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1 - 6 of 6 results

1 - 6 of 6 results

ISMARA / Integrated System for Motif Activity Response Analysis

Enables computational reconstruction of regulatory circuitry from high-throughput data. ISMARA uses motif activity response analysis to identify the key regulators, i.e., transcription factors (TFs) and microRNAs (miRNAs) driving gene expression/chromatin state changes across the samples, the activity profiles of these regulators, their target genes, and the sites on the genome through which these regulators act. The stand-alone client application (called the ISMARA client) automates the process of pre-processing the user’s raw data on her/his own computer.

Octopus-toolkit

Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.

A package to detect genes that show different transcript abundances between two conditions putatively caused by alterations in histone modification. Epigenomix is based on a correlation measure for integrative analysis of ChIP-seq and gene transcription data measured by RNA sequencing or microarrays. We propose quantile normalization for ChIP-seq data and a Bayesian mixture approach involving a mixture of mixtures and distributions of different type (normal and exponential) to classify transcripts based on a measure for the correlation between histone modifications and gene transcription.

A web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq allows users to contextualise their sequencing data with respect to vast amounts of public data in a few minutes without requiring any programming skills. Heat*seq currently contains over 12,000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualise user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.

Facilitates several typical operations related to the quantification of the sequencing signal in a set of genomic regions. compEpiTools provides a number of methods to score these data in regions of interest, leading to the identification of enhancers, lncRNAs, and RNAPII stalling/elongation dynamics. It allows a fast and comprehensive annotation of the resulting genomic regions, and the association of the corresponding genes with non-redundant GeneOntology terms.

Allocates cells measured with single-cell RNA-seq to clones derived from low-coverage single-cell DNA-seq. clonealign is statistical method that constructs a phylogenetic tree using single-cell copy number measurements. It permits the discovery of clone-specific phenotypic properties in real cancer data. This tool is useful in the field of single cell biology including extensions for other multimodal approaches such as methylation-transcription and chromatin accessibility-transcription.

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1 - 8 of 8 results

1 - 8 of 8 results

Bioinformatician OmicX

PhD ès Neurosciences, I worked 8 years on the brain and its diseases. I then specialized in bioinformatics (NGS, epigenetics) and worked in CEA and GENETHON before to join OMICX and help OMICtools community.

aCNViewer MEDOC Bowtie

Big data scientist National Institute of Plant Genome Research

Research Interests Gene fusion detection in Plants Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants. Whole genome and transcriptome sequencing data analysis of Plants In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants. Development of webservers, databases and computational pipelines for plant research Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research. Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies. Professional & Academic Background Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India Awards and Fellowships Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009 Scientific Contributions/ Recognitions Associate editor: Journal of Translational Medicine. Editorial Board Member of Journal: Theoretical Biology and Medical Modelling. Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals. Web Resources/ Databases (Developed/ Contributed) A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/) GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/). Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/). Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/). Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/). Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/). Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/) Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/). A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).

FusionFinder comrad

Mahantesh Biradar

‎Graduate PhD researcher focusing on Cardiovascular Epidemiology & Social Media Enthusiast Research Stash

I'm a Graduate PhD researcher in the area of Biomedical Science and focussing on the Pharmacogenomics/Pharmacogenomics of Diabetes and related complications

PhD Student Institute of Life Sciences

Working on Immunology and Systems Biology.

EuMicrobedbLite Bowtie GATK

Antoine Rousselin

Ingénieur d'étude Centre Franois Baclesse

ONCOCNV CNVkit CNV-seq

olga Adame Guerero

Student Universidad Autónoma de Guerrero

Bioinfomagician Dankook University

Octopus-toolkit

I am an Electrical Engineer and Developer University of Engineering and Technology Lahore

SNPSVM GATK SAMtools

Transcriptomic and epigenomic data integration software tools | RNA sequencing analysis

A variety of NGS-based techniques have been developed. For example, chromatin immunoprecipitation coupled with parallel sequencing (ChIP-seq) is widely used to assess the binding of proteins to the genome (Barski et al., 2007). RNA sequencing (RNA-seq) can estimate the abundance of whole transcripts and their isoforms (Mortazavi et al., 2008). Genome-wide nucleosome positioning and open chromatin can be captured by MNase-seq (Schones et al., 2008) and DNase-seq (4), respectively. As the demand for NGS has increased, several thousand NGS-based data sets have been deposited in public data repositories such as gene expression omnibus (GEO) (Barrett et al., 2013). Notably, novel findings frequently emerge from reanalyzing available NGS-based data sets (Hnisz et al., 2013; Kang et al., 2014). However, there is no easy way to access, download, and process a large set of original (raw) NGS-based data for comparative and integrative analysis, although some web-based applications have been developed to resolve the issue.

References:
(Barski et al., 2007) High-resolution profiling of histone methylations in the human genome. Cell .
(Mortazavi et al., 2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods.
(Schones et al., 2008) Dynamic regulation of nucleosome positioning in the human genome. Cell .
(Boyle et al., 2008) High-resolution mapping and characterization of open chromatin across the genome. Cell .
(Barrett et al., 2013) NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res.
(Hnisz et al., 2013) Super-enhancers in the control of cell identity and disease. Cell .
(Kang et al., 2014) Mammary-specific gene activation is defined by progressive recruitment of STAT5 during pregnancy and the establishment of H3K4me3 marks. Mol Cell Biol.

Source text:
(Kim et al., 2018) Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data. Nucleic Acids Res.

Parent categories

RNA-seq analysis ChIP-seq analysis CAGE analysis

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