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Article
Open AccessThe BRCA1ness signature is associated significantly with response to PARP inhibitor treatment versus control in the I-SPY 2 randomized neoadjuvant setting
Patients with BRCA1-like tumors correlate with improved response to DNA double-strand break-inducing therapy. A gene expression-based classifier was developed to distinguish between BRCA1-like and non-BRCA1-like ...
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Article
Open AccessOncoScape: Exploring the cancer aberration landscape by genomic data fusion
Although large-scale efforts for molecular profiling of cancer samples provide multiple data types for many samples, most approaches for finding candidate cancer genes rely on somatic mutations and DNA copy nu...
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Article
Open AccessIntegration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer
Invasive lobular carcinoma (ILC) is the second most frequently occurring histological breast cancer subtype after invasive ductal carcinoma (IDC), accounting for around 10% of all breast cancers. The molecular...
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Article
Open AccessNext generation sequencing of triple negative breast cancer to find predictors for chemotherapy response
In triple negative breast cancers (TNBC) the initial response to chemotherapy is often favorable, but relapse and chemotherapy resistance frequently occur in advanced disease. Hence there is an urgent need for...
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Article
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
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Article
Open AccessBringing order to protein disorder through comparative genomics and genetic interactions
Intrinsically disordered regions are widespread, especially in proteomes of higher eukaryotes. Recently, protein disorder has been associated with a wide variety of cellular processes and has been implicated i...
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Article
Open AccessHighlights from the 6th International Society for Computational Biology Student Council Symposium at the 18th Annual International Conference on Intelligent Systems for Molecular Biology
This meeting report gives an overview of the keynote lectures and a selection of the student oral and poster presentations at the 6th International Society for Computational Biology Student Council Symposium t...
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Article
Open AccessInteroPORC: an automated tool to predict highly conserved protein interaction networks
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Article
Open AccessCadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator
Cadmium is a persistent pollutant that threatens most biological organisms, including cyanobacteria that support a large part of the biosphere. Using a multifaceted approach, we have investigated the global re...
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Mining Biological Data Using Pyramids
This paper is a review of promising applications of pyramidal classification to biological data. We show that overlap** and ordering properties can give new insights that can not be achieved using more class...