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ComBat-seq: batch effect adjustment for RNA-seq count data.

Yuqing Zhang, Giovanni Parmigiani, W Evan Johnson,

The benefit of integrating batches of genomic data to increase statistical power is often hindered by batch effects, or unwanted variation in data caused by differences in technical factors across batches. It is therefore critical to effectively address batch effects in genomic data to overcome these challenges. Many existing methods ... Read more >>

NAR Genom Bioinform (NAR genomics and bioinformatics)
[2020, 2(3):lqaa078]

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Exploring changes in the human gut microbiota and microbial-derived metabolites in response to diets enriched in simple, refined, or unrefined carbohydrate-containing foods: a post hoc analysis of a randomized clinical trial.

Tyler Faits, Maura E Walker, Jose Rodriguez-Morato, Huicui Meng, Julie E Gervis, Jean M Galluccio, Alice H Lichtenstein, W Evan Johnson, Nirupa R Matthan,

BACKGROUND:Dietary carbohydrate type may influence cardiometabolic risk through alterations in the gut microbiome and microbial-derived metabolites, but evidence is limited. OBJECTIVES:We explored the relative effects of an isocaloric exchange of dietary simple, refined, and unrefined carbohydrate on gut microbiota composition/function, and selected microbial metabolite concentrations. METHODS:Participants [n = 11; age: 65 ± 8 y; ... Read more >>

Am. J. Clin. Nutr. (The American journal of clinical nutrition)
[2020, :]

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ComBat-seq: batch effect adjustment for RNA-seq count data

Yuqing Zhang, Giovanni Parmigiani, W Evan Johnson,

Abstract The benefit of integrating batches of genomic data to increase statistical power is often hindered by batch effects, or unwanted variation in data caused by differences in technical factors across batches. It is therefore critical to effectively address batch effects in genomic data to overcome these challenges. Many existing ... Read more >>

NAR Genom Bioinform (NAR genomics and bioinformatics)
[2020, 2(3):]

Cited: 0 times

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Decontamination of ambient RNA in single-cell RNA-seq with DecontX.

Shiyi Yang, Sean E Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima, Joshua D Campbell,

Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a novel Bayesian method to estimate and ... Read more >>

Genome Biol. (Genome biology)
[2020, 21(1):57]

Cited: 4 times

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Inhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities.

Seiko Ikezu, Hana Yeh, Jean-Christophe Delpech, Maya E Woodbury, Alicia A Van Enoo, Zhi Ruan, Sudhir Sivakumaran, Yang You, Carl Holland, Teresa Guillamon-Vivancos, Asuka Yoshii-Kitahara, Mina B Botros, Charlotte Madore, Pin-Hao Chao, Ankita Desani, Solaiappan Manimaran, Srinidhi Venkatesan Kalavai, W Evan Johnson, Oleg Butovsky, Maria Medalla, Jennifer I Luebke, Tsuneya Ikezu,

Maternal immune activation (MIA) disrupts the central innate immune system during a critical neurodevelopmental period. Microglia are primary innate immune cells in the brain although their direct influence on the MIA phenotype is largely unknown. Here we show that MIA alters microglial gene expression with upregulation of cellular protrusion/neuritogenic pathways, ... Read more >>

Mol. Psychiatry (Molecular psychiatry)
[2020, :]

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Cross-validation of existing signatures and derivation of a novel 29-gene transcriptomic signature predictive of progression to TB in a Brazilian cohort of household contacts of pulmonary TB.

Samantha Leong, Yue Zhao, Rodrigo Ribeiro-Rodrigues, Edward C Jones-López, Carlos Acuña-Villaorduña, Patricia Marques Rodrigues, Moises Palaci, David Alland, Reynaldo Dietze, Jerrold J Ellner, W Evan Johnson, Padmini Salgame,

The goal of this study was to identify individuals at risk of progression and reactivation among household contacts (HHC) of pulmonary TB cases in Vitoria, Brazil. We first evaluated the predictive performance of six published signatures on the transcriptional dataset obtained from peripheral blood mononuclear cell samples from HHC that ... Read more >>

Tuberculosis (Edinb) (Tuberculosis (Edinburgh, Scotland))
[2020, 120:101898]

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The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.

