William Johnson | Profiles RNS

William Evan Johnson, PhD

Adjunct Associate Professor

Boston University Chobanian & Avedisian School of Medicine

Medicine

Computational Biomedicine

PhD, Harvard University
MA, Harvard University
MS, Brigham Young University
BS, Southern Utah University

Websites

	Computational Biomedicine Faculty
	Google Scholar
	NCBI
	Twitter
	LinkedIn
	Lab

ORCID : 0000-0002-6247-6595

Evan Johnson specializes in computational biology and biostatistics, developing new tools to investigate disease prognoses and causes and to help determine effective regimens based on individual patients’ risk factors. He has published in the journals Cell, Proceedings of the National Academy of Sciences, Biometrics, Nature Reviews Genetics, Annals of Applied Statistics, and Biostatistics. His work has been funded by the NIH.

The focus of his group's research is to develop computational and statistical tools to investigate core components that contribute to disease prognosis and etiology, and for the accurate determination of optimal diagnostic, prognostic, and therapeutic regimens for individual patients. They are actively developing methods and software tools for data preprocessing, integration, and downstream analysis, and applying these tools in a variety of clinical and biomedical applications. Their work includes a balance between statistical methods development, algorithm optimization, and clinical application. Statistical innovation focuses on the development of clinically motivated tools that integrate linear modeling, Bayesian methods, factor analysis and structural equations models, Hidden Markov models, mixture models, dynamic programming, and high-performance parallel computing. This work has resulted in widely used tools and algorithms for profiling transcription factors (MAT, MA2C), preprocessing and integrating of genomic data (ComBat, BatchQC, SCAN-UPC), aligning sequencing reads (GNUMAP), developing multi-gene biomarker signatures (ASSIGN), and metagenomic profiling (PathoScope). They have successfully applied their tools in several biomedical and clinical scenarios, ranging from mechanistic studies and to precision genomics.

Adjunct Associate Professor
Boston University School of Public Health
Biostatistics

Member
Boston University
BU-BMC Cancer Center

Member
Boston University
Evans Center for Interdisciplinary Biomedical Research

Full Member
Boston University Medical Center
Boston Nutrition Obesity Research Center

Member
Boston University
Bioinformatics Graduate Program

Member
Boston University
Genome Science Institute

Graduate Faculty (Primary Mentor of Grad Students)
Boston University Chobanian & Avedisian School of Medicine, Graduate Medical Sciences

Founding Associate Professor
Boston University
Computing & Data Sciences Administration

BU Research
NIH RePORTER Research

Microbial Dysbiosis and Epithelial Dysfunction in Vitamin A-deficient Lungs
04/01/2023 - 03/31/2025 (Key Person / Mentor)
NIH/National Heart, Lung, and Blood Institute
5F31HL162523-02

Signature profiling and staging the progression of TB from infection to disease.
07/10/2020 - 06/30/2023 (PI)
NIH/National Institute of Allergy & Infectious Diseases
5R21AI154387-02

Dynamics and immune mechanisms of QFT response in close contacts of TB cases
05/01/2022 - 04/30/2023 (Subcontract PI)
U.S. Civilian Research and Development Foundation National Science Fdn
OISE-9531011

Microbiome-based biomarkers and models of lung cancer development and treatment
12/08/2021 - 08/31/2022 (Multi-PI)
PI: William Evan Johnson, PhD
NIH/National Cancer Institute
1R21CA260382-01A1

Removing batch effects in genomic and epigenomic studies
05/01/2018 - 08/31/2022 (PI)
NIH/National Institute of General Medical Sciences
5R01GM127430-04

Bacterial and Host Heterogeneity in TB latency, persistence and progression
09/23/2021 - 06/30/2022 (Subcontract PI)
Rutgers, The State University of New Jersey NIH NIAID
1U19AI162598-01

Epidemiologic and Genomic Evaluation of Influenza D Among Catlte Workers and Their Community
09/01/2018 - 12/31/2021 (Key Person / Mentor)
PI: Jessica Leibler, DrPH, MS
HHS/CDC/National Institute for Occupational Safety and Health

CFAR Developmental Award: Impact of TB and HIV co-infection on host and microbial gene expression in the upper airway
12/01/2019 - 11/30/2021 (Subcontract PI)
The Miriam Hospital NIH NIAID
5P30AI042853-21

An interactive analysis toolkit for single cell RNA-seq in cancer research
08/01/2017 - 07/31/2021 (PI)
NIH/National Cancer Institute
5U01CA220413-03

Preprocessing and Analysis Tools for High-Throughput Technologies
09/01/2016 - 06/30/2019 (Subcontract PI)
Dana-Farber Cancer Institute NIH NIGMS
5R01GM083084-13

Showing 10 of 15 results. Show All Results

Title

Yr	Title	Project-Sub Proj
2024	Biomarker Signatures of TB Infection in Young Children With and Without HIV	5R01AI175315-02
2024	Systems Biology Core	5U19AI162598-04-6542
2024	Removing batch effects in high-throughput biomedical studies	5R01GM127430-07
2023	Biomarker Signatures of TB Infection in Young Children With and Without HIV	1R01AI175315-01
2023	Microbiome-based biomarkers and models of lung cancer development and treatment	7R21CA260382-02
2023	Systems Biology Core	7U19AI162598-03-6542
2023	Removing batch effects in high-throughput biomedical studies	2R01GM127430-06A1
2022	Microbiome-based biomarkers and models of lung cancer development and treatment	1R21CA260382-01A1
2022	Systems Biology Core	5U19AI162598-02-6542
2021	Systems Biology Core	1U19AI162598-01-6542

Showing 10 of 32 results. Show All Results

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Sanchez GM, Hirsch ES, VanValkenburg A, Mayer DP, Gbedande K, Francis RL, Song W, Antao OQ, Brimmer KE, Lemenze A, Stephens R, Johnson WE, Weinstein JS. Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus. Cell Rep. 2024 Nov 26; 43(11):114978.View Related Profiles.

VanValkenburg, Arthur
Johnson, William

PMID: 39527476

Odom AR, Gill CJ, Pieciak R, Ismail A, Thea D, MacLeod WB, Johnson WE, Lapidot R. Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants. Gates Open Res. 2022; 6:143.View Related Profiles.

Odom, Aubrey
Thea, Donald
Lapidot, Rotem
MacLeod, William
Johnson, William

PMID: 39345284; PMCID: PMC11427455; DOI: 10.12688/gatesopenres.14041.2;

Quiles KR, Shao FZ, Johnson WE, Chen F. EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS. bioRxiv. 2024 Jun 22. PMID: 38948802; PMCID: PMC11212965; DOI: 10.1101/2024.06.21.600110;

Wang X, VanValkenberg A, Odom AR, Ellner JJ, Hochberg NS, Salgame P, Patil P, Johnson WE. Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures. BMC Infect Dis. 2024 Jun 20; 24(1):610.View Related Profiles.

Odom, Aubrey
Hochberg, Natasha
Patil, Prasad
Johnson, William

PMID: 38902649; PMCID: PMC11191245; DOI: 10.1186/s12879-024-09457-z;

Gao X, Johnson WE, Yourick MR, Campasino K, Sprando RL, Yourick JJ. Hepatotoxicity of silver nanoparticles: Benchmark concentration modeling of an in vitro transcriptomics study in human iPSC-derived hepatocytes. Regul Toxicol Pharmacol. 2024 Aug; 151:105653. PMID: 38825064; DOI: 10.1016/j.yrtph.2024.105653;

Goldberg LR, Baskin BM, Adla Y, Beierle JA, Kelliher JC, Yao EJ, Kirkpatrick SL, Reed ER, Jenkins DF, Luong AM, Luttik KP, Scotellaro JA, Drescher TA, Crotts SB, Yazdani N, Ferris MT, Johnson WE, Mulligan MK, Bryant CD. Atp1a2 and Kcnj9 are candidate genes underlying oxycodone behavioral sensitivity and withdrawal in C57BL/6 substrains. bioRxiv. 2024 Apr 17.View Related Profiles.

Baskin, Britahny
Beierle, Jacob
Goldberg, Lisa
Yazdani, Neema
Johnson, William

PMID: 38798314; PMCID: PMC11123399; DOI: 10.1101/2024.04.16.589731;

Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res. 2022; 6:48.View Related Profiles.

Thea, Donald
Lapidot, Rotem
MacLeod, William
Johnson, William

PMID: 39050991; PMCID: PMC11266592; DOI: 10.12688/gatesopenres.13561.2;

Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Alekseev Y, Ma Q, Dayama G, Lau NC, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I. Myc Dysregulation in Activated Macrophages Initiates Iron-Mediated Lipid Peroxidation that Fuels Type I Interferon and Compromises TB Resistance. bioRxiv. 2024 Mar 10.View Related Profiles.

VanValkenburg, Arthur
Kramnik, Igor
Lau, Nelson
Crossland, Nicholas
Araveti, Prasanna
Yabaji, Shivraj
Lata, Suruchi
Johnson, William

PMID: 38496444; PMCID: PMC10942339; DOI: 10.1101/2024.03.05.583602;

Barnard ME, Wang X, Petrick JL, Zirpoli GR, Jones D, Johnson WE, Palmer JR. Psychosocial stressors and breast cancer gene expression in the Black Women's Health Study. Breast Cancer Res Treat. 2024 Apr; 204(2):327-340.View Related Profiles.

Jones, Dennis
Zirpoli, Gary
Petrick, Jessica
Palmer, Julie
Barnard, Mollie
Johnson, William

PMID: 38127176; PMCID: PMC11232497; DOI: 10.1007/s10549-023-07182-w;

Odom AR, McClintock J, Gill CJ, Pieciak R, Ismail A, MacLeod WB, Johnson WE, Lapidot R. Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness. bioRxiv. 2023 Sep 28.View Related Profiles.

Odom, Aubrey
Lapidot, Rotem
MacLeod, William
Johnson, William

PMID: 37808661; PMCID: PMC10557644; DOI: 10.1101/2023.09.27.559805;

Showing 10 of 124 results. Show More

Odom AR, Faits T, Castro-Nallar E, Crandall KA, Johnson WE. Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data. Sci Rep. 2023 Aug 26; 13(1):13957.View Related Profiles.

Odom, Aubrey
Johnson, William

PMID: 37633998; PMCID: PMC10460424; DOI: 10.1038/s41598-023-40799-x;

Khan MM, Frustino J, Villa A, Nguyen BC, Woo SB, Johnson WE, Varelas X, Kukuruzinska M, Monti S. Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer. Hum Genomics. 2023 Aug 04; 17(1):72.View Related Profiles.

Kukuruzinska, Maria
Khan, Mohammed
Monti, Stefano
Johnson, William
Varelas, Xaralabos

PMID: 37542347; PMCID: PMC10403884; DOI: 10.1186/s40246-023-00519-y;

Wang Y, Sarfraz I, Pervaiz N, Hong R, Koga Y, Akavoor V, Cao X, Alabdullatif S, Zaib SA, Wang Z, Jansen F, Yajima M, Johnson WE, Campbell JD. Interactive analysis of single-cell data using flexible workflows with SCTK2. Patterns (N Y). 2023 Aug 11; 4(8):100814.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 37602214; PMCID: PMC10436054; DOI: 10.1016/j.patter.2023.100814;

Li T, Zhang Y, Patil P, Johnson WE. Overcoming the impacts of two-step batch effect correction on gene expression estimation and inference. Biostatistics. 2023 Jul 14; 24(3):635-652. PMID: 34893807; PMCID: PMC10449015; DOI: 10.1093/biostatistics/kxab039;

McClintock J, Odom-Mabey AR, Kebere N, Ismail A, Mwananyanda L, Gill CJ, MacLeod WB, Pieciak RC, Lapidot R, Johnson WE. Postmortem Nasopharyngeal Microbiome Analysis of Zambian Infants With and Without Respiratory Syncytial Virus Disease: A Nested Case Control Study. Pediatr Infect Dis J. 2023 Aug 01; 42(8):637-643.View Related Profiles.

Odom, Aubrey
Gill, Christopher
Mwananyanda, Lawrence
Lapidot, Rotem
MacLeod, William
Johnson, William

PMID: 37093853; PMCID: PMC10348642; DOI: 10.1097/INF.0000000000003941;

Barathi A, Krishnamoorthy Y, Sinha P, Horsburgh C, Hochberg N, Johnson E, Salgame P, Govindarajan S, Senbagavalli PB, Lakshinarayanan S, Roy G, Ellner J, Sarkar S. Effect of treatment adherence on the association between sex and unfavourable treatment outcomes among tuberculosis patients in Puducherry, India: a mediation analysis. J Public Health (Oxf). 2023 Jun 14; 45(2):304-311.View Related Profiles.

Ellner, Jerrold
Hochberg, Natasha
Sinha, Pranay
Johnson, William

PMID: 35692180; PMCID: PMC10273348; DOI: 10.1093/pubmed/fdac062;

Krishnamoorthy Y, Ezhumalai K, Murali S, Rajaa S, Majella MG, Sarkar S, Lakshminarayanan S, Joseph NM, Soundappan G, Prakash Babu S, Horsburgh C, Hochberg N, Johnson WE, Knudsen S, Pentakota SR, Salgame P, Roy G, Ellner J. Development of prognostic scoring system for predicting 1-year mortality among pulmonary tuberculosis patients in South India. J Public Health (Oxf). 2023 Jun 14; 45(2):e184-e195.View Related Profiles.

