A5024793976- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Microbial Community Ecology and Physiology
- Mycorrhizal Fungi and Plant Interactions
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Genome Rearrangement Algorithms
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Evolution and Paleontology Studies
- Plant Diversity and Evolution
- Algorithms and Data Compression
- Genomics and Chromatin Dynamics
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Microbial Metabolic Engineering and Bioproduction
- Protist diversity and phylogeny
- Gut microbiota and health
- Banana Cultivation and Research
- Advanced Graph Theory Research
- Epigenetics and DNA Methylation
- Mosquito-borne diseases and control
University of Connecticut
2015-2024
Solution Spray Technologies (United states)
2024
Indian Institute of Technology Jodhpur
2021
Institute for Systems Biology
2015-2018
Broad Institute
2012-2015
Intel (United States)
2012-2014
Massachusetts Institute of Technology
2009-2014
Harvey Mudd College
2014
Tel Aviv University
2010-2013
Cornell University
2012
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
This study describes comprehensive polling of transcription start and termination sites analysis previously unidentified full-length complementary DNAs derived from the mouse genome. We identify 5' 3' boundaries 181,047 transcripts with extensive variation in arising alternative promoter usage, splicing, polyadenylation. There are 16,247 new protein-coding transcripts, including 5154 encoding proteins. Genomic mapping transcriptome reveals transcriptional forests, overlapping on both...
The laboratory mouse shares the majority of its protein-coding genes with humans, making it premier model organism in biomedical research, yet two mammals differ significant ways. To gain greater insights into both shared and species-specific transcriptional cellular regulatory programs mouse, Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications replication domains throughout genome diverse cell tissue types. By...
Abstract Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal transfer and loss, inferring these in the history of a given fundamental problem comparative genomics with numerous important applications. Solving this requires use reconciliation framework, where input consists phylogeny corresponding species phylogeny, goal to reconcile two postulating loss events. This referred duplication-transfer-loss (DTL) has been extensively...
DupTree is a new software program for inferring rooted species trees from collections of gene using the tree parsimony approach. The implements novel algorithm that significantly improves upon run time standard search heuristics parsimony, and enables first truly genome-scale phylogenetic analyses. In addition, allows users to examine alternate rootings weight reconciliation costs trees. an open source project written in C++.DupTree Mac OS X, Windows, Linux along with sample dataset on-line...
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent duplications and losses. Gene tree parsimony (GTP) a phylogenetic optimization criterion species that minimizes the number of induced set trees selected. The run time performance previous implementations has limited its use on large-scale sets. We used new software incorporates recent algorithmic advances to examine GTP plant consisting 18,896 containing...
Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. based on well established Robinson-Foulds (RF) distance have potential to build supertrees retain much information from Specifically, RF supertree problem seeks a binary minimizes sum distances Thus, an is consistent largest number clusters (or clades) trees.We introduce efficient, local search based,...
Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications. However, sequence data alone often lack enough information to confidently support one topology over competing alternatives. Here, we present novel framework for combining and species information, describe an implementation of this TreeFix, new phylogenetic program improving reconstructions. Given (preferably computed using maximum-likelihood program), TreeFix finds "statistically...
Abstract Background The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as duplication and loss, incomplete lineage sorting (deep coalescence), horizontal transfer. Gene tree parsimony (GTP) addresses this issue seeking a that requires the minimum number reconcile given set incongruent trees....
RANGER-DTL 2.0 is a software program for inferring gene family evolution using Duplication-Transfer-Loss reconciliation. This new highly scalable and easy to use, offers many features not currently available in any other reconciliation program. has particular focus on accuracy can account sources of uncertainty including uncertain tree rooting, topological uncertainty, multiple optimal reconciliations alternative event cost assignments. open-source written C++ Python.Pre-compiled...
Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect tree, many most popular methods consider discordance only due duplication and loss (and sometimes horizontal transfer). Methods do model ILS are either highly parameterized or restricted set histories, thus limiting their applicability...
Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal transfer, and loss, which are fundamental to our understanding of molecular evolution. While duplication–loss (DL) leads unique maximum-parsimony solution, duplication-transfer-loss (DTL) yields multitude optimal solutions, making it difficult infer the true history family. This problem further exacerbated by fact that different event cost assignments yield sets...
Abstract Motivation: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem tree has received considerable attention, most existing methods are only applicable to families unaffected by horizontal transfer. As result, affected transfer remains largely unaddressed problem. Results: In this study, we introduce new and highly effective method for error correction presence Our efficiently models transfers, duplications losses, uses statistical...
Abstract Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts parasites other dependent pairs entities. Reconciliation typically performed using maximum parsimony, in which each event type assigned cost objective to find minimum total cost. It generally understood that reconciliations are sensitive costs, but little about relationship between costs solutions. Moreover, choosing appropriate...
Abstract Background Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use this requires methods that can efficiently analyze extremely large sets and account processes gene evolution, such as duplication loss, incomplete lineage sorting (deep coalescence), or horizontal transfer, cause incongruence among trees. One approach is tree parsimony, which, given set trees, seeks species the smallest number evolutionary events to explain However, only existing...
Abstract Motivation: Deciphering the location of gene duplications and multiple duplication episodes on Tree Life is fundamental to understanding way families genomes evolve. The problem provides a framework for placing events onto nodes given species tree, detecting duplication. One version was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed this problem, but no exact algorithms were known. Results: In article we solve longstanding open providing first...
Almost all standard phylogenetic methods for reconstructing gene trees result in unrooted trees; yet, many of the most useful applications require that be correctly rooted. As a result, several computational have been developed inferring root trees. However, accuracy such has never systematically evaluated on prokaryotic families, where horizontal transfer is often one dominant evolutionary events driving family evolution. In this work, we address gap by conducting thorough comparative...
Abstract Motivation: Horizontal gene transfer (HGT) plays a crucial role in the evolution of prokaryotic species. Typically, no more than few genes are horizontally transferred between any two However, several studies identified pairs species (or linages) which many different were transferred. Such pair is said to be linked by highway sharing. Inferring such highways understanding prokaryotes and for inferring past symbiotic ecological associations among Results: We present new improved...
Abstract Motivation A reconciliation is an annotation of the nodes a gene tree with evolutionary events—for example, speciation, duplication, transfer, loss, etc.—along mapping onto species tree. Many algorithms and software produce or use reconciliations but often using different formats, regarding type events considered whether dated not. This complicates comparison communication between programs. Results Here, we gather consortium developers in to propose endorse format that aims promote...
Abstract Summary SaGePhy is a software package for improved phylogenetic simulation of gene and subgene evolution. can be used to generate species trees, trees or (protein) domain using probabilistic birth–death process that allows duplication, horizontal transfer loss. implements range important features not found in other frameworks/software. These include (i) level evolution inside one more (ii) simultaneous both additive replacing gene/subgene transfers (iii) sampling tree nodes,...
Abstract Summary CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. can be used to efficiently generate profiles thousands simulated tumor cells under more realistic error model and broader range possible CNA mechanisms compared with existing simulators. The implemented in accounts the specific biases sequencing that leads read count fluctuation poor resolution detection. For realism over simulators, (i) WGD, whole-chromosomal...
The NP-hard gene-duplication problem takes as input a collection of gene trees and seeks species tree that requires the fewest number duplications to reconcile trees. An oft-cited, decade-old result by Stege states is fixed parameter tractable when parameterized necessary for reconciliation. Here, we uncover an error in this algorithm show cannot be corrected without sacrificing tractability algorithm. Furthermore, link between minimum rooted triplets inconsistency which implies 1) W[2]-hard...