Resources Publications (current total: 141)

NextBio Authored Articles

• Ontology-based meta-analysis of global collections of high-throughput public data
  Ilya Kupershmidt, Qiaojuan Jane Su, Anoop Grewal, Suman Sundaresh, Inbal Halperin, James Flynn, Mamatha Shekar, Helen Wang, Jenny Park, Wenwu Cui, Gregory D Wall, Robert Wisotzkey, Satnam Alag, Saeid Akhtari, Mostafa Ronaghi
  PLoS One 2010 Sep; 5(9). pii: e13066 (please cite in your publications)
• Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues.
  Johanna Hasmats, Ilya Kupershmidt, Cristina Rodríguez-Antona, Qiaojuan Jane Su, Muhammad Suleman Khan, Carlos Jara, Xabier Mielgo, Joakim Lundeberg, Henrik Green
  Gene. 2012 Sep; 506(1):62-8
• Antipsychotics activate the TGFβ pathway effector SMAD3
  T Cohen, S Sundaresh, F Levine
  Molecular Psychiatry 2012 Jan; doi: 10.1038/mp.2011.186

User Authored Articles Citing NextBio

• Featured Gene Expression Profiling to Identify Potentially Relevant Disease Outcomes and Support Human Health Risk Assessment for Carbon Black Nanoparticle Exposure.
  Julie A. Bourdon, Andrew Williams, Byron Kuo, Ivy Moffat, Paul A. White, Sabina Halappanavar, Ulla Vogel, Hakan Wallin, Carole L. Yauk
  Toxicology 2012 Nov; pii: S0300-483X(12)00366-6. doi: 10.1016/j.tox.2012.10.014
  
  

  "A study by researchers at Environmental Health Science and Research Bureau, Health Canada, showing the utility of toxicogenomics in human health risk assessment for carbon black nanoparticle exposure. Disease prediction was done using the NextBio Disease Atlas and Meta-Analysis apps to study human and mouse gene expression profiles with fibrosis as a phenotype."

• Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility.
  Frédéric Chalmel, Aurélie Lardenois, Bertrand Evrard, Romain Mathieu, Caroline Feig, Philippe Demougin, Alexandre Gattiker, Wolfgang Schulze, Bernard Jégou, Christiane Kirchhoff, Michael Primig
  Human Reproduction. 2012 Nov; 27(11):3233-48
• Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses.
  Arimantas Lionikas, Caroline Meharg, Jonathan M Derry, Aivaras Ratkevicius, Andrew M Carroll, David J Vandenbergh, David A Blizard
  BMC Genomics. 2012 Nov; 13(1):592
• CellLineNavigator: a workbench for cancer cell line analysis.
  Markus Krupp, Timo Itzel, Thorsten Maass, Andreas Hildebrandt, Peter R Galle, Andreas Teufel
  Nucleic Acids Research. 2012 Oct; 1-7
• Genetic Differences in Transcript Responses to Low-Dose Ionizing Radiation Identify Tissue Functions Associated with Breast Cancer Susceptibility.
  Antoine M Snijders, Francesco Marchetti, Sandhya Bhatnagar, Nadire Duru, Ju Han, Zhi Hu, Jian-Hua Mao, Joe W Gray, Andrew J Wyrobek
  PloS One. 2012 Oct; 7(10):e45394. doi: 10.1371/journal.pone.0045394
• A genome-wide approach reveals novel imprinted genes expressed in the human placenta.
  Sandrine Barbaux, Géraldine Gascoin-Lachambre, Christophe Buffat, Paul Monnier, Françoise Mondon, Marie-Béatrice Tonanny, Amélie Pinard, Jana Auer, Bettina Bessières, Anne Barlier, Sébastien Jacques, Umberto Simeoni, Luisa Dandolo, Franck Letourneur, Helene Jammes, Daniel Vaiman
  Epigenetics. 2012 Sep; 7(9):1079-90
• Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas.
  Felix Haglund, Ran Ma, Mikael Huss, Luqman Sulaiman, Ming Lu, Inga-Lena Nilsson, Anders Höög, C Christofer Juhlin, Johan Hartman, Catharina Larsson
  The Journal of Clinical Endocrinology and Metabolism. 2012 Sep;
• Vitamin D: an overview of its role in skeletal muscle physiology in children and adolescents.
