List of works - Amol C Shetty

A Genome-Wide Association Study of Idiopathic Dilated Cardiomyopathy in African Americans.

scientific article published on 26 February 2018

A comparative analysis of library prep approaches for sequencing low input translatome samples

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

scientific article

A phosphorylation-wide sncRNA screen reveals Protein Functional Effector sncRNAs (pfeRNAs) in human lung somatic cells.

scientific article published on 16 March 2017

A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells.

scientific article

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data

scientific article

Alternative Splicing of Differentiated Myeloid Cell Transcripts after Infection by Anaplasma phagocytophilum Impacts a Selective Group of Cellular Programs.

scientific article published on 2 February 2018

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi

scientific article published on 22 July 2016

Association of a Novel Mutation in the Plasmodium falciparum Chloroquine Resistance Transporter With Decreased Piperaquine Sensitivity

scientific article published on August 2017

Best practices on the differential expression analysis of multi-species RNA-seq

publication published on 29 April 2021

Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments.

scientific article published on 23 May 2017

Brain feminization requires active repression of masculinization via DNA methylation

scientific article

Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry.

scientific article published on 11 October 2016

Characterization of microRNA transcriptome in lung cancer by next-generation deep sequencing.

scientific article published on 15 April 2014

Combining microarray-based genomic selection (MGS) with the Illumina Genome Analyzer platform to sequence diploid target regions

scientific article

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli

scientific article

Comprehensive molecular profiling of UV-induced metastatic melanoma in Nme1/Nme2-deficient mice reveals novel markers of survival in human patients

scientific article published on 25 August 2021

Corrigendum: Brain feminization requires active repression of masculinization via DNA methylation.

scientific article published in May 2017

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics

scientific article published on 01 January 2020

Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma.

scientific article

DNA Methylation Patterns in Cord Blood of Neonates Across Gestational Age: Association With Cell-Type Proportions

scientific article published on 25 January 2017

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

scientific article

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

scientific article published in Nature Communications

Determining Aspergillus fumigatus transcription factor expression and function during invasion of the mammalian lung

scientific article published on 29 March 2021

Disruption of RAB40AL function leads to Martin--Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder

scientific article

Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq

scientific article published on 11 July 2015

Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells

Effect of a small molecule Lipid II binder on bacterial cell wall stress.

scientific article published on 28 February 2017

Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire

article published in the Proceedings of the National Academy of Sciences of the United States of America

Genome-Wide Anaplasma phagocytophilum AnkA-DNA Interactions Are Enriched in Intergenic Regions and Gene Promoters and Correlate with Infection-Induced Differential Gene Expression.

scientific article published on 20 September 2016

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

scientific article published on 18 October 2016

Genome-wide small nucleolar RNA expression analysis of lung cancer by next-generation deep sequencing

scientific article published on 4 September 2014

Identification of a gene expression signature associated with the metastasis suppressor function of NME1: prognostic value in human melanoma.

scientific article

Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder

scientific article

Inhibition of EGFR Signaling Protects from Mucormycosis

scientific article published on 14 August 2018

Iron restriction inside macrophages regulates pulmonary host defense against Rhizopus species

scientific article published in Nature Communications

MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL.

scientific article

Map of open and closed chromatin domains in Drosophila genome

scientific article

Microarray oligonucleotide probe designer (MOPeD): A web service

scientific article

Microdeletions of 3q29 confer high risk for schizophrenia

scientific article

Molecular epidemiology and genomics of group A Streptococcus

scientific article

New signaling pathways govern the host response to C. albicans infection in various niches

scientific article published on 9 April 2015

Oral epithelial IL-22/STAT3 signaling licenses IL-17-mediated immunity to oral mucosal candidiasis

scientific article published on 01 June 2020

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

scientific article published in Nature Communications

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates

scientific article published on 12 June 2015

RNAseq Analysis of the Drosophila Response to the Entomopathogenic Nematode Steinernema

scientific article

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys ⬇️

scientific article

SeqAnt: a web service to rapidly identify and annotate DNA sequence variations

scientific article

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

scientific article published on 6 March 2019

Simultaneous transcriptional profiling of bacteria and their host cells

scientific article

Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing.

