List of works - Krishna R Kalari

A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition

scientific article published on 26 September 2019

A cell cycle-dependent BRCA1-UHRF1 cascade regulates DNA double-strand break repair pathway choice

scientific article published on 5 January 2016

A comprehensive analysis of breast cancer microbiota and host gene expression.

scientific article published on 30 November 2017

A knowledge-based approach to predict intragenic deletions or duplications

scientific article published on 21 July 2008

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

scientific article

ATR Inhibition Is a Promising Radiosensitizing Strategy for Triple-Negative Breast Cancer

An integrated model of the transcriptome of HER2-positive breast cancer

scientific article

Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome-Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2

scientific article published on 18 March 2019

Anastrozole has an association between degree of estrogen suppression and outcomes in early breast cancer and is a ligand for estrogen receptor α

scientific article published on 25 February 2020

Antitumor activity of Z-endoxifen in aromatase inhibitor-sensitive and aromatase inhibitor-resistant estrogen receptor-positive breast cancer

scientific article published on 19 May 2020

BBBomics-Human Blood Brain Barrier Transcriptomics Hub.

scientific article published on March 2016

Beta-Poisson model for single-cell RNA-seq data analyses

scientific article

Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: metabolomics-informed genomics.

scientific article

Betaine-homocysteine methyltransferase: Human liver genotype–phenotype correlation ⬇️

scientific article published on October 21, 2010

Breast cancer chemoprevention pharmacogenomics: Deep sequencing and functional genomics of the ZNF423 and CTSO genes

scientific article published on 21 August 2017

CD38 expression, function, and gene resequencing in a human lymphoblastoid cell line-based model system

scientific article

Circular RNAs and their associations with breast cancer subtypes

scientific article

Clonal expansion of antitumor T cells in breast cancer correlates with response to neoadjuvant chemotherapy

scientific article published on 27 May 2016

Comparison of 99mTc-Sestamibi Molecular Breast Imaging and Breast MRI in Patients With Invasive Breast Cancer Receiving Neoadjuvant Chemotherapy

scientific article published on 05 June 2019

Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

scientific article published on 13 June 2020

Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach

scientific article

Correction: Folate receptor-α (FOLR1) expression and function in triple negative tumors.

scientific article published on 30 April 2015

Cytosolic 5'-nucleotidase III (NT5C3): gene sequence variation and functional genomics

scientific article

DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine

scientific article published on 30 April 2018

Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer

scientific article published on 01 October 2019

Detecting gene-gene interactions in prostate disease in African American men

scientific article published on 23 September 2011

Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer.

scientific article published on 10 April 2012

Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer.

scientific article published on 15 April 2016

Differential Effects of Alzheimer's Disease Aβ40 and 42 on Endocytosis and Intraneuronal Trafficking.

scientific article published on 11 January 2018

Discovery of a glucocorticoid receptor (GR) activity signature using selective GR antagonism in ER-negative breast cancer.

scientific article published on 10 April 2018

Ecto-5'-nucleotidase and thiopurine cellular circulation: association with cytotoxicity

scientific article

Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study

scientific article published on 6 December 2017

Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFκB/p65 signaling in triple negative breast cancer

scientific article published on 17 February 2022

Estrogen, SNP-Dependent Chemokine Expression and Selective Estrogen Receptor Modulator Regulation

scientific article published on 11 February 2016

Estrogens and their precursors in postmenopausal women with early breast cancer receiving anastrozole

scientific article

Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy

scientific article

Folate receptor alpha expression associates with improved disease-free survival in triple negative breast cancer patients

scientific article published on 04 February 2020

Folate receptor-α (FOLR1) expression and function in triple negative tumors

scientific article

Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors

scientific article

Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy

scientific article published on 10 October 2016

Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group n9831 Adjuvant Trastuzumab Trial.

scientific article

Germline genome-wide association studies in women receiving neoadjuvant chemotherapy with or without bevacizumab

scientific article published on 01 June 2018

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

scholarly article by Saurabh Baheti published in July 2018

Human S-adenosylhomocysteine hydrolase: common gene sequence variation and functional genomic characterization

scientific article

IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries

scientific article published on 15 December 2014

Identification of genetic variants or genes that are associated with Homoharringtonine (HHT) response through a genome-wide association study in human lymphoblastoid cell lines (LCLs)

scientific article

Impact of histopathology, tumor-infiltrating lymphocytes, and adjuvant chemotherapy on prognosis of triple-negative breast cancer

scientific article published on 14 September 2017

Implementation of preemptive DNA sequence–based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study

scientific article published in 2022

Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing

scientific article (publication date: 25 February 2011)

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

scientific article

Inverse association between programmed death ligand 1 and genes in the VEGF pathway in primary clear cell renal cell carcinoma

scientific article

Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance.

scientific article published on 11 August 2017

Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies.

scientific article

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

scientific article

MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1

Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines

scientific article

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls

scientific article published on 27 June 2016

PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient

scientific article published on 01 December 2018

Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action

scientific article published on 23 July 2020

Protein kinase Cι expression and oncogenic signaling mechanisms in cancer.

scientific article

RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy.

scientific article

SLCO1B1 polymorphisms and plasma estrone conjugates in postmenopausal women with ER+ breast cancer: genome-wide association studies of the estrone pathway.