  Tom J Hazell, Jason R Deguire, Hope A Weiler
  Nutrition Reviews. 2012 Sep; 70(9):520-533
• δ ENaC: A Novel Divergent Amiloride-Inhibitable Sodium Channel.
  Hong-Long Ji, Run-Zhen Zhao, Zai-Xing Chen, Sreerama Shetty, Steven Idell, Sadis Matalon
  American Journal of Physiology. Lung Cellular and Molecular Physiology. 2012 Sep;
• Single Nucleotide Polymorphism in the Interleukin 12B Gene is Associated with Risk for Breast Cancer Development.
  M. H. Kaarvatn, J. Vrbanec, A. Kulic, J. Knezevic, B. Petricevic, S. Balen, D. Vrbanec, Z. Dembic
  Scandinavian Journal of Immunology. 2012 Sep; 76(3):329-35
• The gamma secretase inhibitor MRK-003 attenuates pancreatic cancer growth in preclinical models.
  Masamichi Mizuma, Zeshaan A Rasheed, Shinichi Yabuuchi, Noriyuki Omura, Nathaniel R. Campbell, Roeland F de Wilde, Elizabeth De Oliveira, Qing Zhang, Oscar Puig, William Matsui, Manuel Hidalgo, Anirban Maitra, N.V Rajeshkumar
  Molecular Cancer Therapeutics. 2012 Sep; 11(9):1999-2009
• P2RX7: expression responds to sleep deprivation and associates with rapid cycling in bipolar disorder type 1.
  Lena Backlund, Catharina Lavebratt, Louise Frisén, Pernilla Nikamo, Dzana Hukic Sudic, Lil Träskman-Bendz, Mikael Landén, Gunnar Edman, Marquis P Vawter, Urban ösby, Martin Schalling
  PloS One. 2012 Aug; 7(8):e43057. doi: 10.1371/journal.pone.0043057
• Expression of MicroRNA miR-122 Facilitates an Efficient Replication in Nonhepatic Cells upon Infection with Hepatitis C Virus.
  Takasuke Fukuhara, Hiroto Kambara, Mai Shiokawa, Chikako Ono, Hiroshi Katoh, Eiji Morita, Daisuke Okuzaki, Yoshihiko Maehara, Kazuhiko Koike, Yoshiharu Matsuura
  Journal of Virology. 2012 Aug; 86(15):7918-33
• Dynamic distribution of linker histone H1.5 in cellular differentiation.
  Jing-Yu Li, Michaela Patterson, Hanna K A Mikkola, William E Lowry, Siavash K Kurdistani
  PLoS Genetics. 2012 Aug; (8):e1002879. doi: 10.1371/journal.pgen.1002879
• In silico analysis of expression of orphan G protein-coupled receptor 155 during inflammation - implications for autism.
  A.H. Swiergiel, G.R. Juszczak, K.M. Grochowska
  European Neuropsychopharmacology. 2010 Aug; 20(3):S219-20
• Role of transcriptional coregulator GRIP1 in the anti-inflammatory actions of glucocorticoids.
  Yurii Chinenov, Rebecca Gupte, Jana Dobrovolna, Jamie R Flammer, Bill Liu, Francesco E Michelassi, Inez Rogatsky
  Proc Natl Acad Sci U S A. 2012 Jul; 109(29):11776-81
• Reading cancer's blueprint.
  Michael Eisenstein
  Nature Biotechnology. 2012 Jul; 30(7):581-4
• HNF4α Antagonists Discovered by a High-Throughput Screen for Modulators of the Human Insulin Promoter.
  Alice Kiselyuk, Seung-Hee Lee, Suzette Farber-Katz, Mingjun Zhang, Sonalee Athavankar, Tom Cohen, Anthony B. Pinkerton, Mao Ye, Paul Bushway, Adam D. Richardson, Heather A. Hostetler, Mariam Rodriguez-Lee, Li Huang, Benjamin Spangler, Layton Smith, Jennifer Higginbotham, John Cashman, Hudson Freeze, Pamela Itkin-Ansari, Marcia I. Dawson, Friedhelm Schroeder, Yong Cang, Mark Mercola, and Fred Levine
  Chemistry & Biology. 2012 July; 19(7):806-8
• Data Mining and Meta-Analysis on DNA Microarray Data.
  Triantafyllos Paparountas, Maria Nefeli Nikolaidou-Katsaridou, Gabriella Rustici and Vasilis Aidinis
  International Journal of Systems Biology and Biomedical Technologies. 2012 Jul; 1(3):1-39
• Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression.
  Suhaida A Selamat, Brian S Chung, Luc Girard, Wei Zhang, Ying Zhang, Mihaela Campan, Kimberly D Siegmund, Michael N Koss, Jeffrey A Hagen, Wan L Lam, Stephen Lam, Adi F Gazdar, Ite A Laird-Offringa.
  Genome Research. 2012 Jul; 22(7):1197-211
• Matrix metalloproteinase induction of Rac1b, a key effector of lung cancer progression.
  Melody L Stallings-Mann, Jens Waldmann, Ying Zhang, Erin Miller, Mona L Gauthier, Daniel W Visscher, Gregory P Downey, Evette S Radisky, Alan P Fields, Derek C Radisky
  Science Translational Medicine. 2012 Jul; 4:142ra95
• An unusual case of cat-eye syndrome phenotype and extragonadal mature teratoma: Review of the literature.
  Maria Tzetis, Kalliopi Stefanaki, Areti Syrmou, Konstantina Kosma, Eleni Leze, Krinio Giannikou, Vasilis Oikonomakis, Christalena Sofocleous, Michael Choulakis, Aggeliki Kolialexi, Periklis Makrythanasis, Sophia Kitsiou-Tzeli
  Birth Defects Research. Part A, Clinical and Molecular Teratology. 2012 Jul; 94(7):561-6
• Identification of LMO2 transcriptome and interactome in diffuse large B-cell lymphoma.
  Elena Cubedo, Andrew J Gentles, Chuanxin Huang, Yasodha Natkunam, Shruti Bhatt, Xiaoqing Lu, Xiaoyu Jiang, Isabel Romero-Camarero, Aharon Freud, Shuchun Zhao, Carlos E Bacchi, Jose A Martínez-Climent, Isidro Sánchez-García, Ari Melnick, Izidore S Lossos
  Blood. 2012 Jun; 119:5478-91
• Using whole exome sequencing to identify genetic candidates for carboplatin and gemcitabine induced toxicities.
  J. Hasmats and H. Gréen
  Annals of Oncology. 2012 Jun; 23(5):v12-22
• A genome-wide expression profile of adrenocortical cells in knockout mice lacking steroidogenic acute regulatory protein.
  Tomohiro Ishii, Toshikatsu Mitsui, Sadafumi Suzuki, Yumi Matsuzaki, Tomonobu Hasegawa.
  Endocrinology. 2012 Jun; 153(6):2714-23
• Differential Transcriptomic Analysis of Spontaneous Lung Tumors in B6C3F1 Mice: Comparison to Human Non-Small Cell Lung Cancer.
  Arun R. Pandiri, Robert C. Sills, Vincent Ziglioli, Thai-Vu T. Ton, Hue-Hua L. Hong, Stephanie A. Lahousse, Kevin E. Gerrish, Scott S. Auerbach, Keith R. Shockley, Pierre R. Bushel, Shyamal D. Peddada, and Mark J. Hoenerhoff
  Toxicologic Pathology. 2012 Jun; 40(8):1141-59
• Amino Acid Starvation Induced by Invasive Bacterial Pathogens Triggers an Innate Host Defense Program.
  Ivan Tattoli, Matthew T. Sorbara, Dajana Vuckovic, Arthur Ling, Fraser Soares, Leticia A.M. Carneiro, Chloe Yang, Andrew Emili, Dana J. Philpott, Stephen E. Girardin
  Cell Host & Microbe. 2012 Jun; 11(6):563-575
• NLRP12 Suppresses Colon Inflammation and Tumorigenesis through the Negative Regulation of Noncanonical NFKB Signaling.
  Irving C Allen, Justin E Wilson, Monika Schneider, John D Lich, Reid A Roberts, Janelle C Arthur, Rita-Marie T Woodford, Beckley K Davis, Joshua M Uronis, Hans H Herfarth, Christian Jobin, Arlin B Rogers, Jenny P-Y Ting.
  Immunity. 2012 May; 36(5):742-54
• Testing an aflatoxin B1 gene signature in rat archival tissues.
  B Alex Merrick, Scott S Auerbach, Patricia S Stockton, Julie F Foley, David E Malarkey, Robert C Sills, Richard D Irwin, Raymond R Tice.
  Chemical Research in Toxicology. 2012 May; 25(5):1132-44
• Matrix metalloproteinase-10 is required for lung cancer stem cell maintenance, tumor initiation and metastatic potential.
  Verline Justilien, Roderick P Regala, I-Chu Tseng, Michael P Walsh, Jyotica Batra, Evette S Radisky, Nicole R Murray, Alan P Fields
  PloS One. 2012 Apr; 7(4): e35040
• Cofactors required for TLR7- and TLR9-dependent innate immune responses.
  Chih-Yuan Chiang, Alex Engel, Amanda M Opaluch, Irene Ramos, Ana M Maestre, Ismael Secundino, Paul D De Jesus, Quy T Nguyen, Genevieve Welch, Ghislain M C Bonamy, Loren J Miraglia, Anthony P Orth, Victor Nizet, Ana Fernandez-Sesma, Yingyao Zhou, Gregory M Barton, Sumit K Chanda
  Cell Host & Microbe. 2012 Mar; 11(3):306-18
• SEMG1 may be the candidate gene for idiopathic asthenozoospermia.
  Qing-feng Yu, Qi-zhao Zhou, Qiang Wei, Jing-ping Li, Chun-qiong Feng, Xiang-ming Mao
  Translational Andrology and Urology. 2012 Mar; 1(1): DOI: 10.3978/j.issn.2223-4683.2012.s122
• Beyond differential expression: methods and tools for mining the transcriptomic landscape of human tissue and disease.
  Patrick R Schmid
  MIT Ph.D. Thesis - 2012
• Graphical Models for Biclustering and Information Retrieval in Gene Expression Data.
  Jose Caldas
  Aalto University Ph.D. Thesis - 2012
• Knowledge discovery in microarray data of bioinformatics.
  Fahrġ Salġh Kocabaġ
  Thesis submitted to the Graduate School of Informatics of the Middle East Technical University.
• Semantic Web and the Libraries: An Overview.
  MN Yadagiri, MP Ramesh
  semantic-web-journal.org
• Big Data in Healthcare Hype and Hope.
  B Feldman, EM Martin, T Skotnes
  west-info.eu 2012
• Correlation of Circulating Human Blood RNA Biomarkers and Clinical Outcomes in an Observational Invasive Aspergillosis (IA) Trial.
  Nicholas J. Murgolo, Wei Ding, Jun Li, Radha A. Railkar, Rebecca L. Fox, Cameron M. Douglas, David Mozley, Eunkyung A. Kauh, Robert Iannone, Andrey Loboda, Razvan Cristescu, and Norah J. Shire
  Merck Research Laboratories, USA
• Antipsychotics activate the TGFβ pathway effector SMAD3.
  T Cohen, S Sundaresh, F Levine
  Molecular Psychiatry , (31 January 2012)
• MicroRNA-132 dysregulation in schizophrenia has implications for both neurodevelopment and adult brain function.
  Brooke H Miller, Zane Zeier, Li Xi, Thomas A Lanz, Shibing Deng, Julia Strathmann, David Willoughby, Paul J Kenny, John D Elsworth, Matthew S Lawrence, Robert H Roth, Dieter Edbauer, Robin J Kleiman, Claes Wahlestedt
  Proceedings of the National Academy of Sciences of the United States of America 2012 Feb 21
• The MMP-9/TIMP-1 Axis Controls the Status of Differentiation and Function of Myelin-Forming Schwann Cells in Nerve Regeneration.
  Youngsoon Kim, Albert G Remacle, Andrei V Chernov, Huaqing Liu, Igor Shubayev, Calvin Lai, Jennifer Dolkas, Sergey A Shiryaev, Vladislav S Golubkov, Andrew P Mizisin, Alex Y Strongin, Veronica I Shubayev
  PLoS ONE 2012
• An animal model of MYC-driven medulloblastoma.
  Yanxin Pei, Colin E Moore, Jun Wang, Alok K Tewari, Alexey Eroshkin, Yoon-Jae Cho, Hendrik Witt, Andrey Korshunov, Tracy-Ann Read, Julia L Sun, Earlene M Schmitt, C Ryan Miller, Anne F Buckley, Roger E McLendon, Thomas F Westbrook, Paul A Northcott, Michael D Taylor, Stefan M Pfister, Phillip G Febbo, Robert J Wechsler-Reya
  Cancer cell 2012 Feb 14
• An Improved Meta-Analysis Procedure Reveals Key Transcriptome Signatures Underlying a Renal Damage Phenotype. (PDF file)
  Yu Bai, Jennifer Schmahl
  Biophysical Journal, Volume 102, Issue 3, Supplement 1, 31 January 2012, Page 184a
• Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion.
