Joseph N Paulson
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Differential abundance analysis for microbial marker-gene surveys
JN Paulson, OC Stine, HC Bravo, M Pop
Nature methods 10 (12), 1200-1202, 2013
Simplified and representative bacterial community of maize roots
B Niu, JN Paulson, X Zheng, R Kolter
Proceedings of the National Academy of Sciences 114 (12), E2450-E2459, 2017
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition
M Pop, AW Walker, J Paulson, B Lindsay, M Antonio, MA Hossain, ...
Genome biology 15 (6), 1-12, 2014
Understanding Tissue-Specific Gene Regulation
AR Sonawane, J Platig, M Fagny, CY Chen, JN Paulson, ...
Cell Reports 21 (4), 1077-1088, 2017
metagenomeSeq: Statistical analysis for sparse high-throughput sequencing
JN Paulson, M Pop, HC Bravo
Dynamic metabolic exchange governs a marine algal-bacterial interaction
E Segev, TP Wyche, KH Kim, J Petersen, C Ellebrandt, H Vlamakis, ...
Elife 5, e17473, 2016
Polatuzumab vedotin in relapsed or refractory diffuse large B-cell lymphoma
LH Sehn, AF Herrera, CR Flowers, MK Kamdar, A McMillan, M Hertzberg, ...
Journal of Clinical Oncology 38 (2), 155-165, 2020
Exploring regulation in tissues with eQTL networks
M Fagny, JN Paulson, ML Kuijjer, AR Sonawane, CY Chen, ...
Proceedings of the National Academy of Sciences 114 (37), E7841-E7850, 2017
Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
M Pop, JN Paulson, S Chakraborty, I Astrovskaya, BR Lindsay, S Li, ...
BMC genomics 17 (1), 440, 2016
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
VJ Carrión, J Perez-Jaramillo, V Cordovez, V Tracanna, M De Hollander, ...
Science 366 (6465), 606-612, 2019
Smooth Quantile Normalization
SC Hicks, K Okrah, JN Paulson, J Quackenbush, RA Irizarry, HC Bravo
Biostatistics 19 (2), 185–198, 2018
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
JN Paulson, CY Chen, CM Lopes-Ramos, ML Kuijjer, J Platig, ...
BMC Bioinformatics 18 (1), 437, 2017
Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection
A Morris, JN Paulson, H Talukder, L Tipton, H Kling, L Cui, A Fitch, M Pop, ...
Microbiome 4 (1), 1-11, 2016
Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA gene sequencing as alternative methods of bacterial pathogen detection
B Lindsay, M Pop, M Antonio, AW Walker, V Mai, D Ahmed, J Oundo, ...
Journal of clinical microbiology 51 (10), 3263-3269, 2013
Cancer subtype identification using somatic mutation data
ML Kuijjer, JN Paulson, P Salzman, W Ding, J Quackenbush
British journal of cancer 118 (11), 1492-1501, 2018
A reference map of the human binary protein interactome
K Luck, DK Kim, L Lambourne, K Spirohn, BE Begg, W Bian, R Brignall, ...
Nature 580 (7803), 402-408, 2020
Multisystem analysis of Mycobacterium tuberculosis reveals kinase-dependent remodeling of the pathogen-environment interface
X Carette, J Platig, DC Young, M Helmel, AT Young, Z Wang, LP Potluri, ...
MBio 9 (2), 2018
Regulatory network changes between cell lines and their tissues of origin
CM Lopes-Ramos, JN Paulson, CY Sonawane, ML Kuijjer, M Fagny, ...
BMC genomics 18 (1), 723, 2017
Meta-analysis of the lung microbiota in pulmonary tuberculosis
B Hong, JN Paulson, OC Stine, GM Weinstock, JL Cervantes
Tuberculosis 109, 102-108, 2018
Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing
M Garrine, I Mandomando, D Vubil, T Nhampossa, S Acacio, S Li, ...
PLOS Neglected Tropical Diseases 11 (6), e0005671, 2017
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