Heikham Russiachand Singh

Heikham Russiachand Singh
McGill University | McGill · Department of Plant Science

M.Sc Bioinformatics

About

49
Publications
14,411
Reads
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400
Citations
Additional affiliations
September 2016 - present
McGill University
Position
  • Graduate Scholar
December 2015 - July 2016
Sikkim University
Position
  • Project Scientist
July 2012 - October 2014
Centre for Cellular and Molecular Platforms
Position
  • Bioinformatics Associate
Education
July 2004 - July 2006
Jamia Millia Islamia
Field of study
  • Bioinformatics

Publications

Publications (49)
Conference Paper
Full-text available
Drought stress has an inevitable climate change impact to the agricultural crops. It drastically affected several photosynthetic characters irrespective of genotypes even though tolerance genotypes performed better with respect to carbon assimilation. Photosynthetic response for reduction in the photosynthesis might be due to the limited availabili...
Chapter
Abiotic stress altered various physiological and molecular responses of plants that imposed the plant's survival challenge. Nevertheless, plants regulate their responses either by reducing its growth or by increasing its potential for stress tolerance and survival. Abiotic stress tolerance is a complex process in itself where hormonal interventions...
Article
Full-text available
Background The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is li...
Article
Full-text available
Plant-fungal associations have been explored by routine cultivation based approaches and cultivation based approaches cannot catalogue more than 5% of fungal diversity associated with any niche. In the present study, an attempt has been made to catalogue fungal diversity associated with belowground parts i.e. rhizosphere and cormosphere, of Crocus...
Data
Significance values based on libshuff and Unifrac weighted analysis. (XLSX)
Data
Abundance of fungal (phylum, genus and species) diversity in Bulk soil, cormosphere and rhizosphere of C.sativus during flowering stage. In the table, P represents phylum, g represents genus and s represents species of fungi (XLSX)
Data
Abundance of fungal (phylum, genus and species) diversity in Bulk soil and cormosphere of C.sativus during dormant stage. In the table, P represents phylum, g represents genus and s represents species of fungi (XLSX)
Article
Camptothecin (CPT), a monoterpene indole alkaloid, is a potent inhibitor of DNA topoisomerase I and has applications in treating ovarian, small lung and refractory ovarian cancers. Stem wood tissue of Nothapodytes nimmoniana (Graham) Mabb. (family Icacinaceae) is one of the richest sources of CPT. Since there is no genomic or transcriptome data ava...
Article
Full-text available
Background: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-...
Article
Full-text available
Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are th...
Article
Full-text available
Background Sinopodophyllum hexandrum is an endangered medicinal herb, which is commonly present in elevations ranging between 2,400–4,500 m and is sensitive to temperature. Medicinal property of the species is attributed to the presence of podophyllotoxin in the rhizome tissue. The present work analyzed transcriptome of rhizome tissue of S. hexandr...
Article
Full-text available
Non-coding elements such as miRNAs play key regulatory roles in living systems. These ultra-short, ∼21 bp long, RNA molecules are derived from their hairpin precursors and usually participate in negative gene regulation by binding the target mRNAs. Discovering miRNA candidate regions across the genome has been a challenging problem. Most of the exi...
Data
Total sequences used in training and testing datasets of miR-BAG for different species and benchmarking of various tools. (DOC)
Data
Implementation details for parallelism in miR-BAG. (DOC)
Data
The top 15 feature scores along with the feature names and type of the features obtained after feature selection for every species. (DOC)
Data
Sequence data for novel miRNAs identified in Bos taurus genome, using the NGS module of miR-BAG. (DOC)
Data
The statistics of all conventional features used by previously existing tools. (XLS)
Data
Comparative ROC plots for different precursor identification tools. (TIFF)
Data
Web-server and standalone implementation details for miR-BAG. (PDF)
Data
Energy and Structural profile matrix score plots drawn between the positive and negative instances for all target species, depicting the distribution patterns for positive and negative instances. (DOC)
Article
Full-text available
Picrorhiza kurrooa Royle ex Benth. is an endangered plant species of medicinal importance. The medicinal property is attributed to monoterpenoids picroside I and II, which are modulated by temperature. The transcriptome information of this species is limited with the availability of few hundreds of expressed sequence tags (ESTs) in the public datab...
Data
Top highly represented functional conserved domains found in unknown sequences.
Data
Details on all the transcription factor (TF) families analyzed in P. kurrooa.
Data
Pooled transcriptome data of P. kurrooa. File contains the remaining data of Additional file 1.
Data
Guanine-cytosine (GC) content analysis of P. kurrooa transcripts. The average GC content of each transcript was calculated and highest proportion of transcripts belongs to the GC content range of 40-49%.
Data
Reads per exon kilobase per million (RPKM) based expression of annotated cytochrome P450s (CYPs) in P. kurrooa transcriptome.
Data
Oligonucleotide sequences and polymerase chain reaction (PCR) conditions used in reverse transcriptase (RT-PCR) based expression analysis.
Data
Experimentally validated expressed sequence tags (ESTs) of P. kurrooa available at dbEST NCBI. Methods section has details including URL used in the present analysis.
Data
Top 20 most abundant transcription factor (TF) families analyzed in P. kurrooa. Details of all the TFs are mentioned in Additional file 10.
Data
Pooled transcriptome data of P. kurrooa. Due to large amount, data is divided into Additional file 1 and Additional file 2.
Data
Dissimilar sequence groupings for assembled transcriptome sequences. The grouped sequences are dissimilar from each other, and belong to different regions of common genes. This helps reducing the over-representation of total transcripts, usually missed in assembling.
Data
Simple sequence repeats (SSRs) identified in transcripts of P. kurrooa.
Data
Comparative plots for top ten highest represented molecular function (A) and biological process (B) categories in A. thaliana and P. kurrooa.
Data
Reads per exon kilobase per million (RPKM) based gene expression at 15°C and 25°C in different expression categories ranging from > 10 fold increment to 0.5 fold or lower.
Data
Reads per exon kilobase per million (RPKM) based expression of transcription factors analysed for P. kurrooa transcriptome at 15°C and 25°C.
Data
Reads per exon kilobase per million (RPKM) based expression of targeted genes of mevalonate (MVA), 2-C-methyl-D-erythritol 4-phosphate (MEP) and phenylpropanoid (PP) pathway (pathways associated with picrosides biosynthesis) at 15°C and 25°C.
Data
Reads per exon kilobase per million (RPKM) based expression of annotated glycosyltransferases in P. kurrooa transcriptome.
Article
Full-text available
The non-coding elements of a genome, with many of them considered as junk earlier, have now started gaining long due respectability, with microRNAs as the best current example. MicroRNAs bind preferentially to the 3' untranslated regions 9UTRs) of the target genes and negatively regulate their expression most of the time. Several microRNA: target p...

Questions

Questions (2)
Question
I am new to the metabolomics, and I used MZmine tool for analyzing the profile negative mode dataset from LC-MS.
While using this tool, there is a parameter (no ionization, M+H, M-H, etc.) in the online data search after alignment. However, searching in positive and negative mode gave the different results of a molecular compound.
Any suggestion is much appreciated.
Thanks a lot.
Question
I want to perform a bombardment using biolistics transfection methods for genome editing in wheat. We have Cas9 protein and sgRNA as Ribonucleoprotein complexes and I would like to coat this RNPs on gold nanoparticles for biolistics delivery in calli without using plasmid.
Does anyone have the protocols for coating proteins/RNPs in monocot plant? Please do share me your experience. 
Thank you so much in advance and much appreciated.

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