scientific article published on 25 August 2017

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

scientific article published in Scientific Reports

Targeted sequencing of the human X chromosome exome.

scientific article

The Evolutionary Genomic Dynamics of Peruvians Before, During, and After the Inca Empire

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions

scientific article

Transcriptomic analysis of vulvovaginal candidiasis identifies a role for the NLRP3 inflammasome

scientific article published on 21 April 2015

Unique gene program of rat small resistance mesenteric arteries as revealed by deep RNA sequencing.

scientific article published on July 2015

Venetoclax and pegcrisantaspase for complex karyotype acute myeloid leukemia

scientific article published on 16 November 2020

Whole genome sequence analyses of brain imaging measures in the Framingham Study

scientific article published on 27 December 2017

List of works by Amol C Shetty

A Genome-Wide Association Study of Idiopathic Dilated Cardiomyopathy in African Americans.

A comparative analysis of library prep approaches for sequencing low input translatome samples

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

A phosphorylation-wide sncRNA screen reveals Protein Functional Effector sncRNAs (pfeRNAs) in human lung somatic cells.

A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data

Alternative Splicing of Differentiated Myeloid Cell Transcripts after Infection by Anaplasma phagocytophilum Impacts a Selective Group of Cellular Programs.

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi

Association of a Novel Mutation in the Plasmodium falciparum Chloroquine Resistance Transporter With Decreased Piperaquine Sensitivity

Best practices on the differential expression analysis of multi-species RNA-seq

Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments.

Brain feminization requires active repression of masculinization via DNA methylation

Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry.

Characterization of microRNA transcriptome in lung cancer by next-generation deep sequencing.

Combining microarray-based genomic selection (MGS) with the Illumina Genome Analyzer platform to sequence diploid target regions

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli

Comprehensive molecular profiling of UV-induced metastatic melanoma in Nme1/Nme2-deficient mice reveals novel markers of survival in human patients

Corrigendum: Brain feminization requires active repression of masculinization via DNA methylation.

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics

Cross-species transcriptional analysis reveals conserved and host-specific neoplastic processes in mammalian glioma.

DNA Methylation Patterns in Cord Blood of Neonates Across Gestational Age: Association With Cell-Type Proportions

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

Determining Aspergillus fumigatus transcription factor expression and function during invasion of the mammalian lung

Disruption of RAB40AL function leads to Martin--Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder

Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq

Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells

Effect of a small molecule Lipid II binder on bacterial cell wall stress.

Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire

Genome-Wide Anaplasma phagocytophilum AnkA-DNA Interactions Are Enriched in Intergenic Regions and Gene Promoters and Correlate with Infection-Induced Differential Gene Expression.

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

Genome-wide small nucleolar RNA expression analysis of lung cancer by next-generation deep sequencing

Identification of a gene expression signature associated with the metastasis suppressor function of NME1: prognostic value in human melanoma.

Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder

Inhibition of EGFR Signaling Protects from Mucormycosis

Iron restriction inside macrophages regulates pulmonary host defense against Rhizopus species

MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL.

Map of open and closed chromatin domains in Drosophila genome

Microarray oligonucleotide probe designer (MOPeD): A web service

Microdeletions of 3q29 confer high risk for schizophrenia

Molecular epidemiology and genomics of group A Streptococcus

New signaling pathways govern the host response to C. albicans infection in various niches

Oral epithelial IL-22/STAT3 signaling licenses IL-17-mediated immunity to oral mucosal candidiasis

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates

RNAseq Analysis of the Drosophila Response to the Entomopathogenic Nematode Steinernema

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys ⬇️

SeqAnt: a web service to rapidly identify and annotate DNA sequence variations

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Simultaneous transcriptional profiling of bacteria and their host cells

Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing.

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

Targeted sequencing of the human X chromosome exome.

The Evolutionary Genomic Dynamics of Peruvians Before, During, and After the Inca Empire

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions

Transcriptomic analysis of vulvovaginal candidiasis identifies a role for the NLRP3 inflammasome

Unique gene program of rat small resistance mesenteric arteries as revealed by deep RNA sequencing.

Venetoclax and pegcrisantaspase for complex karyotype acute myeloid leukemia

Whole genome sequence analyses of brain imaging measures in the Framingham Study