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Animesh Ray

Publications and source records attributed to Animesh Ray.

4 recordsLinked to original sources
bioRxiv2016

Modeling Chromosome Maintenance as a Property of Cell Cycle in Saccharomyces cerevisiae

Defects in DNA repair, synthesis, and chromosome transmission can often cause chromosome instability, which are understood with respect to molecular-genetic mechanisms. However, transition from descriptive models to quantitative ones is generally difficult. Here we use a computationally intensive numerical technique based on linear programming to analyze the processes of chromosome maintenance during the cell cycle in yeast, Saccharomyces cerevisiae. We first experimentally identify 19 genes that when ectopically expressed cause chromosome instability. We then build an 18 x 19 matrix by assaying the genetic interactions of pairs of genes that each normally functions to maintain chromosomes, including the 19 genes discovered here. We then use a \"seriation\" algorithm based on linear optimization to find an optimal arrangement of rows and columns to confirm an optimum temporal arrangement of gene influence during cell cycle phases. We experimentally demonstrate that the method yields new biological insights, which we test and validate.

Systems Biology↗
bioRxiv2014

A signature of power law network dynamics

Can one hear the sound of a growing network? We address the problem of recognizing the topology of evolving biological or social networks. Starting from percolation theory, we analytically prove a linear inverse relationship between two simple graph parameters--the logarithm of the average cluster size and logarithm of the ratio of the edges of the graph to the theoretically maximum number of edges for that graph--that holds for all growing power law graphs. The result establishes a novel property of evolving power-law networks in the asymptotic limit of network size. Numerical simulations as well as fitting to real-world citation co-authorship networks demonstrate that the result holds for networks of finite sizes, and provides a convenient measure of the extent to which an evolving family of networks belongs to the same power-law class.

Bioinformatics↗
bioRxiv2013

DCL1, a Protein that Produces Plant MicroRNA, Coordinates Meristem Activity

Abstract Abstract Introduction Results Discussion Materials and Methods Authors' contributions Funding References The ubiquity and importance of short duplex RNAs, termed microRNA (miRNA), for normal development in higher eukaryotes are becoming increasingly clear. We had previously shown that reduction-of-function mutations in Arabidopsis thaliana DCL1 (DICER-LIKE1) gene, affecting the nucleus-localized protein that produces 19-25 nucleotides long miRNA species from longer double stranded RNA precursors, cause a delay in flowering by prolonging the period of juvenile organ development. Here we show that DCL1 transcription is increased at the critical phase of juvenile to reproductive developmental transition, and that DCL1 protein is localized in meri ...

Plant Biology↗
bioRxiv2013

A genome wide dosage suppressor network reveals genetic robustness and a novel mechanism for Huntington’s disease

Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes, revealing 660 suppressor interactions of which 642 are novel. This collection has several distinctive features, including high co-occurrence of mutant-suppressor pairs within protein modules, highly correlated functions between the pairs, and higher diversity of functions among the co-suppressors than previously observed. Dosage suppression of essential genes encoding RNA polymerase subunits and chromosome cohesion complex suggest a surprising degree of functional plasticity of macromolecular complexes and the existence of degenerate pathways for circumventing potentially lethal mutations. The utility of dosage-suppressor networks is illustrated by the discovery of a novel connection between chromosome cohesion-condensation pathways involving homologous recombination, and Huntingtons disease.

Genomics↗