator:Cava, Claudia ; Colaprico, Antonio ; Bertoli, Gloria ; Graudenzi, Alex ; Silva, Tiago ; Olsen, Catharina ; Noushmehr, Houtan ; Bontempi, Gianluca ; Mauri, Giancarlo ; Castiglioni, Isabella
Publisher:Switzerland: MDPI AG
Journal title:International journal of molecular sciences, 2017-02, Vol.18 (2), p.274-274
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Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1
Author / Creator:Mazor, Tali ; Chesnelong, Charles ; Pankov, Aleksandr ; Jalbert, Llewellyn E. ; Hong, Chibo ; Hayes, Josie ; Smirnov, Ivan V. ; Marshall, Roxanne ; Souza, Camila F. ; Shen, Yaoqing ; Viswanath, Pavithra ; Noushmehr, Houtan ; Ronen, Sabrina M. ; Jones, Steven J. M. ; Marra, Marco A. ; Cairncross, J. Gregory ; Perry, Arie ; Nelson, Sarah J. ; Chang, Susan M. ; Bollen, Andrew W. ; Molinaro, Annette M. ; Bengtsson, Henrik ; Olshen, Adam B. ; Weiss, Samuel ; Phillips, Joanna J. ; Luchman, H. Artee ; Costello, Joseph F.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2017-10, Vol.114 (40), p.10743-10748
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New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

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TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]

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Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology

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Interpreting pathways to discover cancer driver genes with Moonlight

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A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants

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Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

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Molecular landscape of IDH-mutant primary astrocytoma Grade IV/glioblastomas

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Expression and regulatory roles of lncRNAs in G-CIMP-low vs G-CIMP-high Glioma: an in-silico analysis

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Impact of developmental state, p53 status, and interferon signaling on glioblastoma cell response to radiation and temozolomide treatment

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Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions

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Correction to: Molecular landscape of IDH-mutant primary astrocytoma Grade IV/Glioblastomas

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Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

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Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

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Transcriptional profiling of endogenous germ layer precursor cells identifies dusp4 as an essential gene in zebrafish endoderm specification

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Fatty Acid Translocase (FAT/CD36) Is Localized on Insulin-Containing Granules in Human Pancreatic β-Cells and Mediates Fatty Acid Effects on Insulin Secretion

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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

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Exploring the cancer methylome

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Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

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SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data

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Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1

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