Alternative empirical Bayes models for adjusting for batch effects in genomic studies by Yuqing Zhang, David F. Jenkins, Solaiappan Manimaran, W. Evan Johnson

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Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50–60Mb) exhibiting reduced methamphetamine sensitivity by Neema Yazdani, Ying Shen, W. Evan Johnson, Camron D. Bryant

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A field guide to genomics research. by Andrea H Bild, Jeffrey T Chang, W Evan Johnson, Stephen R Piccolo

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Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data by Aubrey R. Odom, Tyler Faits, Eduardo Castro-Nallar, Keith A. Crandall, W. Evan Johnson

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animalcules: interactive microbiome analytics and visualization in R by Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti, W. Evan Johnson

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Decontamination of ambient RNA in single-cell RNA-seq with DecontX by Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima, Joshua D. Campbell

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Evaluation of computational methods for human microbiome analysis using simulated data by Matthieu J. Miossec, Sandro L. Valenzuela, Marcos Pérez-Losada, W. Evan Johnson, Keith A. Crandall, Eduardo Castro-Nallar

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Immunopathogenic overlap between COVID-19 and tuberculosis identified from transcriptomic meta-analysis and human macrophage infection by Dylan Sheerin, Abhimanyu, Nashied Peton, William Vo, Cody Charles Allison, Xutao Wang, W. Evan Johnson, Anna Kathleen Coussens

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DNA specificity determinants associate with distinct transcription factor functions. by Peter C Hollenhorst, Katherine J Chandler, Rachel L Poulsen, W Evan Johnson, Nancy A Speck, Barbara J Graves

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Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts. by Molly R Braun, Sarah L Noton, Emmeline L Blanchard, Afzaal Shareef, Philip J Santangelo, W Evan Johnson, Rachel Fearns

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Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures by Xutao Wang, Arthur VanValkenberg, Aubrey R. Odom, Jerrold J. Ellner, Natasha S. Hochberg, Padmini Salgame, Prasad Patil, W. Evan Johnson

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Concordance and discordance of sequence survey methods for molecular epidemiology by Eduardo Castro-Nallar, Nur A. Hasan, Thomas A. Cebula, Rita R. Colwell, Richard A. Robison, W. Evan Johnson, Keith A. Crandall

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Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants [version 2; peer review: 1 approved, 2 approved with reservations] by Donald Thea, Aubrey R. Odom, W. Evan Johnson, William B. MacLeod, Christopher J. Gill, Rotem Lapidot, Rachel Pieciak, Arshad Ismail

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Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes by Jasmine A. McQuerry, David F. Jenkins, Susan E. Yost, Yuqing Zhang, Daniel Schmolze, W. Evan Johnson, Yuan Yuan, Andrea H. Bild

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Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis by Arthur VanValkenburg, Arthur VanValkenburg, Vaishnavi Kaipilyawar, Sonali Sarkar, Subitha Lakshminarayanan, Chelsie Cintron, Senbagavalli Prakash Babu, Selby Knudsen, Noyal Mariya Joseph, C. Robert Horsburgh, C. Robert Horsburgh, Pranay Sinha, Jerrold J. Ellner, Prakash Babu Narasimhan, W. Evan Johnson, W. Evan Johnson, Natasha S. Hochberg, Natasha S. Hochberg, Natasha S. Hochberg, Padmini Salgame

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Xenosurveillance: a novel mosquito-based approach for examining the human-pathogen landscape. by Nathan D Grubaugh, Supriya Sharma, Benjamin J Krajacich, Lawrence S Fakoli, Fatorma K Bolay, Joe W Diclaro, W Evan Johnson, Gregory D Ebel, Brian D Foy, Doug E Brackney

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Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data by Rui Hong, Yusuke Koga, Shruthi Bandyadka, Anastasia Leshchyk, Yichen Wang, Vidya Akavoor, Xinyun Cao, Irzam Sarfraz, Zhe Wang, Salam Alabdullatif, Frederick Jansen, Masanao Yajima, W. Evan Johnson, Joshua D. Campbell

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A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome by Poonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland

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Author Correction: A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome by Poonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland

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Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus by Gina M. Sanchez, Eden S. Hirsch, Arthur VanValkenburg, Daniel P. Mayer, Komi Gbedande, Rebecca L. Francis, Wenzhi Song, Olivia Q. Antao, Kyleigh E. Brimmer, Alexander Lemenze, Robin Stephens, W. Evan Johnson, Jason S. Weinstein

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