Domains, motifs and clusters in the protein universe

J Liu, B Rost - Current Opinion in Chemical Biology, 2003 - Elsevier
The rapid growth of bio-sequence information has resulted in an increasing demand for
reliable methods that group proteins. A few databases with curated alignments of protein …

Artificial neural networks trained to detect viral and phage structural proteins

V Seguritan, N Alves Jr, M Arnoult, A Raymond… - 2012 - journals.plos.org
Phages play critical roles in the survival and pathogenicity of their hosts, via lysogenic
conversion factors, and in nutrient redistribution, via cell lysis. Analyses of phage-and viral …

Repeats with variations: accelerated evolution of the Pin2 family of proteinase inhibitors

E Barta, A Pintar, S Pongor - TRENDS in Genetics, 2002 - cell.com
The Pin2 genes encode potato type II proteinase inhibitors that act against pathogenic
attack. The first examples were found only in the Solanaceae family, but, using new EST and …

Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data

R Eksi, HD Li, R Menon, Y Wen… - PLoS computational …, 2013 - journals.plos.org
Integrating large-scale functional genomic data has significantly accelerated our
understanding of gene functions. However, no algorithm has been developed to differentiate …

Artificial neural network in drug delivery and pharmaceutical research

V Sutariya, A Groshev, P Sadana… - The Open …, 2013 - benthamopen.com
Artificial neural networks (ANNs) technology models the pattern recognition capabilities of
the neural networks of the brain. Similarly to a single neuron in the brain, artificial neuron …

CHOP proteins into structural domain‐like fragments

J Liu, B Rost - Proteins: Structure, Function, and Bioinformatics, 2004 - Wiley Online Library
We developed a method CHOP dissecting proteins into domain‐like fragments. The basic
idea was to cut proteins beginning from very reliable experimental information (PDB) …

Automatic prediction of protein domains from sequence information using a hybrid learning system

N Nagarajan, G Yona - Bioinformatics, 2004 - academic.oup.com
Motivation: We describe a novel method for detecting the domain structure of a protein from
sequence information alone. The method is based on analyzing multiple sequence …

Georeferencing of historical maps using back propagation artificial neural network

I Yilmaz, M Gullu - Experimental Techniques, 2012 - Springer
Historical maps as cartographic heritage contain a great deal of information about the period
they were produced in. Therefore, it is quite important first to conserve historical maps very …

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

C Andorf, D Dobbs, V Honavar - BMC bioinformatics, 2007 - Springer
Background Incorrectly annotated sequence data are becoming more commonplace as
databases increasingly rely on automated techniques for annotation. Hence, there is an …

Methodology development for predicting subcellular localization and other attributes of proteins

HB Shen, J Yang, KC Chou - Expert review of proteomics, 2007 - Taylor & Francis
Facing the explosion of newly generated protein sequences in the postgenomic age, we are
challenged to develop computational methods for the fast and accurate identification of their …