Joao B Xavier, Vincent B Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T Pearson, Paul Macklin, Amir Mitchell, Ilya Shmulevich, Lei Xie, J Gregory Caporaso, Keith A Crandall, Nicole L Simone, Filipa Godoy-Vitorino, Timothy J Griffin, Katrine L Whiteson, Heather H Gustafson, Daniel J Slade, Thomas M Schmidt, Marina R S Walther-Antonio, Tal Korem, Bobbie-Jo M Webb-Robertson, Mark P Styczynski, W Evan Johnson, Christian Jobin, Jason M Ridlon, Andrew Y Koh, Michael Yu, Libusha Kelly, Jennifer A Wargo,

The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions ... Read more >>

Trends Cancer (Trends in cancer)
[2020, 6(3):192-204]

Cited: 3 times

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A Parsimonious Host Inflammatory Biomarker Signature Predicts Incident TB and Mortality in Advanced HIV.

Yukari C Manabe, Bruno B Andrade, Nikhil Gupte, Samantha Leong, Manisha Kintali, Mitch Matoga, Cynthia Riviere, Wadzanai Sameneka, Javier R Lama, Kogieleum Naidoo, Yue Zhao, W Evan Johnson, Jerrold J Ellner, Mina C Hosseinipour, Gregory P Bisson, Padmini Salgame, Amita Gupta, ,

BACKGROUND:People with advanced HIV (CD4<50) remain at high risk of TB or death despite the initiation of antiretroviral therapy. We aimed to identify immunological profiles that were most predictive of incident TB disease and death. METHODS:The REMEMBER randomized clinical trial enrolled 850 participants with HIV (CD4<50 cells/µL) at ART initiation ... Read more >>

Clin Infect Dis (Clinical infectious diseases : an official publication of the Infectious Diseases Society of America)
[2019, :]

Cited: 2 times

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Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes.

Jasmine A McQuerry, David F Jenkins, Susan E Yost, Yuqing Zhang, Daniel Schmolze, W Evan Johnson, Yuan Yuan, Andrea H Bild,

BACKGROUND:Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expression panel compatible with degraded RNA from formalin-fixed, paraffin-embedded (FFPE) patient cancer samples and investigated its utility in pathway activity profiling ... Read more >>

BMC Cancer (BMC cancer)
[2019, 19(1):881]

Cited: 2 times

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scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data.

Zhe Wang, Junming Hu, W Evan Johnson, Joshua D Campbell,

BACKGROUND:Single-cell RNA sequencing (scRNA-seq) enables the high-throughput quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional preprocessing steps such as cell barcode identification or unique molecular identifier (UMI) deconvolution are necessary for preprocessing of data from single cell protocols. R packages that can easily preprocess data ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2019, 20(1):222]

Cited: 1 time

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A Western-Type Dietary Pattern Induces an Atherogenic Gene Expression Profile in the Coronary Arteries of the Ossabaw Pig.

Maura E Walker, Nirupa R Matthan, Stefania Lamon-Fava, Gloria Solano-Aguilar, Saebyeol Jang, Sukla Lakshman, Aleksey Molokin, Joseph F Urban, Tyler Faits, W Evan Johnson, Alice H Lichtenstein,

Background:Current cardiovascular risk reduction guidance focuses on shifts in dietary patterns, rather than single foods or nutrients. Experimental studies are needed to identify the mechanisms by which food-based diets affect the development and progression of atherosclerosis. Objectives:The aim of this study was to investigate the effect of 2 food-based dietary ... Read more >>

(Current developments in nutrition)
[2019, 3(5):nzz023]

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A Western-type dietary pattern and atorvastatin induce epicardial adipose tissue interferon signaling in the Ossabaw pig.

Maura E Walker, Nirupa R Matthan, Gloria Solano-Aguilar, Saebyeol Jang, Sukla Lakshman, Aleksey Molokin, Tyler Faits, Joseph F Urban, W Evan Johnson, Stefania Lamon-Fava, Alice H Lichtenstein,

Epicardial adipose tissue (EAT) inflammation is thought to potentiate the development of coronary artery disease (CAD). Overall diet quality and statin therapy are important modulators of inflammation and CAD progression. Our objective was to examine the effects and interaction of dietary patterns and statin therapy on EAT gene expression in ... Read more >>

J Nutr Biochem (The Journal of nutritional biochemistry)
[2019, 67:212-218]

Cited: 1 time

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Exploring Host-Microbe Interactions in Lung Cancer.