Horsburgh, C.
Hochberg, Natasha
Johnson, William

PMID: 36038507; PMCID: PMC10273380; DOI: 10.1093/pubmed/fdac087;

Hawkins DY, Zuch DT, Huth J, Rodriguez-Sastre N, McCutcheon KR, Glick A, Lion AT, Thomas CF, Descoteaux AE, Johnson WE, Bradham CA. ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes. Bioinformatics. 2023 May 04; 39(5).View Related Profiles.

Bradham, Cynthia
Johnson, William

PMID: 37086439; PMCID: PMC10172037; DOI: 10.1093/bioinformatics/btad278;

Kukuruzinska, Maria
Khan, Mohammed
Monti, Stefano
Johnson, William
Varelas, Xaralabos

PMID: 36993637; PMCID: PMC10055367; DOI: 10.1101/2023.03.24.534064;

Wang X, VanValkenberg A, Odom-Mabey AR, Ellner JJ, Hochberg NS, Salgame P, Patil P, Johnson WE. Comparison of gene set scoring methods for reproducible evaluation of multiple tuberculosis gene signatures. bioRxiv. 2023 Jan 30.View Related Profiles.

Hochberg, Natasha
Patil, Prasad
Johnson, William

PMID: 36711818; PMCID: PMC9882404; DOI: 10.1101/2023.01.19.520627;

Chitale P, Lemenze AD, Fogarty EC, Shah A, Grady C, Odom-Mabey AR, Johnson WE, Yang JH, Eren AM, Brosch R, Kumar P, Alland D. Author Correction: A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome. Nat Commun. 2022 Dec 07; 13(1):7538. PMID: 36477679; PMCID: PMC9729191; DOI: 10.1038/s41467-022-35402-2;

Chitale P, Lemenze AD, Fogarty EC, Shah A, Grady C, Odom-Mabey AR, Johnson WE, Yang JH, Eren AM, Brosch R, Kumar P, Alland D. A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome. Nat Commun. 2022 Nov 18; 13(1):7068.View Related Profiles.

Odom, Aubrey
Johnson, William

PMID: 36400796; PMCID: PMC9673877; DOI: 10.1038/s41467-022-34853-x;

Leibler JH, Abdelgadir A, Seidel J, White RF, Johnson WE, Reynolds SJ, Gray GC, Schaeffer JW. Influenza D virus exposure among US cattle workers: A call for surveillance. Zoonoses Public Health. 2023 Mar; 70(2):166-170.View Related Profiles.

Leibler, Jessica
White, Roberta
Johnson, William

PMID: 36370131; PMCID: PMC10099784; DOI: 10.1111/zph.13008;

VanValkenburg A, Kaipilyawar V, Sarkar S, Lakshminarayanan S, Cintron C, Babu SP, Knudsen S, Joseph NM, Horsburgh CR, Sinha P, Ellner JJ, Narasimhan PB, Johnson WE, Hochberg NS, Salgame P. Corrigendum: Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis. Front Immunol. 2022; 13:1064883.View Related Profiles.

VanValkenburg, Arthur
Hochberg, Natasha
Sinha, Pranay
Johnson, William

PMID: 36341454; PMCID: PMC9632611; DOI: 10.3389/fimmu.2022.1064883;

Kaipilyawar V, Zhao Y, Wang X, Joseph NM, Knudsen S, Prakash Babu S, Muthaiah M, Hochberg NS, Sarkar S, Horsburgh CR, Ellner JJ, Johnson WE, Salgame P. Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoString nCounter Platform. Clin Infect Dis. 2022 Sep 29; 75(6):1022-1030.View Related Profiles.

Ellner, Jerrold
Hochberg, Natasha
Johnson, William

PMID: 35015839; PMCID: PMC9522394; DOI: 10.1093/cid/ciac010;

VanValkenburg A, Kaipilyawar V, Sarkar S, Lakshminarayanan S, Cintron C, Prakash Babu S, Knudsen S, Joseph NM, Horsburgh CR, Sinha P, Ellner JJ, Narasimhan PB, Johnson WE, Hochberg NS, Salgame P. Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis. Front Immunol. 2022; 13:1011166.View Related Profiles.

VanValkenburg, Arthur
Hochberg, Natasha
Sinha, Pranay
Johnson, William

PMID: 36248906; PMCID: PMC9554585; DOI: 10.3389/fimmu.2022.1011166;

Wang Z, Yang S, Koga Y, Corbett SE, Shea CV, Johnson WE, Yajima M, Campbell JD. Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data. NAR Genom Bioinform. 2022 Sep; 4(3):lqac066.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 36110899; PMCID: PMC9469931; DOI: 10.1093/nargab/lqac066;

Sheerin D, Abhimanyu, Peton N, Vo W, Allison CC, Wang X, Johnson WE, Coussens AK. Immunopathogenic overlap between COVID-19 and tuberculosis identified from transcriptomic meta-analysis and human macrophage infection. iScience. 2022 Jun 17; 25(6):104464. PMID: 35634577; PMCID: PMC9130411; DOI: 10.1016/j.isci.2022.104464;

Hong R, Koga Y, Bandyadka S, Leshchyk A, Wang Y, Akavoor V, Cao X, Sarfraz I, Wang Z, Alabdullatif S, Jansen F, Yajima M, Johnson WE, Campbell JD. Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data. Nat Commun. 2022 Mar 30; 13(1):1688.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 35354805; PMCID: PMC8967915; DOI: 10.1038/s41467-022-29212-9;

Petrick JL, Wilkinson JE, Michaud DS, Cai Q, Gerlovin H, Signorello LB, Wolpin BM, Ruiz-Narváez EA, Long J, Yang Y, Johnson WE, Shu XO, Huttenhower C, Palmer JR. The oral microbiome in relation to pancreatic cancer risk in African Americans. Br J Cancer. 2022 02; 126(2):287-296.View Related Profiles.

