List of works - Trupti Joshi

A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies

scientific article published on 25 November 2015

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

AccuCalc: A Python Package for Accuracy Calculation in GWAS

scientific article published in 2023

An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum

article

An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus

scientific article published on 09 September 2014

An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data

scientific article

An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants

scientific article published on 7 April 2010

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data

scientific article

Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting

scientific article

Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean

scientific article

Correction: Stuckel, et al.; Enhanced CXCR4 Expression Associates with Increased Gene Body 5-Hydroxymethylcytosine Modification but Not Decreased Promoter Methylation in Colorectal Cancer. Cancers 2020, 12, 539

scientific article published on 23 October 2020

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

scientific article published on 20 January 2017

Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings

scientific article published on 6 June 2015

Elongation factor 1 alpha1 and genes associated with Usher syndromes are downstream targets of GBX2

scientific journal article

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

scientific article published on 05 June 2013

Erratum: Genome sequence of the palaeopolyploid soybean

scientific article published in Nature

Establishment of a protein reference map for soybean root hair cells

scientific article published on 26 November 2008

Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.

scientific article published on 13 February 2016

FcgammaR-induced production of superoxide and inflammatory cytokines is differentially regulated by SHIP through its influence on PI3K and/or Ras/Erk pathways

scientific article published on 16 March 2006

G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers

scientific article published on 01 July 2021

GeneFAS: A tool for prediction of gene function using multiple sources of data

scientific article

Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection

scientific article

Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean

scientific article

Genome sequence of the palaeopolyploid soybean

scientific article

Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae

scientific article

Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response

scientific article published on 27 December 2014

Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions

scientific article published on 15 January 2016

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

scientific article

IL-21 mediates apoptosis through up-regulation of the BH3 family member BIM and enhances both direct and antibody-dependent cellular cytotoxicity in primary chronic lymphocytic leukemia cells in vitro

scientific article published on 8 January 2008

Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655

scientific article

Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection.

scientific article published on 14 May 2015

Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C

scientific article published on 23 May 2015

Inferring gene regulatory networks from multiple microarray datasets

scientific article published on 24 July 2006

Landscape of genomic diversity and trait discovery in soybean

scientific article published on 31 March 2016

Large-scale analysis of putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development

scientific article published on 15 September 2009

Legume transcription factor genes: what makes legumes so special?

scientific article published on 02 September 2009

Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes

scientific article

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

scientific article

Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7.

scientific article published on 31 March 2017

Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE.

scientific article

Prediction of novel miRNAs and associated target genes in Glycine max.

scientific article

Quantitative assessment of relationship between sequence similarity and function similarity

scientific article

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

scientific article

SNP discovery by high-throughput sequencing in soybean

scientific article

Single feature polymorphism discovery in rice

scientific article

SoyDB: a knowledge database of soybean transcription factors

scientific article

Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis

scientific article published on 11 July 2015

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

scientific article

Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

scientific article

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

scientific article (publication date: 2014)

Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance

scientific article published on 13 August 2015

System analysis of an Arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism

scientific article published on 11 March 2009

System approaches to study root hairs as a single cell plant model: current status and future perspectives

scientific article

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

scientific article

Targeting CD37-positive lymphoid malignancies with a novel engineered small modular immunopharmaceutical

scientific article

The Evolution of Soybean Knowledge Base (SoyKB).

scientific article published on January 2017

The NS1 protein of the parvovirus MVM Aids in the localization of the viral genome to cellular sites of DNA damage

scientific article published on 16 October 2020

The humanized CD40 antibody SGN-40 demonstrates pre-clinical activity that is enhanced by lenalidomide in chronic lymphocytic leukaemia

scientific article published on 12 January 2009

Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

scientific article published in May 2008

Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress

article

Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress

scientific article

Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores

scientific article

Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe).

scientific article

List of works by Trupti Joshi

A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

AccuCalc: A Python Package for Accuracy Calculation in GWAS

An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum

An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus

An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data

An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data

Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting

Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean

Correction: Stuckel, et al.; Enhanced CXCR4 Expression Associates with Increased Gene Body 5-Hydroxymethylcytosine Modification but Not Decreased Promoter Methylation in Colorectal Cancer. Cancers 2020, 12, 539

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings

Elongation factor 1 alpha1 and genes associated with Usher syndromes are downstream targets of GBX2

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

Erratum: Genome sequence of the palaeopolyploid soybean

Establishment of a protein reference map for soybean root hair cells

Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing.

FcgammaR-induced production of superoxide and inflammatory cytokines is differentially regulated by SHIP through its influence on PI3K and/or Ras/Erk pathways

G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers

GeneFAS: A tool for prediction of gene function using multiple sources of data

Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection

Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean

Genome sequence of the palaeopolyploid soybean

Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae

Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response

Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

IL-21 mediates apoptosis through up-regulation of the BH3 family member BIM and enhances both direct and antibody-dependent cellular cytotoxicity in primary chronic lymphocytic leukemia cells in vitro

Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655

Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection.

Identification of quantitative trait loci underlying resistance to southern root-knot and reniform nematodes in soybean accession PI 567516C

Inferring gene regulatory networks from multiple microarray datasets

Landscape of genomic diversity and trait discovery in soybean

Large-scale analysis of putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development

Legume transcription factor genes: what makes legumes so special?

Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7.

Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE.

Prediction of novel miRNAs and associated target genes in Glycine max.

Quantitative assessment of relationship between sequence similarity and function similarity

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

SNP discovery by high-throughput sequencing in soybean

Single feature polymorphism discovery in rice

SoyDB: a knowledge database of soybean transcription factors

Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance

System analysis of an Arabidopsis mutant altered in de novo fatty acid synthesis reveals diverse changes in seed composition and metabolism

System approaches to study root hairs as a single cell plant model: current status and future perspectives

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

Targeting CD37-positive lymphoid malignancies with a novel engineered small modular immunopharmaceutical

The Evolution of Soybean Knowledge Base (SoyKB).

The NS1 protein of the parvovirus MVM Aids in the localization of the viral genome to cellular sites of DNA damage

The humanized CD40 antibody SGN-40 demonstrates pre-clinical activity that is enhanced by lenalidomide in chronic lymphocytic leukaemia

Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

Transcriptional and Physiological Responses of Bradyrhizobium japonicum to Desiccation-Induced Stress

Transcriptional and physiological responses of Bradyrhizobium japonicum to desiccation-induced stress

Transcriptional responses of Arabidopsis thaliana to chewing and sucking insect herbivores

Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe).