Literature DB >> 22101971

The NIH National Center for Integrative Biomedical Informatics (NCIBI).

Brian D Athey1, James D Cavalcoli, H V Jagadish, Gilbert S Omenn, Barbara Mirel, Matthias Kretzler, Charles Burant, Raphael D Isokpehi, Charles DeLisi.   

Abstract

The National Center for Integrative and Biomedical Informatics (NCIBI) is one of the eight NCBCs. NCIBI supports information access and data analysis for biomedical researchers, enabling them to build computational and knowledge models of biological systems to address the Driving Biological Problems (DBPs). The NCIBI DBPs have included prostate cancer progression, organ-specific complications of type 1 and 2 diabetes, bipolar disorder, and metabolic analysis of obesity syndrome. Collaborating with these and other partners, NCIBI has developed a series of software tools for exploratory analysis, concept visualization, and literature searches, as well as core database and web services resources. Many of our training and outreach initiatives have been in collaboration with the Research Centers at Minority Institutions (RCMI), integrating NCIBI and RCMI faculty and students, culminating each year in an annual workshop. Our future directions include focusing on the TranSMART data sharing and analysis initiative.

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Year:  2011        PMID: 22101971      PMCID: PMC3277628          DOI: 10.1136/amiajnl-2011-000552

Source DB:  PubMed          Journal:  J Am Med Inform Assoc        ISSN: 1067-5027            Impact factor:   4.497


  15 in total

1.  Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.

Authors:  Scott A Tomlins; Daniel R Rhodes; Sven Perner; Saravana M Dhanasekaran; Rohit Mehra; Xiao-Wei Sun; Sooryanarayana Varambally; Xuhong Cao; Joelle Tchinda; Rainer Kuefer; Charles Lee; James E Montie; Rajal B Shah; Kenneth J Pienta; Mark A Rubin; Arul M Chinnaiyan
Journal:  Science       Date:  2005-10-28       Impact factor: 47.728

2.  SAGA: a subgraph matching tool for biological graphs.

Authors:  Yuanyuan Tian; Richard C McEachin; Carlos Santos; David J States; Jignesh M Patel
Journal:  Bioinformatics       Date:  2006-11-16       Impact factor: 6.937

3.  A bioinformatics analysis of the cell line nomenclature.

Authors:  Sirarat Sarntivijai; Alexander S Ade; Brian D Athey; David J States
Journal:  Bioinformatics       Date:  2008-10-10       Impact factor: 6.937

4.  An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

Authors:  Xiao-Song Wang; John R Prensner; Guoan Chen; Qi Cao; Bo Han; Saravana M Dhanasekaran; Rakesh Ponnala; Xuhong Cao; Sooryanarayana Varambally; Dafydd G Thomas; Thomas J Giordano; David G Beer; Nallasivam Palanisamy; Maureen A Sartor; Gilbert S Omenn; Arul M Chinnaiyan
Journal:  Nat Biotechnol       Date:  2009-11-01       Impact factor: 54.908

5.  Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.

Authors:  Daniel R Rhodes; Shanker Kalyana-Sundaram; Vasudeva Mahavisno; Radhika Varambally; Jianjun Yu; Benjamin B Briggs; Terrence R Barrette; Matthew J Anstet; Colleen Kincead-Beal; Prakash Kulkarni; Sooryanaryana Varambally; Debashis Ghosh; Arul M Chinnaiyan
Journal:  Neoplasia       Date:  2007-02       Impact factor: 5.715

Review 6.  Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

Authors:  Sebastian Martini; Felix Eichinger; Viji Nair; Matthias Kretzler
Journal:  Rev Endocr Metab Disord       Date:  2008-12       Impact factor: 6.514

7.  Cross-domain neurobiology data integration and exploration.

Authors:  Weijian Xuan; Manhong Dai; Josh Buckner; Barbara Mirel; Jean Song; Brian Athey; Stanley J Watson; Fan Meng
Journal:  BMC Genomics       Date:  2010-12-01       Impact factor: 3.969

8.  Open Biomedical Ontology-based Medline exploration.

Authors:  Weijian Xuan; Manhong Dai; Barbara Mirel; Jean Song; Brian Athey; Stanley J Watson; Fan Meng
Journal:  BMC Bioinformatics       Date:  2009-05-06       Impact factor: 3.169

9.  Michigan molecular interactions r2: from interacting proteins to pathways.

Authors:  V Glenn Tarcea; Terry Weymouth; Alex Ade; Aaron Bookvich; Jing Gao; Vasudeva Mahavisno; Zach Wright; Adriane Chapman; Magesh Jayapandian; Arzucan Ozgür; Yuanyuan Tian; Jim Cavalcoli; Barbara Mirel; Jignesh Patel; Dragomir Radev; Brian Athey; David States; H V Jagadish
Journal:  Nucleic Acids Res       Date:  2008-10-31       Impact factor: 16.971

10.  The Edinburgh human metabolic network reconstruction and its functional analysis.

Authors:  Hongwu Ma; Anatoly Sorokin; Alexander Mazein; Alex Selkov; Evgeni Selkov; Oleg Demin; Igor Goryanin
Journal:  Mol Syst Biol       Date:  2007-09-18       Impact factor: 11.429

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  7 in total

1.  National Centers for Biomedical Computing: from the BISTI report to the future.

Authors:  Jeremy M Berg
Journal:  J Am Med Inform Assoc       Date:  2012-01-18       Impact factor: 4.497

2.  Exposome informatics: considerations for the design of future biomedical research information systems.

Authors:  Fernando Martin Sanchez; Kathleen Gray; Riccardo Bellazzi; Guillermo Lopez-Campos
Journal:  J Am Med Inform Assoc       Date:  2013-11-01       Impact factor: 4.497

3.  Disseminating informatics knowledge and training the next generation of leaders.

Authors:  Lucila Ohno-Machado
Journal:  J Am Med Inform Assoc       Date:  2014 Nov-Dec       Impact factor: 4.497

Review 4.  Omics databases on kidney disease: where they can be found and how to benefit from them.

Authors:  Theofilos Papadopoulos; Magdalena Krochmal; Katryna Cisek; Marco Fernandes; Holger Husi; Robert Stevens; Jean-Loup Bascands; Joost P Schanstra; Julie Klein
Journal:  Clin Kidney J       Date:  2016-03-21

5.  Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients.

Authors:  Stein Hallan; Maryam Afkarian; Leila R Zelnick; Bryan Kestenbaum; Shoba Sharma; Rintaro Saito; Manjula Darshi; Gregory Barding; Daniel Raftery; Wenjun Ju; Matthias Kretzler; Kumar Sharma; Ian H de Boer
Journal:  EBioMedicine       Date:  2017-10-31       Impact factor: 8.143

6.  Recent trends in biomedical informatics: a study based on JAMIA articles.

Authors:  Xiaoqian Jiang; Krystal Tse; Shuang Wang; Son Doan; Hyeoneui Kim; Lucila Ohno-Machado
Journal:  J Am Med Inform Assoc       Date:  2013-11-08       Impact factor: 4.497

7.  A Functional Landscape of CKD Entities From Public Transcriptomic Data.

Authors:  Ferenc Tajti; Christoph Kuppe; Asier Antoranz; Mahmoud M Ibrahim; Hyojin Kim; Francesco Ceccarelli; Christian H Holland; Hannes Olauson; Jürgen Floege; Leonidas G Alexopoulos; Rafael Kramann; Julio Saez-Rodriguez
Journal:  Kidney Int Rep       Date:  2019-11-13
  7 in total

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