Petrick, Jessica
Palmer, Julie
Johnson, William

PMID: 34718358; PMCID: PMC8770575; DOI: 10.1038/s41416-021-01578-5;

Huang X, Qiao Y, Brady SW, Factor RE, Downs-Kelly E, Farrell A, McQuerry JA, Shrestha G, Jenkins D, Johnson WE, Cohen AL, Bild AH, Marth GT. Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies. Genome Med. 2021 Oct 28; 13(1):170. PMID: 34711268; PMCID: PMC8555066; DOI: 10.1186/s13073-021-00989-6;

Krishnamoorthy Y, Ezhumalai K, Murali S, Rajaa S, Jose M, Sathishkumar A, Soundappan G, Horsburgh C, Hochberg N, Johnson WE, Knudsen S, Salgame P, Ellner J, Prakash Babu S, Sarkar S. Prevalence and risk factors associated with latent tuberculosis infection among household contacts of smear positive pulmonary tuberculosis patients in South India. Trop Med Int Health. 2021 12; 26(12):1645-1651.View Related Profiles.

Horsburgh, C.
Ellner, Jerrold
Hochberg, Natasha
Johnson, William

PMID: 34654061

Goldberg LR, Yao EJ, Kelliher JC, Reed ER, Wu Cox J, Parks C, Kirkpatrick SL, Beierle JA, Chen MM, Johnson WE, Homanics GE, Williams RW, Bryant CD, Mulligan MK. A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity. Genes Brain Behav. 2021 11; 20(8):e12774.View Related Profiles.

Bryant, Camron
Beierle, Jacob
Goldberg, Lisa
Johnson, William

PMID: 34677900; PMCID: PMC9083095; DOI: 10.1111/gbb.12774;

Cintron C, Narasimhan PB, Locks L, Babu S, Sinha P, Rajkumari N, Kaipilyawar V, Bhargava A, Maloomian K, Chandrasekaran P, Verma S, Joseph N, Johnson WE, Wanke C, Horsburgh CR, Ellner JJ, Sarkar S, Salgame P, Lakshminarayanan S, Hochberg NS. Tuberculosis-Learning the Impact of Nutrition (TB LION): protocol for an interventional study to decrease TB risk in household contacts. BMC Infect Dis. 2021 Oct 12; 21(1):1058.View Related Profiles.

Horsburgh, C.
Ellner, Jerrold
Locks, Lindsey
Hochberg, Natasha
Sinha, Pranay
Johnson, William

PMID: 34641820; PMCID: PMC8506078; DOI: 10.1186/s12879-021-06734-z;

Borrelli KN, Yao EJ, Yen WW, Phadke RA, Ruan QT, Chen MM, Kelliher JC, Langan CR, Scotellaro JL, Babbs RK, Beierle JC, Logan RW, Johnson WE, Wachman EM, Cruz-Martín A, Bryant CD. Sex Differences in Behavioral and Brainstem Transcriptomic Neuroadaptations following Neonatal Opioid Exposure in Outbred Mice. eNeuro. 2021 Sep-Oct; 8(5).View Related Profiles.

Bryant, Camron
Wachman, Elisha
Borrelli, Kristyn
Logan, Ryan
Johnson, William

PMID: 34479978; PMCID: PMC8454922; DOI: 10.1523/ENEURO.0143-21.2021;

Delpech JC, Pathak D, Varghese M, Kalavai SV, Hays EC, Hof PR, Johnson WE, Ikezu S, Medalla M, Luebke JI, Ikezu T. Wolframin-1-expressing neurons in the entorhinal cortex propagate tau to CA1 neurons and impair hippocampal memory in mice. Sci Transl Med. 2021 09 15; 13(611):eabe8455.View Related Profiles.

Luebke, Jennifer
Medalla, Maria
Ikezu, Seiko
Ikezu, Tsuneya
Johnson, William

PMID: 34524859; PMCID: PMC8763211; DOI: 10.1126/scitranslmed.abe8455;

Zhang Y, Patil P, Johnson WE, Parmigiani G. Robustifying genomic classifiers to batch effects via ensemble learning. Bioinformatics. 2021 07 12; 37(11):1521-1527.View Related Profiles.

Patil, Prasad
Johnson, William

PMID: 33245114; PMCID: PMC8485848; DOI: 10.1093/bioinformatics/btaa986;

Braun MR, Noton SL, Blanchard EL, Shareef A, Santangelo PJ, Johnson WE, Fearns R. Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts. PLoS Pathog. 2021 05; 17(5):e1009589.View Related Profiles.

Fearns, Rachel
Noton, Sarah
Johnson, William

PMID: 34003848; PMCID: PMC8162694; DOI: 10.1371/journal.ppat.1009589;

Zhao Y, Federico A, Faits T, Manimaran S, Segrè D, Monti S, Johnson WE. animalcules: interactive microbiome analytics and visualization in R. Microbiome. 2021 03 28; 9(1):76.View Related Profiles.

Segre, Daniel
Monti, Stefano
Johnson, William

PMID: 33775256; PMCID: PMC8006385; DOI: 10.1186/s40168-021-01013-0;

Johnson WE, Odom A, Cintron C, Muthaiah M, Knudsen S, Joseph N, Babu S, Lakshminarayanan S, Jenkins DF, Zhao Y, Nankya E, Horsburgh CR, Roy G, Ellner J, Sarkar S, Salgame P, Hochberg NS. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis. 2021 Jan 22; 21(1):106.View Related Profiles.

Odom, Aubrey
Horsburgh, C.
Ellner, Jerrold
Hochberg, Natasha
Johnson, William

PMID: 33482742; PMCID: PMC7821401; DOI: 10.1186/s12879-020-05598-z;

Manabe YC, Andrade BB, Gupte N, Leong S, Kintali M, Matoga M, Riviere C, Samaneka W, Lama JR, Naidoo K, Zhao Y, Johnson WE, Ellner JJ, Hosseinipour MC, Bisson GP, Salgame P, Gupta A. A Parsimonious Host Inflammatory Biomarker Signature Predicts Incident Tuberculosis and Mortality in Advanced Human Immunodeficiency Virus. Clin Infect Dis. 2020 12 17; 71(10):2645-2654.View Related Profiles.

Ellner, Jerrold
Johnson, William

PMID: 31761933; PMCID: PMC7744990; DOI: 10.1093/cid/ciz1147;

Faits T, Walker ME, Rodriguez-Morato J, Meng H, Gervis JE, Galluccio JM, Lichtenstein AH, Johnson WE, Matthan NR. 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. Am J Clin Nutr. 2020 12 10; 112(6):1631-1641.View Related Profiles.

