It is becoming increasingly necessary to develop computerized methods for identifying the few disease-causing variants from hundreds discovered in each individual patient. This problem is especially relevant for Copy Number Variants (CNVs), which can...
The Gram-negative bacterium Xanthomonas euvesicatoria (Xcv) is the causal agent of bacterial spot disease in pepper and tomato. Xcv pathogenicity depends on a type III secretion (T3S) system that delivers effector proteins into host cells to suppress...
MOTIVATION: As the quantity of genomic mutation data increases, the likelihood of finding patients with similar genomic profiles, for various disease inferences, increases. However, so does the difficulty in identifying them. Similarity search based ...
BMC medical informatics and decision making
May 20, 2015
BACKGROUND: Alterations of a genome can lead to changes in protein functions. Through these genetic mutations, a protein can lose its native function (loss-of-function, LoF), or it can confer a new function (gain-of-function, GoF). However, when a mu...
The number of mutated genes in cancer cells is far larger than the number of mutations that drive cancer. The difficulty this creates for identifying relevant alterations has stimulated the development of various computational approaches to distingui...
With the advent of high-throughput measurement techniques, scientists and engineers are starting to grapple with massive data sets and encountering challenges with how to organize, process and extract information into meaningful structures. Multidime...
Interdisciplinary sciences, computational life sciences
Mar 21, 2015
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...
This paper reports an experimental comparison of artificial neural network (ANN) and support vector machine (SVM) ensembles and their "nonensemble" variants for lung cancer prediction. These machine learning classifiers were trained to predict lung c...
UNLABELLED: Dysregulation of the tumor suppressor gene adenomatous polyposis coli (APC) is a canonical step in colorectal cancer development by promoting activation of the WNT/β-catenin pathway. Curiously, most colorectal tumors carry biallelic mutat...
UNLABELLED: Preinvasive breast cancer, or ductal carcinoma in situ (DCIS), shares many morphologic and genomic features with invasive breast cancer, yet most DCIS tumors remain indolent over decades. In this study, we performed spatial analyses of so...
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