  Gillian H Little, Houtan Noushmehr, Sanjeev K Baniwal, Benjamin P Berman, Gerhard A Coetzee, Baruch Frenkel
  Nucleic acids research 2011 Dec 19
• Growth of lung cancer cells in three-dimensional microenvironments reveals key features of tumor malignancy.
  Magdalena A Cichon, Vladimir G Gainullin, Ying Zhang, Derek C Radisky
  Integrative biology : quantitative biosciences from nano to macro 2012 Apr
• Characterization of polybrominated diphenyl ether toxicity in Wistar Han rats and use of liver microarray data for predicting disease susceptibilities.
  June K Dunnick, A Brix, H Cunny, M Vallant, K R Shockley
  Toxicologic pathology 2012
• Toward a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation.
  Antony J Williams, Sean Ekins, Valery Tkachenko
  Drug discovery today 2012 Mar 8
• A specific increase in inositol 1,4,5-trisphosphate 3-kinase B expression upon differentiation of human embryonic stem cells.
  Catherine Hoofd, Fabienne Devreker, Laurence Deneubourg, Sandrine Deleu, Thi Mai Uyen Nguyen, Karen Sermon, Yvon Englert, Christophe Erneux
  Cellular signalling 2012 Mar 13
• Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
  José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G Nicholson, Sakari Knuutila, Alvis Brazma, Samuel Kaski
  Bioinformatics (Oxford, England) 2012 Jan 15
• In search of the Golden Fleece: unraveling principles of morphogenesis by studying the integrative biology of skin appendages.
  Michael W Hughes, Ping Wu, Ting-Xin Jiang, Sung-Jan Lin, Chen-Yuan Dong, Ang Li, Fon-Jou Hsieh, Randall B Widelitz, Cheng Ming Chuong
  Integrative biology : quantitative biosciences from nano to macro 2011 Apr
• ProKinO: an ontology for integrative analysis of protein kinases in cancer.
  Gurinder Gosal, Krys J Kochut, Natarajan Kannan
  PloS one 2011
• Identification of aberrant pathways and network activities from high-throughput data.
  Jinlian Wang, Yuji Zhang, Catalin Marian, Habtom W Ressom
  Briefings in bioinformatics 2012 Jan 27
• Genetic dissection of the canq1 locus governing variation in extent of the collateral circulation.
  Shiliang Wang, Hua Zhang, Tim Wiltshire, Robert Sealock, James E Faber
  PloS one 2012
• A genome-wide search for genetic influences and biological pathways related to the brain's white matter integrity.
  Lorna M Lopez, Mark E Bastin, Susana Muñoz Maniega, Lars Penke, Gail Davies, Andrea Christoforou, Maria C Valdés Hernández, Natalie A Royle, Albert Tenesa, John M Starr, David J Porteous, Joanna M Wardlaw, Ian J Deary
  Neurobiology of aging 2012 Mar 15
• Gene regulation by cohesin in cancer: is the ring an unexpected party to proliferation?
  Jenny M Rhodes, Miranda McEwan, Julia A Horsfield
  Molecular cancer research : MCR 2011 Dec
• Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas.
  Lloyd D Graham, Susanne K Pedersen, Glenn S Brown, Thu Ho, Zena Kassir, Audrey T Moynihan, Emma K Vizgoft, Robert Dunne, Letitia Pimlott, Graeme P Young, Lawrence C Lapointe, Peter L Molloy
  Genes & cancer 2011 Aug
• SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: online resources and useful tools - a compass in the land of biomarker discovery.
  Davide Bedognetti, James M Balwit, Ena Wang, Mary L Disis, Cedrik M Britten, Lucia G Delogu, Sara Tomei, Bernard A Fox, Thomas F Gajewski, Francesco M Marincola, Lisa H Butterfield
  Journal of translational medicine 2011
• SNPedia: a wiki supporting personal genome annotation, interpretation and analysis.
  Michael Cariaso, Greg Lennon
  Nucleic acids research 2012 Jan
• Comprehensive literature review and statistical considerations for microarray meta-analysis.
  George C Tseng, Debashis Ghosh, Eleanor Feingold
  Nucleic acids research 2012 Jan 19
• Characterization of NLRP12 during the development of allergic airway disease in mice.