Walker, Maura
Johnson, William

PMID: 32936872; PMCID: PMC7727488; DOI: 10.1093/ajcn/nqaa254;

Sheerin D, Abhimanyu, Wang X, Johnson WE, Coussens A. Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis. medRxiv. 2020 Nov 26. PMID: 33269371; PMCID: PMC7709192; DOI: 10.1101/2020.11.25.20236646;

Zhang Y, Parmigiani G, Johnson WE. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom Bioinform. 2020 Sep; 2(3):lqaa078. PMID: 33015620; PMCID: PMC7518324; DOI: 10.1093/nargab/lqaa078;

Miossec MJ, Valenzuela SL, Pérez-Losada M, Johnson WE, Crandall KA, Castro-Nallar E. Evaluation of computational methods for human microbiome analysis using simulated data. PeerJ. 2020; 8:e9688. PMID: 32864214; PMCID: PMC7427543; DOI: 10.7717/peerj.9688;

Ruan QT, Yazdani N, Reed ER, Beierle JA, Peterson LP, Luttik KP, Szumlinski KK, Johnson WE, Ash PEA, Wolozin B, Bryant CD. 5' UTR variants in the quantitative trait gene Hnrnph1 support reduced 5' UTR usage and hnRNP H protein as a molecular mechanism underlying reduced methamphetamine sensitivity. FASEB J. 2020 07; 34(7):9223-9244.View Related Profiles.

Wolozin, Benjamin
Bryant, Camron
Reed, Eric
Beierle, Jacob
Yazdani, Neema
Ash, Peter
Johnson, William

PMID: 32401417; PMCID: PMC8006537; DOI: 10.1096/fj.202000092R;

Babbs RK, Beierle JA, Yao EJ, Kelliher JC, Medeiros AR, Anandakumar J, Shah AA, Chen MM, Johnson WE, Bryant CD. The effect of the demyelinating agent cuprizone on binge-like eating of sweetened palatable food in female and male C57BL/6 substrains. Appetite. 2020 07 01; 150:104678.View Related Profiles.

Bryant, Camron
Beierle, Jacob
Johnson, William

PMID: 32209386; PMCID: PMC7206526; DOI: 10.1016/j.appet.2020.104678;

Yang S, Corbett SE, Koga Y, Wang Z, Johnson WE, Yajima M, Campbell JD. Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biol. 2020 03 05; 21(1):57.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 32138770; PMCID: PMC7059395; DOI: 10.1186/s13059-020-1950-6;

Ikezu S, Yeh H, Delpech JC, Woodbury ME, Van Enoo AA, Ruan Z, Sivakumaran S, You Y, Holland C, Guillamon-Vivancos T, Yoshii-Kitahara A, Botros MB, Madore C, Chao PH, Desani A, Manimaran S, Kalavai SV, Johnson WE, Butovsky O, Medalla M, Luebke JI, Ikezu T. Inhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities. Mol Psychiatry. 2021 06; 26(6):1808-1831.View Related Profiles.

Luebke, Jennifer
Medalla, Maria
Woodbury, Maya
Ikezu, Seiko
Ikezu, Tsuneya
Johnson, William
You, Yang
Ruan, Zhi

PMID: 32071385; PMCID: PMC7431382; DOI: 10.1038/s41380-020-0671-2;

Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer. 2020 03; 6(3):192-204. PMID: 32101723; PMCID: PMC7098063; DOI: 10.1016/j.trecan.2020.01.004;

Leong S, Zhao Y, Ribeiro-Rodrigues R, Jones-López EC, Acuña-Villaorduña C, Rodrigues PM, Palaci M, Alland D, Dietze R, Ellner JJ, Johnson WE, Salgame P. 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. Tuberculosis (Edinb). 2020 01; 120:101898.View Related Profiles.

Ellner, Jerrold
Johnson, William

PMID: 32090859; PMCID: PMC7066850; DOI: 10.1016/j.tube.2020.101898;

Buwembo W, Munabi IG, Kaddumukasa M, Kiryowa H, Mbabali M, Nankya E, Johnson WE, Okello E, Sewankambo NK. Non-surgical oral hygiene interventions on disease activity of Rheumatoid arthritis patients with periodontitis: A randomized controlled trial. J Dent Res Dent Clin Dent Prospects. 2020; 14(1):26-36. PMID: 32454955; PMCID: PMC7235694; DOI: 10.34172/joddd.2020.004;

Buwembo W, Munabi IG, Kaddumukasa M, Kiryowa H, Nankya E, Johnson WE, Okello E, Sewankambo N. Periodontitis and Rheumatoid Arthritis in sub-Saharan Africa, gaps and way forward: a systematic review and meta-analysis. Open J Stomatol. 2019 Oct; 9(10):215-226. PMID: 31695961; PMCID: PMC6834353; DOI: 10.4236/ojst.2019.910023;

McQuerry JA, Jenkins DF, Yost SE, Zhang Y, Schmolze D, Johnson WE, Yuan Y, Bild AH. Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. BMC Cancer. 2019 Sep 05; 19(1):881. PMID: 31488082; PMCID: PMC6727561; DOI: 10.1186/s12885-019-6052-z;

Wang Z, Hu J, Johnson WE, Campbell JD. scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data. BMC Bioinformatics. 2019 May 02; 20(1):222.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 31046658; PMCID: PMC6498700; DOI: 10.1186/s12859-019-2797-2;

Walker ME, Matthan NR, Lamon-Fava S, Solano-Aguilar G, Jang S, Lakshman S, Molokin A, Urban JF, Faits T, Johnson WE, Lichtenstein AH. A Western-Type Dietary Pattern Induces an Atherogenic Gene Expression Profile in the Coronary Arteries of the Ossabaw Pig. Curr Dev Nutr. 2019 May; 3(5):nzz023.View Related Profiles.

Walker, Maura
Johnson, William

PMID: 31049488; PMCID: PMC6488722; DOI: 10.1093/cdn/nzz023;

Walker ME, Matthan NR, Solano-Aguilar G, Jang S, Lakshman S, Molokin A, Faits T, Urban JF, Johnson WE, Lamon-Fava S, Lichtenstein AH. A Western-type dietary pattern and atorvastatin induce epicardial adipose tissue interferon signaling in the Ossabaw pig. J Nutr Biochem. 2019 05; 67:212-218.View Related Profiles.

Walker, Maura
Johnson, William

PMID: 30981985; PMCID: PMC6935368; DOI: 10.1016/j.jnutbio.2019.02.003;

Bryant CD, Bagdas D, Goldberg LR, Khalefa T, Reed ER, Kirkpatrick SL, Kelliher JC, Chen MM, Johnson WE, Mulligan MK, Imad Damaj M. C57BL/6 substrain differences in inflammatory and neuropathic nociception and genetic mapping of a major quantitative trait locus underlying acute thermal nociception. Mol Pain. 2019 Jan-Dec; 15:1744806918825046.View Related Profiles.

