Saakshi Jalali

Saakshi Jalali
Institute of Genomics and Integrative Biology | IGIB · Genome Informatics and Structural Biology Research Area (IGIB)

Computational Biologist

About

44
Publications
6,265
Reads
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882
Citations
Additional affiliations
October 2017 - present
Reliance Industries Limited
Position
  • Researcher
April 2017 - October 2017
Institute of Genomics and Integrative Biology
Position
  • Research Associate
March 2009 - March 2017
Institute of Genomics and Integrative Biology
Position
  • Senior Researcher

Publications

Publications (44)
Article
Full-text available
Background Jatropha (Jatropha curcas L.) has been considered as a potential bioenergy crop and its genetic improvement is essential for higher seed yield and oil content which has been hampered due to lack of desirable molecular markers. Methods and results An F2 population was created using an intraspecific cross involving a Central American line...
Article
Full-text available
Jatropha is a non-edible, important bioenergy plant, which can grow in marginalized land. The seeds possess about 36% oil and this would be converted into biodiesel or biojet-fuel. Jatropha provides an option for sustainable feed and fuel production due to its inherent qualities including hardy nature, drought tolerance and surviving with limited a...
Chapter
Long noncoding RNAs are well studied for their regulatory actions through interaction with DNA regulating biological roles of DNA, RNA, or protein. However, direct binding of lncRNA with DNA is rarely demonstrated in experiments. The present protocol explains genome wide computational strategies to choose lncRNAs that can bind directly to the chrom...
Article
The outbreak of the infectious and rapidly expanding coronavirus disease 19 (COVID-19) caused by the SARS-CoV-2 virus has led to a devastating effect on public health and the global economy. The daily country-wise updates from the World Health Organization on the number of infected cases and death rates show diverse statistics. In this study, the m...
Article
Full-text available
Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements’ (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We...
Article
Full-text available
Efficient management of an epidemic requires identification and isolation of infected individuals from healthy population to curb community spread of the pathogen. Therefore, a faster and efficient diagnostic method for population screening is desirable to flatten the curve of daily raise of cases. This will also help medical professional to treat...
Article
Full-text available
Jatropha curcas is one of the major sources of renewable energy due to potential use of its oil as a biofuel. The genome of this crop is constituted by the high content of repetitive elements. We employed the Hi-C proximity ligation technique to re-scaffold our existing hybrid genome assembly of an elite genotype (RJC1) developed using Illumina and...
Article
Full-text available
Jatropha curcas is an important perennial, drought tolerant plant that has been identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of J. curcas generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for Jatropha Mosaic Virus (JMV) resistance. In this study, we ge...
Data
Distribution of RNA binding proteins CLIPdb-CIMS (CSTF2), starBase (AGO1), CLIPdb-CITS (HNRNPC), doRiNA (AGO2), Clipdb-PARalyzer (AGO2), and CLIPdb-Piranha-non-stranded (AGO2) across lncRNA, Protein Coding Transcript and Random Genomic Loci. X-axis of the graph represents random RBPs selected from each dataset and Y-axis depicts the normalized freq...
Data
(A,B) Distribution of RNA binding proteins from CLIPdb-Piranha-stranded across six biotypes of lncRNA genes and protein-coding genes. X-axis of the graph shows the distribution of RNA binding protein interaction sites in subclasses of lncRNAs and protein coding genes frequency of binding sites.
Data
Distribution of RNA binding proteins from (A) starBase, (B) CLIPdb-CITS, (C) doRiNA, (D) Clipdb-PARalyzer, and (E) CLIPdb-Piranha-non-stranded across 6 biotypes of lncRNA genes and protein-coding genes. X-axis of the graph shows the distribution of RNA binding protein interaction sites in subclasses of lncRNAs and protein coding genes frequency of...
Article
Full-text available
Background: Long non-coding RNAs (lncRNAs), are being reported to be extensively involved in diverse regulatory roles and have exhibited numerous disease associations. LncRNAs modulate their function through interaction with other biomolecules in the cell including DNA, RNA, and proteins. The availability of genome-scale experimental datasets of RN...
Article
Full-text available
Background: Only a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there have been detailed investigations on lncRNA-miRNA and lncRNA-protein interactions, the interaction of lncRNAs with DNA have not bee...
Article
Full-text available
Background Our understanding of the transcriptional potential of the genome and its functional consequences has undergone a significant change in the last decade. This has been largely contributed by the improvements in technology which could annotate and in many cases functionally characterize a number of novel gene loci in the human genome. Keepi...
Article
Full-text available
Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit patho-genic organisms has been well recognized. Approaches to identify the microbiome as...
