Janga Lab – Page 2 – The Janga Lab

Two studies first authored by graduate master’s students from the lab are accepted for paper presentation at ICIBM’19 conference in Columbus, Ohio

Two studies from the lab are accepted as full length papers and invited for oral presentation for the upcoming International Conference on Intelligent Biology and Medicine (ICIBM 2019) in Columbus, Ohio

Title: Long non-coding RNA expression levels modulate cell-type specific splicing patterns by altering their interaction landscape with RNA-binding proteins

Authors: Felipe Wendt Porto, Swapna Vidhur Daulatabad and Sarath Chandra Janga

Title: Human protein-RNA interaction network is highly stable across vertebrates

Author: Aarthi Ramakrishnan and Sarath Chandra Janga

Dr. Sarath Janga and Dr. Heidi Dvinge are hosting a special session “RNA Sequence to Structure” at Great Lakes Bioinformatics Conference at UW Madison in May 2019

Dr. Sarath Janga and Dr. Heidi Dvinge are hosting a special session “RNA Sequence to Structure” at Great Lakes Bioinformatics Conference at UW Madison in May 2019.

Please see the links below for submission tracks and program details.

https://www.iscb.org/glbio2019-special-sessions

http://www.iupui.edu/~jangalab/rss_glbio19/

Direct RNA sequencing based cytosine methylation prediction work employing deep learning models gets invited for a lightening talk at NCM-2018

Click here for agenda.

New study on Il9 enhancer landscape in Nature Communications

Our lab member co-authored study on the transcriptional landscape of enhancer modulating Il9 expression in multiple lineages is now published in Nature Communications.

Raja Kadumuri’s work on identification of m5C modification events at single molecule resolution

Raja Kadumuri’s work on identification of m5C modification events at single molecule resolution from direct RNA sequencing of human cell lines is invited for an oral presentation at Rustbelt RNA Meeting 2018 in Columbus, Ohio” and link to the rustbelt meeting talk slots

https://rustbeltrna.org/2018/agenda.php

Researchers at IUPUI propose new model for gene regulation

In a paper titled “Epitranscriptomic code and its alterations in human disease,” researchers Raja Shekar Kadumuri and Sarath Chandra Janga explore the factors that control the proteins that translate DNA to RNA.

Click here

Epitomy: Database for exploring post-transcriptional modifications on RNA transcripts

Epitomy is a database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs. Epitomy provides various search options such as searching by modification name, Pubmed ID, coordinates and gene name and is powered by IGV JS genome browser, plotly heatmap module for seamless data visualization and elastic search in the back-end for efficient data storage and retrieval.

Click to have a look at Epitomy!

Lantern: A genome-scale lncRNA ontology annotation extractor and cellular network repository

Lantern is a repository of high quality controlled lncRNA ontology annotations, extracted by mining recent lncRNA literature using a robust NLP based approach. It also houses extensive lncRNA omics annotations like: tissue specific lncRNA expression, RBP interactions, lncRNA-protein co-expression, coding potential, sub-cellular localization and SNPs in lncRNA. Thereby making it a holistic resource for improving the understanding of the noncoding transcriptome. The extracted annotations for around 11,000 lncRNAs are available at

Click to have a look at Lantern!

SliceIt: CRISPR/Cas9 guide RNA prediction search engine

SliceIt is a genome-wide database of predicted sgRNAs based on CRISPR/Cas9 system to enable the systematic design of both low (gene or binding site centric) and high-throughput (genome-wide) CRISPR screens to understand the impact of editing the RNA-Binding Proteins’ binding sites in the human genome. SliceIt is powered by IGV JS genome browser for seamless data visualization and elastic search in the backend for efficient data storage and retrieval.

Click to have a look at Sliceit!

Express: Transcriptome database for mouse eye tissues across multiple developmental stages

Express contains transcript level expression data obtained from 21 lens and 35 retina RNA-Seq mouse samples. We downloaded the raw datasets, aligned them to reference genome and quantified transcript level expression for known and novel transcripts. When then downloaded the reference gene and transcript information and organized them along with the expression data in a MySQL database. We finally developed a PHP backend to interact with the database and a frontend to interact with the user and to visualize the query results.

Click to have a look at Express!