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J. Foox · SciRah

Researcher profile · Semantic Scholar

J. Foox

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J. Foox — researcher profile on SciRah

h-index: 34
Works: 101
Citations: 4,640

Most-cited papers

Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep Space Exploration
Ebrahim Afshinnekoo, Ryan T. Scott, Matthew Mackay, E. Pariset +34 more
2020Cell400 citations Open access
Semantic Scholar
Comprehensive Multi-Omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact
W. D. da Silveira, Hossein Fazelinia, S. Rosenthal, E. Laiakis +34 more
2020Cell352 citations Open access
Semantic Scholar
The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection
André F. Rendeiro, Hiranmayi Ravichandran, Y. Bram, V. Chandar +14 more
2021Nature313 citations Open access
Semantic Scholar
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Alexa B. R. McIntyre, R. Ounit, Ebrahim Afshinnekoo, Robert J. Prill +16 more
2017Genome Biology301 citations Open access
Semantic Scholar
Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection
Vijendra Ramlall, P. Thangaraj, Cem Meydan, J. Foox +8 more
2020Nature Medicine296 citations Open access
Semantic Scholar
Investigation of product derived lymphoma following infusion of piggyBac modified CD19 chimeric antigen receptor T-cells.
K. Micklethwaite, K. Gowrishankar, B. Gloss, Ziduo Li +16 more
2021Blood204 citations Open access
Semantic Scholar
DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
Yang Liu, Wojciech Rosikiewicz, Ziwei Pan, Nathaniel L. Jillette +7 more
2021Genome Biology198 citations Open access
Semantic Scholar
Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts
Joseph W. Guarnieri, Joseph M. Dybas, Hossein Fazelinia, Man S. Kim +47 more
2023Science Translational Medicine165 citations Open access
Semantic Scholar
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
D. Butler, C. Mozsary, Cem Meydan, J. Foox +75 more
2021Nature Communications128 citations Open access
Semantic Scholar
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
J. Foox, S. Tighe, C. Nicolet, J. Zook +23 more
2021Nature Biotechnology114 citations Open access
Semantic Scholar
Relationships between SARS-CoV-2 in Wastewater and COVID-19 Clinical Cases and Hospitalizations, with and without Normalization against Indicators of Human Waste
Qin Zhan, K. Babler, M. Sharkey, A. Amirali +29 more
2022ACS ES&T water103 citations Open access
Semantic Scholar
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
Li Tai Fang, Bin Zhu, Yong-Mei Zhao, Wan-Qiu Chen +75 more
2021Nature Biotechnology103 citations Open access
Semantic Scholar
A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood
Dianna L. Ng, Andrea C Granados, Yale A. Santos, V. Servellita +28 more
2021Science Advances94 citations Open access
Semantic Scholar
Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius
J. Rosenfeld, D. Reeves, M. Brugler, A. Narechania +23 more
2016Nature Communications93 citations Open access
Semantic Scholar
The Space Omics and Medical Atlas (SOMA) and international astronaut biobank
Eliah G. Overbey, Jangkeun Kim, Braden T. Tierney, Jiwoon Park +105 more
2024Nature92 citations Open access
Semantic Scholar
Temporal Telomere and DNA Damage Responses in the Space Radiation Environment.
Jared J. Luxton, M. McKenna, Lynn Taylor, K. George +14 more
2020Cell Reports86 citations Open access
Semantic Scholar
Role of miR-2392 in driving SARS-CoV-2 infection
J. Mcdonald, F. Enguita, Deanne M. Taylor, R. Griffin +44 more
2021Cell Reports75 citations Open access
Semantic Scholar
Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight
Braden T. Tierney, Jangkeun Kim, Eliah G. Overbey, Krista A. Ryon +33 more
2024Nature Microbiology71 citations Open access
Semantic Scholar
Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions
D. Butler, C. Mozsary, Cem Meydan, D. Danko +48 more
2020bioRxiv64 citations Open access
Semantic Scholar
Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight
Jangkeun Kim, Braden T. Tierney, Eliah G. Overbey, E. Dantas +46 more
2024Nature Communications60 citations Open access
Semantic Scholar
Molecular and physiological changes in the SpaceX Inspiration4 civilian crew
Christopher W. Jones, Eliah G. Overbey, Jérôme Lacombe, Adrian J. Ecker +55 more
2024Nature59 citations Open access
Semantic Scholar
Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
Yong-Mei Zhao, L. Fang, Tsai-Wei Shen, Sulbha Choudhari +34 more
2021Scientific Data57 citations Open access
Semantic Scholar
Clonal Hematopoiesis Before, During, and After Human Spaceflight
Nuria Mencia-Trinchant, Matthew Mackay, Christopher R. Chin, Ebrahim Afshinnekoo +16 more
2020Cell Reports56 citations Open access
Semantic Scholar
Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).
S. Tighe, Ebrahim Afshinnekoo, Tara M. Rock, K. McGrath +32 more
2017Journal of Biomolecular Techniques55 citations Open access