Bryant, Camron
Reed, Eric
Goldberg, Lisa
Johnson, William

PMID: 30632432; PMCID: PMC6365993; DOI: 10.1177/1744806918825046;

Zhao Y, Johnson WE. Exploring Host-Microbe Interactions in Lung Cancer. Am J Respir Crit Care Med. 2018 11 01; 198(9):1116-1118. PMID: 30063838

Zhang Y, Jenkins DF, Manimaran S, Johnson WE. Alternative empirical Bayes models for adjusting for batch effects in genomic studies. BMC Bioinformatics. 2018 07 13; 19(1):262. PMID: 30001694; PMCID: PMC6044013; DOI: 10.1186/s12859-018-2263-6;

Wang J, Huang M, Torre E, Dueck H, Shaffer S, Murray J, Raj A, Li M, Zhang NR. Gene expression distribution deconvolution in single-cell RNA sequencing. Proc Natl Acad Sci U S A. 2018 07 10; 115(28):E6437-E6446. PMID: 29946020; PMCID: PMC6048536; DOI: 10.1073/pnas.1721085115;

Griffin PJ, Zhang Y, Johnson WE, Kolaczyk ED. Detection of multiple perturbations in multi-omics biological networks. Biometrics. 2018 12; 74(4):1351-1361. PMID: 29772079

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2018 02 05; 9(1):572.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 29402882; PMCID: PMC5799176; DOI: 10.1038/s41467-017-02383-6;

Leong S, Zhao Y, Joseph NM, Hochberg NS, Sarkar S, Pleskunas J, Hom D, Lakshminarayanan S, Horsburgh CR, Roy G, Ellner JJ, Johnson WE, Salgame P. Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India. Tuberculosis (Edinb). 2018 03; 109:41-51.View Related Profiles.

Horsburgh, C.
Ellner, Jerrold
Hochberg, Natasha
Johnson, William

PMID: 29559120

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2017 11 01; 8(1):1231.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 29093439; PMCID: PMC5666005; DOI: 10.1038/s41467-017-01174-3;

Goldberg LR, Kirkpatrick SL, Yazdani N, Luttik KP, Lacki OA, Keith Babbs R, Jenkins DF, Evan Johnson W, Bryant CD. Casein kinase 1-epsilon deletion increases mu opioid receptor-dependent behaviors and binge eating1. Genes Brain Behav. 2017 Sep; 16(7):725-738.View Related Profiles.

Bryant, Camron
Goldberg, Lisa
Yazdani, Neema
Johnson, William

PMID: 28594147; PMCID: PMC6180211; DOI: 10.1111/gbb.12397;

Shared Gene Expression Alterations in Nasal and Bronchial Epithelium for Lung Cancer Detection. J Natl Cancer Inst. 2017 Jul 01; 109(7).View Related Profiles.

Lenburg, Marc
Johnson, William

PMID: 28376173; PMCID: PMC6059169; DOI: 10.1093/jnci/djw327;

Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. Genome Med. 2017 Apr 26; 9(1):40.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 28446242; PMCID: PMC5406893; DOI: 10.1186/s13073-017-0429-x;

Rahman M, Macneil S, Jenkins DF, Johnson WE. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. Genome Medicine. 2017; 9(1). View Publication

Kirkpatrick SL, Goldberg LR, Yazdani N, Babbs RK, Wu J, Reed ER, Jenkins DF, Bolgioni AF, Landaverde KI, Luttik KP, Mitchell KS, Kumar V, Johnson WE, Mulligan MK, Cottone P, Bryant CD. Cytoplasmic FMR1-Interacting Protein 2 Is a Major Genetic Factor Underlying Binge Eating. Biol Psychiatry. 2017 May 01; 81(9):757-769.View Related Profiles.

Bolgioni-Smith, Amanda
Bryant, Camron
Mitchell, Karen
Goldberg, Lisa
Yazdani, Neema
Cottone, Pietro
Johnson, William

PMID: 27914629; PMCID: PMC5386810; DOI: 10.1016/j.biopsych.2016.10.021;

Lam S, Mandrekar SJ, Gesthalter Y, Allen Ziegler KL, Seisler DK, Midthun DE, Mao JT, Aubry MC, McWilliams A, Sin DD, Shaipanich T, Liu G, Johnson E, Bild A, Lenburg ME, Ionescu DN, Mayo J, Yi JE, Tazelaar H, Harmsen WS, Smith J, Spira AE, Beane J, Limburg PJ, Szabo E. A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia. Cancer Prev Res (Phila). 2016 Dec; 9(12):906-914.View Related Profiles.

Spira, Avrum
Liu, Gang
Beane-Ebel, Jennifer
Lenburg, Marc
Johnson, William

PMID: 27658890; PMCID: PMC5136333; DOI: 10.1158/1940-6207.CAPR-15-0254;

Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE. BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinformatics. 2016 Dec 15; 32(24):3836-3838. PMID: 27540268; PMCID: PMC5167063; DOI: 10.1093/bioinformatics/btw538;

Shrestha G, MacNeil SM, McQuerry JA, Jenkins DF, Sharma S, Bild AH. The value of genomics in dissecting the RAS-network and in guiding therapeutics for RAS-driven cancers. Semin Cell Dev Biol. 2016 10; 58:108-17. PMID: 27338857; PMCID: PMC5951171; DOI: 10.1016/j.semcdb.2016.06.012;

Yazdani N, Shen Y, Johnson WE, Bryant CD. Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50-60Mb) exhibiting reduced methamphetamine sensitivity. Genom Data. 2016 Jun; 8:77-80.View Related Profiles.

Bryant, Camron
Yazdani, Neema
Johnson, William

PMID: 27222804; PMCID: PMC4856813; DOI: 10.1016/j.gdata.2016.03.009;

Hilton SK, Castro-Nallar E, Pérez-Losada M, Toma I, McCaffrey TA, Hoffman EP, Siegel MO, Simon GL, Johnson WE, Crandall KA. Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology. Front Microbiol. 2016; 7:484. PMID: 27092134; PMCID: PMC4823605; DOI: 10.3389/fmicb.2016.00484;

Piccolo SR, Hoffman LM, Conner T, Shrestha G, Cohen AL, Marks JR, Neumayer LA, Agarwal CA, Beckerle MC, Andrulis IL, Spira AE, Moos PJ, Buys SS, Johnson WE, Bild AH. Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility. Mol Syst Biol. 2016 Mar 10; 12(3):860.View Related Profiles.

Spira, Avrum
Piccolo, Stephen
Johnson, William

PMID: 26969729; PMCID: PMC4812528; DOI: 10.15252/msb.20156506;

Yazdani N, Parker CC, Shen Y, Reed ER, Guido MA, Kole LA, Kirkpatrick SL, Lim JE, Sokoloff G, Cheng R, Johnson WE, Palmer AA, Bryant CD. Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity. PLoS Genet. 2015 Dec; 11(12):e1005713.View Related Profiles.