scientific article

Single-nucleotide polymorphism biomarkers of adjuvant anastrozole-induced estrogen suppression in early breast cancer

scientific article published on 08 July 2020

TCL1A Single-Nucleotide Polymorphisms and Estrogen-Mediated Toll-Like Receptor-MYD88-Dependent Nuclear Factor-κB Activation: Single-Nucleotide Polymorphism- and Selective Estrogen Receptor Modulator-Dependent Modification of Inflammation and Immune

scientific article published on 14 June 2017

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

scientific article (publication date: 15 January 2012)

TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics

scientific article published on 23 February 2016

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease

scientific article published on 03 August 2016

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data

scientific article

The lncRNA MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1

Transcriptome analysis of garlic-induced hepatoprotection against alcoholic fatty liver.

scientific article

Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites

scientific article published on 8 January 2014

Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy

scientific article published on January 2017

Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer

scientific article

Vitamin D Levels, Vitamin D Receptor Polymorphisms, and Inflammatory Cytokines in Aromatase Inhibitor-Induced Arthralgias: An Analysis of CCTG MA.27.

scientific article published on 16 October 2017

List of works by Krishna R Kalari

A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition

A cell cycle-dependent BRCA1-UHRF1 cascade regulates DNA double-strand break repair pathway choice

A comprehensive analysis of breast cancer microbiota and host gene expression.

A knowledge-based approach to predict intragenic deletions or duplications

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

ATR Inhibition Is a Promising Radiosensitizing Strategy for Triple-Negative Breast Cancer

An integrated model of the transcriptome of HER2-positive breast cancer

Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome-Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2

Anastrozole has an association between degree of estrogen suppression and outcomes in early breast cancer and is a ligand for estrogen receptor α

Antitumor activity of Z-endoxifen in aromatase inhibitor-sensitive and aromatase inhibitor-resistant estrogen receptor-positive breast cancer

BBBomics-Human Blood Brain Barrier Transcriptomics Hub.

Beta-Poisson model for single-cell RNA-seq data analyses

Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: metabolomics-informed genomics.

Betaine-homocysteine methyltransferase: Human liver genotype–phenotype correlation ⬇️

Breast cancer chemoprevention pharmacogenomics: Deep sequencing and functional genomics of the ZNF423 and CTSO genes

CD38 expression, function, and gene resequencing in a human lymphoblastoid cell line-based model system

Circular RNAs and their associations with breast cancer subtypes

Clonal expansion of antitumor T cells in breast cancer correlates with response to neoadjuvant chemotherapy

Comparison of 99mTc-Sestamibi Molecular Breast Imaging and Breast MRI in Patients With Invasive Breast Cancer Receiving Neoadjuvant Chemotherapy

Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type

Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach

Correction: Folate receptor-α (FOLR1) expression and function in triple negative tumors.

Cytosolic 5'-nucleotidase III (NT5C3): gene sequence variation and functional genomics

DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine

Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer

Detecting gene-gene interactions in prostate disease in African American men

Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer.

Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer.

Differential Effects of Alzheimer's Disease Aβ40 and 42 on Endocytosis and Intraneuronal Trafficking.

Discovery of a glucocorticoid receptor (GR) activity signature using selective GR antagonism in ER-negative breast cancer.

Ecto-5'-nucleotidase and thiopurine cellular circulation: association with cytotoxicity

Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study

Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFκB/p65 signaling in triple negative breast cancer

Estrogen, SNP-Dependent Chemokine Expression and Selective Estrogen Receptor Modulator Regulation

Estrogens and their precursors in postmenopausal women with early breast cancer receiving anastrozole

Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy

Folate receptor alpha expression associates with improved disease-free survival in triple negative breast cancer patients

Folate receptor-α (FOLR1) expression and function in triple negative tumors

Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors

Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy

Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group n9831 Adjuvant Trastuzumab Trial.

Germline genome-wide association studies in women receiving neoadjuvant chemotherapy with or without bevacizumab

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

Human S-adenosylhomocysteine hydrolase: common gene sequence variation and functional genomic characterization

IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries

Identification of genetic variants or genes that are associated with Homoharringtonine (HHT) response through a genome-wide association study in human lymphoblastoid cell lines (LCLs)

Impact of histopathology, tumor-infiltrating lymphocytes, and adjuvant chemotherapy on prognosis of triple-negative breast cancer

Implementation of preemptive DNA sequence–based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study

Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Inverse association between programmed death ligand 1 and genes in the VEGF pathway in primary clear cell renal cell carcinoma

Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance.

Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies.

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1

Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls

PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient

Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action

Protein kinase Cι expression and oncogenic signaling mechanisms in cancer.

RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy.

SLCO1B1 polymorphisms and plasma estrone conjugates in postmenopausal women with ER+ breast cancer: genome-wide association studies of the estrone pathway.

Single-nucleotide polymorphism biomarkers of adjuvant anastrozole-induced estrogen suppression in early breast cancer

TCL1A Single-Nucleotide Polymorphisms and Estrogen-Mediated Toll-Like Receptor-MYD88-Dependent Nuclear Factor-κB Activation: Single-Nucleotide Polymorphism- and Selective Estrogen Receptor Modulator-Dependent Modification of Inflammation and Immune

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data

The lncRNA MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1

Transcriptome analysis of garlic-induced hepatoprotection against alcoholic fatty liver.

Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites

Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy

Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer

Vitamin D Levels, Vitamin D Receptor Polymorphisms, and Inflammatory Cytokines in Aromatase Inhibitor-Induced Arthralgias: An Analysis of CCTG MA.27.