  Irving C Allen, John D Lich, Janelle C Arthur, Corey M Jania, Reid A Roberts, Justin B Callaway, Stephen L Tilley, Jenny P-Y Ting
  PloS one 2012
• RNA-Seq Atlas - A reference database for gene expression profiling in normal tissue by next generation sequencing.
  Markus Krupp, Jens U Marquardt, Ugur Sahin, Peter R Galle, John Castle, Andreas Teufel
  Bioinformatics (Oxford, England) 2012 Feb 17
• DNA Sequencing Caught in Deluge of Data (PDF file)
  Andrew Pollack
  The New York Times, Nov 30 2011
• An Emerging Era of Big Data.
  National Institutes of Mental Health Director’s Blog
• CIWI: Albert, Flavelle & Pineau - Introduction to the Semantic Web. (DOCX file)
  C Commons - zenportfolios.com
• Evaluación de metabuscadores gratuitos especializados en ciencias de la salud.
  Sílvia Sastre-Suárez,Elena Pastor-Ramon
  El Profesional de la Informacion 2011. Volume 20, Number 6 / November-December 2011
• Increased cellular accumulation and distribution of amrubicin contribute to its activity in anthracycline-resistant cancer cells
  Vidya Mamidipudi, Tao Shi, Helen Brady, Sekhar Surapaneni, Rajesh Chopra, Sharon L. Aukermany, Carla Heise, Victoria Sung,
  Cancer Chemotherapy and Pharmacology, November 2011
• Essential Roles of ECAT15-2/Dppa2 in Functional Lung Development.
  Tomonori Nakamura, Masato Nakagawa, Tomoko Ichisaka, Arufumi Shiota , Shinya Yamanaka
  Molecular and cellular biology, November 2011
• Metabolic syndrome in mice induced by expressing a transcriptional activator in adipose tissue.
  Liwen Zhang, Yuchen Zhou, Amber Ying Zhu, Xiang-qing Li, Steven S. Mundt, Ling Gao, JeanMarie Lisnock, Melba Hernandez, Magdalena Alonso-Galicia, Martin S. Springer, Edward A. O'Neill, Bruce L. Daugherty, Oscar Puig
  Transgenic Research, October 2011
• Discovery of NSAID and Anticancer Drugs Enhancing Reprogramming and IPS Cell Generation
  Chao-Shun Yang, Claudia G. Lopez, Tariq M. Rana
  Stem Cells Volume 29, Issue 10, pages 1528-1536, Oct 2011
• Aloe vera Non-Decolorized Whole Leaf Extract-Induced Large Intestinal Tumors in F344 Rats Share Similar Molecular Pathways with Human Sporadic Colorectal Tumors
  Arun Pandiri, Robert Sills, Mark Hoenerhoff, Shyamal Peddada, Thai-Vu Ton, Hue-Hua Hong, Gordon Flake, David Malarkey, Greg Olson, Igor Pogribny, Nigel Walker, Mary Boudreau
  Toxicol Pathol 0192623311422081, September 21, 2011
• Loss of breast epithelial marker hCLCA2 promotes epithelial-to-mesenchymal transition and indicates higher risk of metastasis.
  V Walia , Y Yu, J R McLean , B G Hollier, J Cheng, S A Mani, L Premkumar, R C Elble, K Rao
  Oncogene, September 12, 2011
• Transcription factor Dlx2 protects from TGFβ-induced cell-cycle arrest and apoptosis
  Mahmut Yilmaz , Dorothea 0Maaß, Neha Tiwari , Lorenz Waldmeier, Petra Schmidt, François Lehembre, Gerhard Christofori
  The EMBO journal, September 6,2011
• Homozygosity mapping and targeted genomic sequencing reveal locomotion in a consanguineous kindred the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred
  Suleyman Gulsuner, Ayse B Tekinay, Katja Doerschner, Huseyin Boyaci, Kaya Bilguvar, Hilal Unal, Aslihan Ors, O. Emre Onat, Ergin Atalar, A. Nazli Basak, Haluk Topaloglu, Tulay Kansu, Meliha Tan, Uner Tan, Murat Gunel, Tayfun Ozcelik
  Genome Research - published online September 1, 2011
• Speak, RNA. A trip through the transcriptome.
  Jeffrey Perkel
  The Scientist, September 2011
• New system for nitrosation of alkyl-substituted gem-dichlorocyclopropanes.