Bryant, Camron
Reed, Eric
Yazdani, Neema
Johnson, William

PMID: 26658939; PMCID: PMC4675533; DOI: 10.1371/journal.pgen.1005713;

Piccolo SR, Andrulis IL, Cohen AL, Conner T, Moos PJ, Spira AE, Buys SS, Johnson WE, Bild AH. Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility. BMC Med Genomics. 2015; 8:72.View Related Profiles.

Spira, Avrum
Piccolo, Stephen
Johnson, William

PMID: 26538066; PMCID: PMC4634735; DOI: 10.1186/s12920-015-0145-6;

Castro-Nallar E, Shen Y, Freishtat RJ, Pérez-Losada M, Manimaran S, Liu G, Johnson WE, Crandall KA. Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities. BMC Med Genomics. 2015; 8:50.View Related Profiles.

Liu, Gang
Johnson, William

PMID: 26277095; PMCID: PMC4537781; DOI: 10.1186/s12920-015-0121-1;

Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR. Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. Bioinformatics. 2015 Nov 15; 31(22):3666-72.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 26209429; PMCID: PMC4804769; DOI: 10.1093/bioinformatics/btv377;

MacNeil SM, Johnson WE, Li DY, Piccolo SR, Bild AH. Inferring pathway dysregulation in cancers from multiple types of omic data. Genome Med. 2015; 7(1):61.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 26170901; PMCID: PMC4499940; DOI: 10.1186/s13073-015-0189-4;

Hong C, Manimaran S, Johnson WE. PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets. Cancer Inform. 2014; 13(Suppl 1):167-76. PMID: 25983538; PMCID: PMC4429651; DOI: 10.4137/CIN.S13890;

Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong C, Johnson WE, Bass BL. Genome-wide profiling of the C. elegans dsRNAome. RNA. 2015 May; 21(5):786-800. PMID: 25805852; PMCID: PMC4408787; DOI: 10.1261/rna.048801.114;

Grubaugh ND, Sharma S, Krajacich BJ, Fakoli Iii LS, Bolay FK, Diclaro Ii JW, Johnson WE, Ebel GD, Foy BD, Brackney DE. Xenosurveillance: a novel mosquito-based approach for examining the human-pathogen landscape. PLoS Negl Trop Dis. 2015 Mar; 9(3):e0003628.View Related Profiles.

Sharma, Supriya
Johnson, William

PMID: 25775236; PMCID: PMC4361501; DOI: 10.1371/journal.pntd.0003628;

Mortenson JB, Heppler LN, Banks CJ, Weerasekara VK, Whited MD, Piccolo SR, Johnson WE, Thompson JW, Andersen JL. Histone deacetylase 6 (HDAC6) promotes the pro-survival activity of 14-3-3? via deacetylation of lysines within the 14-3-3? binding pocket. J Biol Chem. 2015 May 15; 290(20):12487-96.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 25770209; PMCID: PMC4432270; DOI: 10.1074/jbc.M114.607580;

Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA. Concordance and discordance of sequence survey methods for molecular epidemiology. PeerJ. 2015; 3:e761. PMID: 25737810; PMCID: PMC4338773; DOI: 10.7717/peerj.761;

Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. Bioinformatics. 2015 Jun 1; 31(11):1745-53.View Related Profiles.

Monti, Stefano
Piccolo, Stephen
Johnson, William

PMID: 25617415; PMCID: PMC4443674; DOI: 10.1093/bioinformatics/btv031;

Shah DJ, Rohlfing F, Anand S, Johnson WE, Alvarez MT, Cobell J, King J, Young SA, Kauwe JS, Graves SW. Discovery and Subsequent Confirmation of Novel Serum Biomarkers Diagnosing Alzheimer's Disease. J Alzheimers Dis. 2015; 49(2):317-27. PMID: 26484917; DOI: 10.3233/JAD-150498;

Anand S, Bench Alvarez TM, Johnson WE, Esplin MS, Merrell K, Porter TF, Graves SW. Serum biomarkers predictive of pre-eclampsia. Biomark Med. 2015; 9(6):563-75. PMID: 26079961; DOI: 10.2217/bmm.15.21;

Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA. 2015 Feb; 21(2):164-71.View Related Profiles.

Spira, Avrum
Liu, Gang
Beane-Ebel, Jennifer
Tedrow, John
Campbell, Joshua
Luo, Lingqi
Lenburg, Marc
Monti, Stefano
Johnson, William
Alekseyev, Yuriy

PMID: 25519487; PMCID: PMC4338344; DOI: 10.1261/rna.046060.114;

Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics. 2014; 15:918. PMID: 25336203; PMCID: PMC4218995; DOI: 10.1186/1471-2164-15-918;

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome. 2014; 2:33. PMID: 25225611; PMCID: PMC4164323; DOI: 10.1186/2049-2618-2-33;

Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA, Johnson WE. Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinformatics. 2014; 15:262. PMID: 25091138; PMCID: PMC4131054; DOI: 10.1186/1471-2105-15-262;

El-Chaar NN, Piccolo SR, Boucher KM, Cohen AL, Chang JT, Moos PJ, Bild AH. Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer. Mol Oncol. 2014 Oct; 8(7):1339-54.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24908424; PMCID: PMC4450766; DOI: 10.1016/j.molonc.2014.05.005;

Bild AH, Chang JT, Johnson WE, Piccolo SR. A field guide to genomics research. PLoS Biol. 2014 Jan; 12(1):e1001744.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24409093; PMCID: PMC3883637; DOI: 10.1371/journal.pbio.1001744;

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE. Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. BMC Bioinformatics. 2013; 14:337. PMID: 24261665; PMCID: PMC3924334; DOI: 10.1186/1471-2105-14-337;

Piccolo SR, Withers MR, Francis OE, Bild AH, Johnson WE. Multiplatform single-sample estimates of transcriptional activation. Proc Natl Acad Sci U S A. 2013 Oct 29; 110(44):17778-83.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24128763; PMCID: PMC3816418; DOI: 10.1073/pnas.1305823110;

Cohen AL, Piccolo SR, Cheng L, Soldi R, Han B, Johnson WE, Bild AH. Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers. BMC Med Genomics. 2013; 6:35.View Related Profiles.