Article
Full-text available
Long noncoding RNAs (lncRNAs) form the largest class of non-protein coding genes in the human genome. While a small subset of well-characterized lncRNAs has demonstrated their significant role in diverse biological functions like chromatin modifications, post-transcriptional regulation, imprinting etc., the functional significance of a vast majorit...
Article
Full-text available
A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis tha...
Article
Non-protein coding RNAs have increasingly been shown to be an important class of regulatory RNAs having significant roles in regulation of gene expression. The long non-coding RNA gene family presently constitutes a large number of noncoding RNA loci almost equalling the number of protein-coding genes. Nevertheless the biological roles and mechanis...
Article
Full-text available
These authors contributed equally to this work. zAuthors are listed in the descending order based on their microattributions credits in the Zebrafish GenomeWiki database. §Authors provided technical assistance for creating and maintaining the database and related infrastructure.
Article
Full-text available
Long non-coding RNAs (lncRNA) represent an assorted class of transcripts having little or no protein coding capacity and have recently gained importance for their function as regulators of gene expression. Molecular studies on lncRNA have uncovered multifaceted interactions with protein coding genes. It has been suggested that lncRNAs are an additi...
Article
Full-text available
Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platfo...
Data
Full-text available
The table lists the metadata used in MitoLSDB in column one and the status of corresponding metadata listed as minimal requirements for LSDBs in the second column. (PDF)
Data
Full-text available
The table lists the phenotype as obtained from literature along with their ethnic background. The third column list the number of individuals in each phenotype category. The last column provides MeSH terms for the phenotype as obtained from http://www.ncbi.nlm.nih.gov/mesh. The controlled vocabulary is used to ensure standardization in reporting di...
Article
Full-text available
Background: Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs, which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. The functional role of many of the members of this class has been an enigma, except a few of them like Malat and HOTAIR. Littl...
Data
List of all transcripts with the Ago binding sites. (DOC)
Data
Schematic of the proposed hypothesis. (TIF)
Data
Distribution of Ago binding sites across the length of lncRNAs divided in bins of 10 percent. A) The panel shows the number of Ago sites in each bin. B) The panel shows the individual Ago binding sites in lncRNAs transcripts. (TIF)
Article
Full-text available
The advent of high-throughput genome scale technologies has enabled us to unravel a large amount of the previously unknown transcriptionally active regions of the genome. Recent genome-wide studies have provided annotations of a large repertoire of various classes of noncoding transcripts. Long noncoding RNAs (lncRNAs) form a major proportion of th...
Article
Full-text available
Background: The availability of sequencing technology has enabled understanding of transcriptomes through genome-wide approaches including RNA-sequencing. Contrary to the previous assumption that large tracts of the eukaryotic genomes are not transcriptionally active, recent evidence from transcriptome sequencing approaches have revealed pervasive...
Data
Tabular summary of lncRNAs and small RNA clusters mappings to lncRNA exons derived from lncRNAdb.
Data
Tabular summary of lncRNAs and small RNA clusters mapping to lncRNA exons derived from Gencode database.
Data
Graph showing the size distribution of deepBase clusters mapped to lncRNA exons from Gencode dataset.
Data
Graph depicting the length distribution of lncRNAs derived from lncRNAdb.
Data
Table summarizing small RNA clusters discovered in our analysis, catalogued as miRNA, pasRNA and nasRNA; A) small RNA clusters mapped to lncRNA exons from lncRNAdb catalogued as different types of small RNAs B) small RNA clusters mapped to lncRNA exons from Gencode database catalogued as different types of small RNAs.
Data
Pie chart depicting the distribution of small RNA clusters in the 5’ Region, 3’ Region and Mid Region along the length of lncRNAs: A) Lengths of lncRNAs derived from lncRNAdb B) Lengths of lncRNAs derived from Gencode database.
Data
The DOC file containing the mapping of small RNA clusters in Tug1 lncRNA derived from lncRNAdb.
Article
Full-text available
Introduction: Long non-coding RNAs (lncRNAs) are a recently discovered class of non-coding functional RNA which has attracted immense research interest. The growing corpus of literature in the field provides ample evidence to suggest the important role of lncRNAs as regulators in a wide spectrum of biological processes. Recent evidence also sugges...
Article
Full-text available
Background: Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe Mi- ToLSDB, an int...
Article
Full-text available
The advancements in genomics technologies and the amenability to large-scale computational analysis have contributed immensely to the understanding of the zebrafish genome, its organization, and its functional correlates. Translating genomics information into biological meaning would require integration and amenability of data and tools. FishMap is...