  Oksana B. Bondarenko, Anna Yu. Gavrilova, Dilovar S. Murodov, Nikolai V. Zyk , Nikolai S. Zefirov ,M. V. Lomonosov
  Mendeleev Communications, Volume 21, Issue 4, July-August 2011
• TGF-β in the Bone Microenvironment: Role in Breast Cancer Metastases.
  Jeroen T Buijs,Keith R Stayrook, Theresa A Guise
  Cancer microenvironment : official journal of the International Cancer Microenvironment Society, July 12, 2011
• Matrix Metalloproteinase-10 Promotes Kras-Mediated Bronchio-Alveolar Stem Cell Expansion and Lung Cancer Formation.
  Roderick P. Regala, Verline Justilien, Michael P. Walsh, Capella Weems, Nicole R. Murray, Alan P. Fields, Andras Khoor
  PLoS ONE 6(10): e26439. doi:10.1371/journal.pone.0026439
• Wide-scale comparison of transcriptome data and the role of microRNA in major depression and suicide.
  Raymond Lim, B. Sc, University of British Columbia, 2008.
  
• Developing an Interactive Communicative Search Agent.
  Lauren Akif, University of Gothenburg, Department of Applied Information Technology, Gothenburg, Sweden, June 2011.
  
• Approaches for defining the Hsp90-dependent proteome
  Steven D. Hartson, Robert L. Matts,
  Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, In Press, Uncorrected Proof, Available online 27 August 2011
• Cheminformatic/bioinformatic analysis of large corporate databases: Application to drug repurposing
  William Loging, Raul Rodriguez-Esteban, Jon Hill, Tom Freeman, John Miglietta
  Drug Discovery Today: Therapeutic Strategies, In Press, Corrected Proof, Available online 9 August 2011
• Intradomain cleavage of the inhibitory prodomain is essential to the pro-tumorigenic function of membrane type-1 matrix metalloproteinase (MT1-MMP) in vivo
  Vladislav S Golubkov, Andrei V Chernov, Alex Y Strongin
  The Journal of biological chemistry 2011 Aug 8
• Lenalidomide downregulates the cell survival factor, interferon regulatory factor-4, providing a potential mechanistic link for predicting response
  Antonia Lopez-Girona, Daniel Heintel, Ling-Hua Zhang, Derek Mendy, Svetlana Gaidarova, Helen Brady, Justin Blake Bartlett, Peter H Schafer, Martin Schreder, Arnold Bolomsky, Bernadette Hilgarth, Niklas Zojer, Heinz Gisslinger, Heinz Ludwig, Tom Daniel, Ulrich Jäger, Rajesh Chopra
  British journal of haematology 2011 Aug
• Learning Biomarkers of Pluripotent Stem Cells in Mouse
  Lena Scheubert, Rainer Schmidt, Dirk Repsilber, Mitja Lustrek, Georg Fuellen
  DNA research: an international journal for rapid publication of reports on genes and genomes 2011 Jul 26
• Characterization of BCAR4, a novel oncogene causing endocrine resistance in human breast cancer cells
  Marcia Godinho, Danielle Meijer, Buddy Setyono-Han, Lambert C J Dorssers, Ton van Agthoven
  Journal of cellular physiology 2011 Jul
• Genetic variation in BDNF is associated with allergic asthma and allergic rhinitis in an ethnic Chinese population in Singapore
  Anand Kumar Andiappan, Pallavi Nilkanth Parate, Ramani Anantharaman, Bani Kaur Suri, De Yun Wang, Fook Tim Chew
  Cytokine, In Press, Corrected Proof, Available online 30 June 2011
• Genetic variation in an MiRNA-1827 binding site in MYCL1 alters susceptibility to small cell lung cancer
  Fang Xiong, Chen Wu, Jiang Chang, Dianke Yu, Binghe Xu, Peng Yuan, Kan Zhai, Jian Xu, Wen Tan, Dongxin Lin
  Cancer research 2011 Jun 15
• Histone deacetylase inhibitor MGCD0103 synergizes with gemcitabine in human pancreatic cells
  Victoria Sung, Normand Richard, Helen Brady, Armin Maier, Gerhard Kelter, Carla Heise
  Cancer science 2011 Jun
• Global Gene Expression Profiling of Spontaneous Hepatocellular Carcinoma in B6C3F1 Mice: Similarities in the Molecular Landscape with Human Liver Cancer
  Mark J Hoenerhoff, Arun R Pandiri, Stephanie A Lahousse, Hue-Hua Hong, Thai-Vu Ton, Tiwanda Masinde, Scott S Auerbach, Kevin Gerrish, Pierre R Bushel, Keith R Shockley, Shyamal D Peddada, Robert C Sills
  Toxicologic pathology 2011 May 13
• Human ESC-Derived Neural Crest Model Reveals a Key Role for SOX2 in Sensory Neurogenesis
  Flavio Cimadamore, Katherine Fishwick, Elena Giusto, Ksenia Gnedeva, Giulio Cattarossi, Amber Miller, Stefano Pluchino, Laurence M Brill, Marianne Bronner-Fraser, Alexey V Terskikh
  Cell stem cell 2011 May 6
• Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
  Jonathan M.J. Derry, Lara M. Mangravite, Christine Suver, Matt Furia, David Henderson, Xavier Schildwachter, Jonathan Izant, Solveig K. Sieberts, Michael R. Kellen, Stephen H. Friend
  Nature Precedings : doi:10.1038/npre.2011.5883.1 : Posted 4 Apr 2011
• Horizons in therapy for corneal angiogenesis
  Surekha Maddula, Don K Davis, Soumya Maddula, Michael K Burrow, Balamurali K Ambati
  Ophthalmology 2011 Mar
• The 'persons' and 'genomics' of personal genomics
  J Reardon