Yue Zhao, W Evan Johnson,

Am. J. Respir. Crit. Care Med. (American journal of respiratory and critical care medicine)
[2018, 198(9):1116-1118]

Cited: 0 times

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Alternative empirical Bayes models for adjusting for batch effects in genomic studies.

Yuqing Zhang, David F Jenkins, Solaiappan Manimaran, W Evan Johnson,

BACKGROUND:Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or require the sequential generation of data. However, significant technical heterogeneity is commonly observed across multiple batches of data that are generated from different processing or reagent batches, experimenters, ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2018, 19(1):262]

Cited: 1 time

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Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK)

David Jenkins, Tyler Faits, Emma Briars, Sebastian Carrasco Pro, Steve Cunningham, Joshua Campbell, Masanao Yajima, Evan Johnson,

Abstract Single cell RNA-sequencing (scRNA-Seq) allows researchers to profile transcriptional activity in individual cells. However, the complex nature of these data and variability in study design and data generation requires sophisticated computational tools and informed analytical decisions. Here, we present the Single Cell Toolkit (SCTK), an interactive scRNA-Seq analysis package ... Read more >>

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Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India.

Samantha Leong, Yue Zhao, Noyal M Joseph, Natasha S Hochberg, Sonali Sarkar, Jane Pleskunas, David Hom, Subitha Lakshminarayanan, C Robert Horsburgh, Gautam Roy, Jerrold J Ellner, W Evan Johnson, Padmini Salgame,

Several studies have identified blood transcriptomic signatures that can distinguish active from latent Tuberculosis (TB). The purpose of this study was to assess how well these existing gene profiles classify TB disease in a South Indian population. RNA sequencing was performed on whole blood PAXgene samples collected from 28 TB patients ... Read more >>

Tuberculosis (Edinb) (Tuberculosis (Edinburgh, Scotland))
[2018, 109:41-51]

Cited: 5 times

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Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.

Samuel W Brady, Jasmine A McQuerry, Yi Qiao, Stephen R Piccolo, Gajendra Shrestha, David F Jenkins, Ryan M Layer, Brent S Pedersen, Ryan H Miller, Amanda Esch, Sara R Selitsky, Joel S Parker, Layla A Anderson, Brian K Dalley, Rachel E Factor, Chakravarthy B Reddy, Jonathan P Boltax, Dean Y Li, Philip J Moos, Joe W Gray, Laura M Heiser, Saundra S Buys, Adam L Cohen, W Evan Johnson, Aaron R Quinlan, Gabor Marth, Theresa L Werner, Andrea H Bild,

The originally published version of this Article contained an error in Figure 4. In panel a, grey boxes surrounding the subclones associated with patients #2 and #4 obscured adjacent portions of the heatmap. This error has now been corrected in both the PDF and HTML versions of the Article. ... Read more >>

Nat Commun (Nature communications)
[2018, 9(1):572]

Cited: 0 times

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Combating subclonal evolution of resistant cancer phenotypes.

Samuel W Brady, Jasmine A McQuerry, Yi Qiao, Stephen R Piccolo, Gajendra Shrestha, David F Jenkins, Ryan M Layer, Brent S Pedersen, Ryan H Miller, Amanda Esch, Sara R Selitsky, Joel S Parker, Layla A Anderson, Brian K Dalley, Rachel E Factor, Chakravarthy B Reddy, Jonathan P Boltax, Dean Y Li, Philip J Moos, Joe W Gray, Laura M Heiser, Saundra S Buys, Adam L Cohen, W Evan Johnson, Aaron R Quinlan, Gabor Marth, Theresa L Werner, Andrea H Bild,

Metastatic breast cancer remains challenging to treat, and most patients ultimately progress on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations (subclones) within heterogeneous tumors. Here, we track the genetic and phenotypic subclonal evolution of four breast cancers through years of treatment to better understand how breast ... Read more >>

Nat Commun (Nature communications)
[2017, 8(1):1231]

Cited: 17 times

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Shared Gene Expression Alterations in Nasal and Bronchial Epithelium for Lung Cancer Detection.