Semantic Scholar
Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers
D. Bezdan, K. Grigorev, Cem Meydan, Fanny A. Pelissier Vatter +27 more
2020bioRxiv54 citations Open access
Semantic Scholar
IDH2 and TET2 mutations synergize to modulate T Follicular Helper cell functional interaction with the AITL microenvironment.
J. Leca, F. Lemonnier, Cem Meydan, J. Foox +17 more
2023Cancer Cell52 citations Open access
Semantic Scholar
Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction
Keith Siew, Kevin A. Nestler, Charlotte A. Nelson, V. D'Ambrosio +101 more
2024Nature Communications48 citations Open access
Semantic Scholar
The SEQC2 epigenomics quality control (EpiQC) study
J. Foox, J. Nordlund, C. Lalancette, Ting Gong +53 more
2020Genome Biology45 citations Open access
Semantic Scholar
The Road To Cnidaria: History of Phylogeny of the Myxozoa
J. Foox, M. Siddall
2015Journal of Parasitology43 citations
Semantic Scholar
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
W. Jones, Bin-Sheng Gong, N. Novoradovskaya, Dan Li +70 more
2021Genome Biology42 citations Open access
Semantic Scholar
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
Nicolae Sapoval, M. Mahmoud, M. Jochum, Yunxi Liu +16 more
2021Genome Research39 citations Open access
Semantic Scholar
Haplotype diversity and sequence heterogeneity of human telomeres
K. Grigorev, J. Foox, D. Bezdan, D. Butler +8 more
2020bioRxiv39 citations Open access
Semantic Scholar
System-wide transcriptome damage and tissue identity loss in COVID-19 patients
Jiwoon Park, J. Foox, Tyler D. Hether, D. Danko +44 more
2022Cell Reports Medicine37 citations Open access
Semantic Scholar
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan +51 more
2022Genome Biology36 citations Open access
Semantic Scholar
Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome
Vijendra Ramlall, P. Thangaraj, Cem Meydan, J. Foox +7 more
2020medRxiv32 citations Open access
Semantic Scholar
Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Authors:
D. Butler, C. Mozsary, Cem Meydan, D. Danko +45 more
202032 citations
Semantic Scholar
TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION
Joseph W. Guarnieri, Joseph M. Dybas, Hossein Fazelinia, Man S. Kim +39 more
2022bioRxiv31 citations Open access
Semantic Scholar
Transcriptional response modules characterize IL-1β and IL-6 activity in COVID-19
L. C. Bell, Cem Meydan, Jacob Kim, J. Foox +5 more
2020iScience31 citations Open access
Semantic Scholar
PRMT5 supports multiple oncogenic pathways in mantle cell lymphoma.
S. Sloan, F. Brown, Mackenzie E Long, C. Weigel +27 more
2023Blood27 citations Open access
Semantic Scholar
The spatial landscape of lung pathology during COVID-19 progression - immune activation IMC data
A. Rendeiro, Hiranmayi Ravichandran, Y. Bram, Junbum Kim +13 more
202127 citations
Semantic Scholar
Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
Nicolae Sapoval, M. Mahmoud, M. Jochum, Yunxi Liu +16 more
2020bioRxiv27 citations Open access
Semantic Scholar
Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes
J. Foox, M. Brugler, M. Siddall, E. Rodríguez
2016Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis27 citations
Semantic Scholar
Towards geospatially-resolved public-health surveillance via wastewater sequencing
Braden T. Tierney, J. Foox, Krista A. Ryon, Daniel Butler +34 more
2024Nature Communications26 citations Open access
Semantic Scholar
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Bin-Sheng Gong, Dan Li, Rebecca Kusko, N. Novoradovskaya +147 more
2021Genome Biology26 citations Open access
Semantic Scholar
Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight
J. S. Garcia-Medina, K. Sienkiewicz, S. Narayanan, Eliah G. Overbey +39 more
2024Precision Clinical Medicine23 citations Open access
Semantic Scholar
Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells
J. Fortin, Ming-Feng Chiang, Cem Meydan, J. Foox +19 more
2023Proceedings of the National Academy of Sciences of the United States of America23 citations Open access
Semantic Scholar
In silico hybridization enables transcriptomic illumination of the nature and evolution of Myxozoa
J. Foox, M. Ringuette, S. Desser, M. Siddall
2015BMC Genomics22 citations Open access
Semantic Scholar
Comparative analysis of single-cell RNA Sequencing Platforms and Methods
J. Ashton, H. Rehrauer, Jason R. Myers, Jacqueline Myers +9 more
2020bioRxiv21 citations Open access
Semantic Scholar
Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep-Space Exploration
Ebrahim Afshinnekoo, Ryan T. Scott, Matthew Mackay, E. Pariset +34 more
2021Cell20 citations Open access
Semantic Scholar
Identification of Radioresponsive Genes in Esophageal Cancer from Longitudinal and Single Cell Exome Sequencing.
Ling Yang, Xiaoyan Zhang, Matthew Mackay, J. Foox +7 more
2020International Journal of Radiation Oncology, Biology, Physics19 citations
Semantic Scholar

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