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The Cytoscape app article collection. PDF available through Get Fulltext Research

Pico, Alexander R Bader, Gary D Demchak, Barry Guitart Pla, Oriol Hull, Timothy Longabaugh, William Lopes, Christian Lotia, Samad Molenaar, Piet Montojo, Jason ...

Published in F1000Research

As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online "cookbook" for app developers. This article collection is another resource to help res...

An integrated map of HIV-human protein complexes that facilitate viral infection. PDF available through Get Fulltext Research

Emig-Agius, Dorothea Olivieri, Kevin Pache, Lars Shih, Hsin Ling Pustovalova, Olga Bessarabova, Marina Young, John A T Chanda, Sumit K Ideker, Trey

Published in PloS one

Recent proteomic and genetic studies have aimed to identify a complete network of interactions between HIV and human proteins and genes. This HIV-human interaction network provides invaluable information as to how HIV exploits the host machinery and can be used as a starting point for further functional analyses. We integrated this network with com...

Development of ultra-high-density screening tools for microbial "omics". PDF available through Get Fulltext Research

Bean, Gordon J Jaeger, Philipp A Bahr, Sondra Ideker, Trey

Published in PloS one

High-throughput genetic screens in model microbial organisms are a primary means of interrogating biological systems. In numerous cases, such screens have identified the genes that underlie a particular phenotype or a set of gene-gene, gene-environment or protein-protein interactions, which are then used to construct highly informative network maps...

Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PDF available through Get Fulltext Research

Joshi, Shweta Singh, Alok R Zulcic, Muamera Bao, Lei Messer, Karen Ideker, Trey Dutkowski, Janusz Durden, Donald L

Published in PloS one

Although it is well-established that the macrophage M1 to M2 transition plays a role in tumor progression, the molecular basis for this process remains incompletely understood. Herein, we demonstrate that the small GTPase, Rac2 controls macrophage M1 to M2 differentiation and the metastatic phenotype in vivo. Using a genetic approach, combined with...

Matrin 3 co-immunoprecipitates with the heat shock proteins glucose-regulated protein 78 (GRP78), GRP75 and glutathione ... PDF available through Get Fulltext Research

Osman, Ahmed M. van Loveren, Henk

Published in Biochimie

•Matrin 3 coimmunoprecipitates with GRP78, GRP75 and GSTπ2 in thymoma cells.•We identified MATR3 and its partners by MS/MS analysis and confirmed by immunoblot.•It is suggested that these proteins may assist MATR3 in its functional role in cells.•We propose that TBTO triggers MATR3 degradation via caspase cascade pathway.•The broad-spectrum caspase...

A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. PDF available through Get Fulltext Research

Srivas, Rohith Costelloe, Thomas Carvunis, Anne-Ruxandra Sarkar, Sovan Malta, Erik Sun, Su Ming Pool, Marijke Licon, Katherine van Welsem, Tibor van Leeuwen, Fred ...

Published in Cell reports

Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. ...

Network-based stratification of tumor mutations. PDF available through Get Fulltext Research

Hofree, Matan Shen, John P Carter, Hannah Gross, Andrew Ideker, Trey

Published in Nature methods

Many forms of cancer have multiple subtypes with different causes and clinical outcomes. Somatic tumor genome sequences provide a rich new source of data for uncovering these subtypes but have proven difficult to compare, as two tumors rarely share the same mutations. Here we introduce network-based stratification (NBS), a method to integrate somat...

Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease.

Sharma, Kumar Karl, Bethany Mathew, Anna V Gangoiti, Jon A Wassel, Christina L Saito, Rintaro Pu, Minya Sharma, Shoba You, Young-Hyun Wang, Lin ...

Published in Journal of the American Society of Nephrology : JASN

Diabetic kidney disease is the leading cause of ESRD, but few biomarkers of diabetic kidney disease are available. This study used gas chromatography-mass spectrometry to quantify 94 urine metabolites in screening and validation cohorts of patients with diabetes mellitus (DM) and CKD(DM+CKD), in patients with DM without CKD (DM-CKD), and in healthy...

Integrative approaches for finding modular structure in biological networks.

Mitra, Koyel Carvunis, Anne-Ruxandra Ramesh, Sanath Kumar Ideker, Trey

Published in Nature reviews. Genetics

A central goal of systems biology is to elucidate the structural and functional architecture of the cell. To this end, large and complex networks of molecular interactions are being rapidly generated for humans and model organisms. A recent focus of bioinformatics research has been to integrate these networks with each other and with diverse molecu...

Proteome-wide discovery of mislocated proteins in cancer.

Lee, KiYoung Byun, Kyunghee Hong, Wonpyo Chuang, Han-Yu Pack, Chan-Gi Bayarsaikhan, Enkhjargal Paek, Sun Ha Kim, Hyosil Shin, Hye Young Ideker, Trey ...

Published in Genome research

Several studies have sought systematically to identify protein subcellular locations, but an even larger task is to map which of these proteins conditionally relocates in disease (the mislocalizome). Here, we report an integrative computational framework for mapping conditional location and mislocation of proteins on a proteome-wide scale, called a...

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