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Background:We previously derived and validated a bronchial epithelial gene expression biomarker to detect lung cancer in current and former smokers. Given that bronchial and nasal epithelial gene expression are similarly altered by cigarette smoke exposure, we sought to determine if cancer-associated gene expression might also be detectable in the more ... Read more >>

J. Natl. Cancer Inst. (Journal of the National Cancer Institute)
[2017, 109(7):]

Cited: 5 times

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Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

Mumtahena Rahman, Shelley M MacNeil, David F Jenkins, Gajendra Shrestha, Sydney R Wyatt, Jasmine A McQuerry, Stephen R Piccolo, Laura M Heiser, Joe W Gray, W Evan Johnson, Andrea H Bild,

The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components, or pathways, and the inability to study complex signaling networks in patient tumors. Here, pathway-specific genomic signatures were used to ... Read more >>

Genome Med (Genome medicine)
[2017, 9(1):40]

Cited: 3 times

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Cytoplasmic FMR1-Interacting Protein 2 Is a Major Genetic Factor Underlying Binge Eating.

Stacey L Kirkpatrick, Lisa R Goldberg, Neema Yazdani, R Keith Babbs, Jiayi Wu, Eric R Reed, David F Jenkins, Amanda F Bolgioni, Kelsey I Landaverde, Kimberly P Luttik, Karen S Mitchell, Vivek Kumar, W Evan Johnson, Megan K Mulligan, Pietro Cottone, Camron D Bryant,

BACKGROUND:Eating disorders are lethal and heritable; however, the underlying genetic factors are unknown. Binge eating is a highly heritable trait associated with eating disorders that is comorbid with mood and substance use disorders. Therefore, understanding its genetic basis will inform therapeutic development that could improve several comorbid neuropsychiatric conditions. METHODS:We ... Read more >>

Biol Psychiatry (Biological psychiatry)
[2017, 81(9):757-769]

Cited: 18 times

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BatchQC: interactive software for evaluating sample and batch effects in genomic data.

Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T Leek, John Quackenbush, Benjamin Haibe-Kains, Hector Corrada Bravo, W Evan Johnson,

Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are several existing batch adjustment tools for '-omics' data, but they do not indicate a priori whether adjustment ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2016, 32(24):3836-3838]

Cited: 8 times

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Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50-60Mb) exhibiting reduced methamphetamine sensitivity.

Neema Yazdani, Ying Shen, W Evan Johnson, Camron D Bryant,

Addiction to psychostimulants such as Methamphetamine (MA) is a significant public health issue in the United States and currently, there are no FDA approved pharmacological interventions. Previously, using short term-selected mouse lines for high and low MA sensitivity that were derived from an F2 cross between C57BL/6J (B6) and DBA/2J ... Read more >>

(Genomics data)
[2016, 8:77-80]

Cited: 2 times

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Discovery and Subsequent Confirmation of Novel Serum Biomarkers Diagnosing Alzheimer's Disease.

Dipti Jigar Shah, Frederick Rohlfing, Swati Anand, W Evan Johnson, MeiHwa Tanielle Bench Alvarez, Jesse Cobell, Jackson King, Sydney A Young, John S K Kauwe, Steven W Graves,

Alzheimer's disease (AD) remains challenging to diagnose, especially early disease. Having serum AD biomarkers would be of significant interest both in the clinical setting and in drug development efforts.We applied a novel serum proteomic approach to interrogate the low-molecular weight proteome for serum AD biomarkers.A discovery study used sera from ... Read more >>

J. Alzheimers Dis. (Journal of Alzheimer's disease : JAD)
[2016, 49(2):317-327]

Cited: 3 times

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Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

Stephen R Piccolo, Irene L Andrulis, Adam L Cohen, Thomas Conner, Philip J Moos, Avrum E Spira, Saundra S Buys, W Evan Johnson, Andrea H Bild,

Women with a family history of breast cancer face considerable uncertainty about whether to pursue standard screening, intensive screening, or prophylactic surgery. Accurate and individualized risk-estimation approaches may help these women make more informed decisions. Although highly penetrant genetic variants have been associated with familial breast cancer (FBC) risk, many ... Read more >>

BMC Med Genomics (BMC medical genomics)
[2015, 8:72]

Cited: 3 times

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