Evolution of Protein Structure and Function

ExoLocator - an online view into genetic makeup of vertebrate proteins

Published date : 23 Nov 2013

ExoLocator (http://exolocator.eopsf.org) collects in a single place information needed for comparative analysis of protein-coding exons from vertebrate species. The main source of data—the genomic sequences, and the existing exon and homology annotation—is the ENSEMBL database of completed vertebrate genomes.

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Journal Paper
journal
Nucleic Acids Research, 2013, 1–3, doi:10.1093/nar/gkt1164
Impact Factor
8.278

Cube - an online tool for comparison and contrasting of protein sequences

Published date : 20 Nov 2013

When comparing sequences of similar proteins, two kinds of questions can be asked, and the related two kinds of inference made. First, one may ask to what degree they are similar, and then, how they differ. In the first case one may tentatively conclude that the conserved elements common to all sequences are of central and common importance to the protein’s function. In the latter case the regions of specialization may be discriminative of the function or binding partners across

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Journal Paper
journal
PLoS One, Nov 2013, Vol. 8, Issue 11, doi:10.1371/journal.pone.0079480
Impact Factor
3.73

TRF2 Interaction with Ku Heterotetramerization Interface Gives Insight into c-NHEJ Prevention at Human Telomeres

Published date : 02 Oct 2013

Telomeres are protected from nonhomologous end-joining (NHEJ) to avoid deleterious chromosome fusions, yet they associate with the Ku heterodimer that is principal in the classical NHEJ (c-NHEJ) pathway. T-loops have been proposed to inhibit Ku's association with telomeric ends, thus inhibiting c-NHEJ; however, deficiencies in the t-loop model suggest additional mechanisms are in effect. We demonstrate that TRF2 interacts with Ku at telomeres and via residues in Ku70 helix 5 (α5), which are vital for NHEJ.

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Journal Paper
journal
Cell Reports, Vol. 5, Issue 1, 3 Oct 2013, Pg 194-206, 2013, doi: 10.1016/j.celrep.2013.08.040

Epidemic centrality - is there an underestimated epidemic impact of network peripheral nodes?

Published date : 01 Oct 2013

In the study of disease spreading on empirical complex networks in SIR model, initially infected nodes can be ranked according to some measure of their epidemic impact. The highest ranked nodes, also referred to as “superspreaders”, are associated to dominant epidemic risks and therefore deserve special attention. In simulations on studied empirical complex networks, it is shown that the ranking depends on the dynamical regime of the disease spreading. A possible mechanism leading to this dependence is illustrated in an analytically tractable example.

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Journal Paper
journal
The European Physical Journal B, Oct 2013, Vol. 86, Issue 356, doi: 10.1140/epjb/e2013-31025-5

SW# - GPU enabled exact alignments on genome scale

Published date : 17 Jul 2013

Summary: We propose SW#, a new CUDA GPU enabled and memory efficient implementation of dynamic programming algorithms for local alignment. It can be use as either a standalone application or a library. Although there are other GPU implementations of the Smith-Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.

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Journal Paper
journal
Bioinformatics 2013, doi: 10.1093/bioinformatics/btt410

FastSIR algorithm: A fast algorithm for the simulation of the epidemic spread in large networks by using the susceptible-infected-recovered compartment model

Published date : 25 Mar 2013

We propose two efficient epidemic spreading algorithms (Naive SIR and FastSIR) for arbitrary network structures, based on the SIR (susceptible–infected–recovered) compartment model. The Naive SIR algorithm models full epidemic dynamics of the well-known SIR model and uses data structures efficiently to reduce running time. The FastSIR algorithm is based on the probability distribution over the number of infected nodes and uses the concept of generation time instead of explicit time in treating the spreading dynamics.

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Journal Paper
journal
Information Sciences, Vol. 239, 2013, Pg. 226-240

Large-Scale Functional Organiztion of Long-Range Chromatin Interaction Networks

Published date : 25 Oct 2012

Chromatin interactions play important roles in transcription regulation. To better understand the underlying evolutionary and functional constraints of these interactions, we implemented a systems approach to examine RNA polymerase-II-associated chromatin interactions in human cells. We found that 40% of the total genomic elements involved in chromatin interactions converged to a giant, scale-free-like, hierarchical network organized into chromatin communities. The communities were enriched in specific functions and were syntenic through evolution.

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Journal Paper
journal
Cell Reports 2012, Pg 1-13, doi: 10.1016/J.celrep.2012.09.22

Defining the phenotype in congenital disorder of glycosylation due to ALG1 mutations.

Published date : 10 Sep 2012

Deficiency of β-1,4 mannosyltransferase (MT-1) congenital disorder of glycosylation (CDG), due to ALG1 gene mutations. Features in 9 patients reported previously consisted of prenatal growth retardation, pregnancy-induced maternal hypertension and fetal hydrops. Four patients died before 5 years of age, and survivors showed a severe psychomotor retardation. We report on 7 patients with psychomotor delay, microcephaly, strabismus and coagulation abnormalities, seizures and abnormal fat distribution. Four children had a stable clinical course, two had visual impairment, and 1 had hearing loss.

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Journal Paper
journal
Pediatrics Vol. 130 No. 4, 1 Oct 2012, pg 1034-1039 doi: 10.1542/peds.2011-2711
Impact Factor
5.391

BioMe: biologically relevant metals

Published date : 12 Jun 2012

In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites.

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Journal Paper
journal
Nucleic Acids Research, 2012, Vol. 40, Pg 352-357, doi: 10.1093/nar/gks514
Impact Factor
7.836

Cube-DB: detection of functional divergence in human protein families

Published date : 01 Dec 2011

Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. The analysis is organized around the nomenclature associated with the human proteins, but based on all currently available vertebrate genomes. Using full genomes enables us, through a mutual-best-hit strategy, to construct comparable taxonomical samples for all paralogues under consideration. Functional specialization is scored on the residue level according to two models of behavior after divergence: heterotachy and homotachy.

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Journal Paper
journal
Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr1129