  Personalized Medicine, January 2011, Vol. 8, No. 1, Pages 95-107
• Gene Signatures Derived from a c-MET-Driven Liver Cancer Mouse Model Predict Survival of Patients with Hepatocellular Carcinoma.
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• Mouse ghrelin-O-acyltransferase (GOAT) plays a critical role in bile acid reabsorption.
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• NMNAT suppresses Tau-induced neurodegeneration by promoting clearance of hyperphosphorylated Tau oligomers in a Drosophila model of tauopathy.
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• CREB-activity and nmnat2 transcription are down-regulated prior to neurodegeneration, while NMNAT2 over-expression is neuroprotective, in a mouse model of human tauopathy.
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• Mechanisms of Action of Bisphenol A and Other Biochemical/Molecular Interactions.
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• Up-Regulated Dicer Expression in Patients with Cutaneous Melanoma
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• STAT3 Activation in Skeletal Muscle Links Muscle Wasting and the Acute Phase Response in Cancer Cachexia
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• The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods
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• Schizophrenia: A Pathogenetic Autoimmune Disease Caused by Viruses and Pathogens and Dependent on Genes
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• A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogaster
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• Sorafenib efficacy in ovarian clear cell carcinoma revealed by transcriptome profiling
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• CWM Global Search - The Internet Search Engine for Chemists and Biologists
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• The class-I HDAC inhibitor MGCD0103 induces apoptosis in Hodgkin lymphoma cell lines and synergizes with proteasome inhibitors by an HDAC6-independent mechanism
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• SNP-SNP Interactions between dNTP Supply Enzymes and Mismatch DNA Repair in Breast Cancer
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• Genome-wide expression profiling revealed peripheral effects of cannabinoid receptor 1 inverse agonists in improving insulin sensitivity and metabolic parameters
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• Azacitidine and decitabine have different mechanisms of action in non-small cell lung cancer cell lines (external link)
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• Transcriptome profiling and network analysis of genetically hypertensive mice identifies potential pharmacological targets of hypertension
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• Microarray-based transcriptional and epigenetic profiling of matrix metalloproteinases, collagens and related genes in cancer
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• Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma
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• Urinary trypsin inhibitor: miraculous medicine in many surgical situations?
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• Influence of Sublethal Total-Body Irradiation on Immune Cell Populations in the Intestinal Mucosa
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• Distinct pathogenesis and host responses during infection of C. elegans by P. aeruginosa and S. aureus
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• Targeted disruption of Ing2 results in defective spermatogenesis and development of soft-tissue sarcomas
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• Human BAHD1 promotes heterochromatic gene silencing
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• Gene Transcript Abundance Profiles Distinguish Kawasaki Disease from Adenovirus Infection
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• Deregulated direct targets of the hepatitis B viral (HBV) protein, HBx, identified through chromatin immunoprecipitation and expression microarray profiling
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• A pluripotency signature predicts histological transformation and influences survival in follicular lymphoma patients
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• Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery
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• Scientific Publishing: Disruption and Semantic Build-Up (external link)
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• Cell cycle-dependent variation of a CD133 epitope in human embryonic stem cell, colon cancer, and melanoma cell lines
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