Evolution of web services in bioinformatics

PBT Neerincx, JAM Leunissen - Briefings in bioinformatics, 2005‏ - academic.oup.com
Bioinformaticians have developed large collections of tools to make sense of the rapidly
growing pool of molecular biological data. Biological systems tend to be complex and in …

Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data

MF Ochs, L Rink, C Tarn, S Mburu, T Taguchi… - Cancer …, 2009‏ - aacrjournals.org
Cell signaling plays a central role in the etiology of cancer. Numerous therapeutics in use or
under development target signaling proteins; however, off-target effects often limit …

Automated extraction of reported statistical analyses: towards a logical representation of clinical trial literature

W Hsu, W Speier, RK Taira - AMIA Annual Symposium …, 2012‏ - pmc.ncbi.nlm.nih.gov
Randomized controlled trials are an important source of evidence for guiding clinical
decisions when treating a patient. However, given the large number of studies and their …

Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis

EJ Fertig, A Markovic, LV Danilova, DA Gaykalova… - PloS one, 2013‏ - journals.plos.org
Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based
on their etiology, human papillomavirus (HPV)-positive and–negative. Global DNA …

Incorporation of gene ontology annotations to enhance microarray data analysis

MF Ochs, AJ Peterson, A Kossenkov… - Microarray Data Analysis …, 2007‏ - Springer
Typical microarray or GeneChip™ experiments now provide genome-wide measurements
on gene expression across many conditions. Analysis often focuses on only a few of the …

Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer

AS Afshar, J Xu, J Goutsias - PloS one, 2014‏ - journals.plos.org
MicroRNAs (miRNAs) have attracted a great deal of attention in biology and medicine. It has
been hypothesized that miRNAs interact with transcription factors (TFs) in a coordinated …

High level of chromosomal aberration in ovarian cancer genome correlates with poor clinical outcome

L Cope, RC Wu, IM Shih, TL Wang - Gynecologic oncology, 2013‏ - Elsevier
OBJECTIVES: Structural aberration in chromosomes characterizes almost all human solid
cancers and analysis of those alterations may reveal the history of chromosomal instability …

Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell …

EJ Fertig, Q Ren, H Cheng, H Hatakeyama, AP Dicker… - BMC genomics, 2012‏ - Springer
Background Aberrant activation of signaling pathways downstream of epidermal growth
factor receptor (EGFR) has been hypothesized to be one of the mechanisms of cetuximab (a …

ClutrFree: cluster tree visualization and interpretation

G Bidaut, MF Ochs - Bioinformatics, 2004‏ - academic.oup.com
ClutrFree facilitates the visualization and interpretation of clusters or patterns computed from
microarray data through a graphical user interface that displays patterns, membership …

OligoRAP–An Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

PBT Neerincx, H Rauwerda, H Nie, MAM Groenen… - BMC proceedings, 2009‏ - Springer
Background High throughput gene expression studies using oligonucleotide microarrays
depend on the specificity of each oligonucleotide (oligo or probe) for its target gene …