Piccolo, Stephen
Johnson, William

PMID: 24079712; PMCID: PMC3850967; DOI: 10.1186/1755-8794-6-35;

Imholte GC, Scott-Boyer MP, Labbe A, Deschepper CF, Gottardo R. iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data. Bioinformatics. 2013 Nov 01; 29(21):2797-8. PMID: 23958729; PMCID: PMC3799478; DOI: 10.1093/bioinformatics/btt485;

Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE. Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res. 2013 Oct; 23(10):1721-9. PMID: 23843222; PMCID: PMC3787268; DOI: 10.1101/gr.150151.112;

O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013; 5(3):28. PMID: 23537139; PMCID: PMC3706896; DOI: 10.1186/gm432;

Woolstenhulme CJ, Parajuli S, Healey DW, Valverde DP, Petersen EN, Starosta AL, Guydosh NR, Johnson WE, Wilson DN, Buskirk AR. Nascent peptides that block protein synthesis in bacteria. Proc Natl Acad Sci U S A. 2013 Mar 5; 110(10):E878-87. PMID: 23431150; PMCID: PMC3593848; DOI: 10.1073/pnas.1219536110;

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics. 2012 Dec; 100(6):337-44.View Related Profiles.

Campbell, Joshua
Lenburg, Marc
Piccolo, Stephen
Johnson, William

PMID: 22959562; PMCID: PMC3508193; DOI: 10.1016/j.ygeno.2012.08.003;

Warf MB, Shepherd BA, Johnson WE, Bass BL. Effects of ADARs on small RNA processing pathways in C. elegans. Genome Res. 2012 Aug; 22(8):1488-98. PMID: 22673872; PMCID: PMC3409262; DOI: 10.1101/gr.134841.111;

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012 Mar 15; 28(6):882-3. PMID: 22257669; PMCID: PMC3307112; DOI: 10.1093/bioinformatics/bts034;

Lyon GJ, Jiang T, Van Wijk R, Wang K, Johnson WE. 29th World Congress of Psychiatric Genetics 2011. Whole exome sequencing reveals the genetic basis of a case of idiopathic hemolytic anemia and suggests candidate rare variants for ADHD in a Utah pedigree. 2012; 3.

Cohen AL, Soldi R, Zhang H, Gustafson AM, Wilcox R, Welm BE, Chang JT, Johnson E, Spira A, Jeffrey SS, Bild AH. A pharmacogenomic method for individualized prediction of drug sensitivity. Mol Syst Biol. 2011; 7:513.View Related Profiles.

Spira, Avrum
Johnson, William

PMID: 21772261; PMCID: PMC3159972; DOI: 10.1038/msb.2011.47;

Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, Tian L, Robison RJ, Clement M, Lin Y, Zhang P, Liu Y, Moore B, Glessner JT, Elia J, Reimherr F, van Solinge WW, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K. Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med. 2011 Jul; 12(62):41-55. PMID: 21794208; PMCID: PMC3544941

Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet. 2011 Jul 15; 89(1):28-43. PMID: 21700266; PMCID: PMC3135802; DOI: 10.1016/j.ajhg.2011.05.017;

Evan Johnson W, Welker NC, Bass BL. Dynamic linear model for the identification of miRNAs in next-generation sequencing data. Biometrics. 2011 Dec; 67(4):1206-14. PMID: 21385162; PMCID: PMC3116054; DOI: 10.1111/j.1541-0420.2010.01570.x;

Warf MB, Johnson WE, Bass BL. Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer. RNA. 2011 Apr; 17(4):563-77. PMID: 21307183; PMCID: PMC3062169; DOI: 10.1261/rna.2432311;

Rope A, Wang K, Evjenth R, Johnson WE et. al. Massively parallel sequencing identifies a previously unrecognized X-linked disorder resulting in lethality in male infants owing to amino-terminal acetyltransferase deficiency. Genome Biology. 2011; 12(1). View Publication

Clement NL, Clement MJ, Snell Q, Johnson WE. Parallel Mapping Approaches for GNUMAP. IPDPS. 2011; 435-443. PMID: 23396612; PMCID: PMC3565456

Rai K, Sarkar S, Broadbent TJ, Voas M, Grossmann KF, Nadauld LD, Dehghanizadeh S, Hagos FT, Li Y, Toth RK, Chidester S, Bahr TM, Johnson WE, Sklow B, Burt R, Cairns BR, Jones DA. DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell. 2010 Sep 17; 142(6):930-42. PMID: 20850014; PMCID: PMC2943938; DOI: 10.1016/j.cell.2010.08.030;

Thyagarajan B, Blaszczak AG, Chandler KJ, Watts JL, Johnson WE, Graves BJ. ETS-4 is a transcriptional regulator of life span in Caenorhabditis elegans. PLoS Genet. 2010 Sep; 6(9):e1001125. PMID: 20862312; PMCID: PMC2940738; DOI: 10.1371/journal.pgen.1001125;

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010 Oct; 11(10):733-9. PMID: 20838408; PMCID: PMC3880143; DOI: 10.1038/nrg2825;

Hollenhorst PC, Chandler KJ, Poulsen RL, Johnson WE, Speck NA, Graves BJ. DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet. 2009 Dec; 5(12):e1000778. PMID: 20019798; PMCID: PMC2787013; DOI: 10.1371/journal.pgen.1000778;

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE. The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics. 2010 Jan 1; 26(1):38-45. PMID: 19861355; PMCID: PMC6276904; DOI: 10.1093/bioinformatics/btp614;

Johnson WE, Liu JS, Liu S. New Developments in Biostatistics and Bioinformatics. Analysis of ChIP-chip Data on Genome Tiling Microarrays. 2009; 239-257. View Publication
Johnson WE, Liu S, Liu JS. Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays. The Annals of Applied Statistics. 2009; 3(3). View Publication

Gottardo R, Li W, Johnson WE, Liu XS. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments. Biometrics. 2008 Jun; 64(2):468-78. PMID: 17888037

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biol. 2007; 8(8):R178. PMID: 17727723; PMCID: PMC2375008; DOI: 10.1186/gb-2007-8-8-r178;

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12457-62. PMID: 16895995; PMCID: PMC1567901; DOI: 10.1073/pnas.0601180103;

Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007 Jan; 8(1):118-27. PMID: 16632515

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 124 publications over 18 distinct years, with a maximum of 13 publications in 2015

Bar chart showing 124 publications over 18 distinct years, with a maximum of 13 publications in 2015

Year	Publications
2006	2
2007	2
2009	4
2010	3
2011	7
2012	4
2013	7
2014	6
2015	13
2016	7
2017	5
2018	6
2019	6
2020	12
2021	11
2022	9
2023	12
2024	8

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In addition to these self-described keywords below, a list of MeSH based concepts is available here.

batch effects
Bayesian biostatistics
Computational biology
genomic medicine
infectious disease diagnostics
metagenomics
single cell sequencing
tumor heterogeneity

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