W. Evan Johnson (@wejlab) header
W. Evan Johnson (@wejlab) profile picture

W. Evan Johnson

@wejlab

Developing computational algorithms for genomic medicine (tuberculosis/cancer genomics and clinical metagenomics).

 Boston, MA
jlab.bu.edu/
Joined August 2012
  • Tweets482
  • Following313
  • Followers593
Excited that this work from our group is finally through peer review! Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants gatesopenresearch.org/articl…
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A cool paper from our group on reproducibility in TB gene signature analysis: bmcinfectdis.biomedcentral.c…
Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures

Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures

BMC Infectious Diseases - Blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease. However, an unresolved issue is whether gene...

link.springer.com
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This paper is a little different than we usually publish, but we helped with some complex batch effect correction: sciencedirect.com/science/ar…
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Wow! Finally published! This took a long time to get done! Nice work @rotemlapidot and @tylerfaits! Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory.... Lapidot R et al., published by Gates Open Research, gatesopenresearch.org/articl…
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Students in #datascience: it's not too late to register for our student-focused conference this May, to talk science, learn new skills, connect with industry, and experience beautiful Southern Utah! (Faculty, send your students!) redrockdatascience.com
HOME | Red Rock DataScience

HOME | Red Rock DataScience

redrockdatascience.com
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Students in Data Science! Here is a conference for you! Come join us in for science, learning, networking, while experiencing the outdoors and beauty of Southern Utah! Conference information and registration link is in the comments! #DataScience #redrockdatascience
Image from W. Evan Johnson (@wejlab)
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redrockdatascience.com/stude…
Student Conference 2024 | Red Rock DataScience

Student Conference 2024 | Red Rock DataScience

redrockdatascience.com
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Happy to share this exciting publication from our group! @crandallkeith nature.com/articles/s41598-0…
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

Scientific Reports - Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data

nature.com
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Excited for our new paper on our work studying on the developing microbiome and associated infectious disease pathogenesis in Zambia: journals.lww.com/pidj/Fullte…
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Shout out to our new publication with @JessicaLeibler! Its is gaining momentum: already an Altmetric score of 340, 42 news outlets have picked it up, including NPR: onlinelibrary.wiley.com/doi/… npr.org/sections/goatsandsod…

Influenza D virus exposure among US cattle workers: A call for surveillance

Although cattle are a reservoir for influenza D virus (IDV), little is known about human exposure to IDV. We assessed IDV exposure and associated health effects among United States dairy workers, a...

onlinelibrary.wiley.com
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Here is a link to the paper: onlinelibrary.wiley.com/doi/…

Influenza D virus exposure among US cattle workers: A call for surveillance

Although cattle are a reservoir for influenza D virus (IDV), little is known about human exposure to IDV. We assessed IDV exposure and associated health effects among United States dairy workers, a...

onlinelibrary.wiley.com
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Super excited to publish this work in Frontiers in Immunology! frontiersin.org/articles/10.…
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Excited for this publication from our group! Will be the basis for a lot of our upcoming TB biomarker work! academic.oup.com/cid/advance…
Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoSt...

Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoSt...

The NanoString nCounter platform is an expedient approach for validating a panel of tuberculosis biomarkers and benchmarking them against each other and fo

academic.oup.com
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Here is a really fun and exctiign paper we have posted on medRviv! Hopng to get it peer reviewed soon! medrxiv.org/content/10.1101/…
Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young...

Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young...

Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles...

medrxiv.org
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So excited for this paper! We spent a long time on it and I think it has some important conclusions! Great job @li_tenglong @yuqingzBU academic.oup.com/biostatisti…
Overcoming the impacts of two-step batch effect correction on gene expression estimation and...

Overcoming the impacts of two-step batch effect correction on gene expression estimation and...

Summary. Nonignorable technical variation is commonly observed across data from multiple experimental runs, platforms, or studies. These so-called batch ef

academic.oup.com
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Our paper for our animalcules microbiome analysis toolkit is now live! Nice teamwork @jasonzhao0307 @MontiLab @dsegre @BU_CBM microbiomejournal.biomedcent…
animalcules: interactive microbiome analytics and visualization in R

animalcules: interactive microbiome analytics and visualization in R

Microbiome - Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial...

link.springer.com
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Just realized that I never tweeted about this exciting and important published work from our group by @yuqingzBU! When is it best to merge batches of data, and when to learn from each batch and ensemble the results?! Read here: academic.oup.com/bioinformat…

Robustifying genomic classifiers to batch effects via ensemble learning

AbstractMotivation. Genomic data are often produced in batches due to practical restrictions, which may lead to unwanted variation in data caused by discre

academic.oup.com
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Our paper on profiling TB signatures is finally available! bmcinfectdis.biomedcentral.c…
Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler

Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler

BMC Infectious Diseases - Gene expression signatures have been used as biomarkers of tuberculosis (TB) risk and outcomes. Platforms are needed to simplify access to these signatures and determine...

link.springer.com
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Have been working on this one for a while. Glad to get it out and hope it makes a difference! biorxiv.org/content/10.1101/…
Overcoming the impacts of two-step batch effect correction on gene expression estimation and...

Overcoming the impacts of two-step batch effect correction on gene expression estimation and...

Non-ignorable technical variation is commonly observed across data from multiple experimental runs, platforms, or studies. These so-called batch effects can lead to difficulty in merging data from...

biorxiv.org
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Super excited for this one to finally be out! Nice work @yuqingzBU ComBat-seq : batch effect adjustment for RNA-seq count data academic.oup.com/nargab/arti…
ComBat-seq: batch effect adjustment for RNA-seq count data

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

Abstract. The benefit of integrating batches of genomic data to increase statistical power is often hindered by batch effects, or unwanted variation in dat

academic.oup.com
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