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Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations.
Published in:
Environmental Microbiome, 2022, v. 17, n. 1, p. 1, doi. 10.1186/s40793-022-00455-9
By:
- Sierra, Maria A.;
- Ryon, Krista A.;
- Tierney, Braden T.;
- Foox, Jonathan;
- Bhattacharya, Chandrima;
- Afshin, Evan;
- Butler, Daniel;
- Green, Stefan J.;
- Thomas, W. Kelley;
- Ramsdell, Jordan;
- Bivens, Nathan J.;
- McGrath, Ken;
- Mason, Christopher E.;
- Tighe, Scott W.
Publication type:
Article
Elevated A-to-I RNA editing in COVID-19 infected individuals.
Published in:
NAR Genomics & Bioinformatics, 2023, v. 5, n. 4, p. 1, doi. 10.1093/nargab/lqad092
By:
- Merdler-Rabinowicz, Rona;
- Gorelik, David;
- Park, Jiwoon;
- Meydan, Cem;
- Foox, Jonathan;
- Karmon, Miriam;
- Roth, Hillel S;
- Cohen-Fultheim, Roni;
- Shohat-ophir, Galit;
- Eisenberg, Eli;
- Ruppin, Eytan;
- Mason, Christopher E;
- Levanon, Erez Y
Publication type:
Article
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21361-7
By:
- Butler, Daniel;
- Mozsary, Christopher;
- Meydan, Cem;
- Foox, Jonathan;
- Rosiene, Joel;
- Shaiber, Alon;
- Danko, David;
- Afshinnekoo, Ebrahim;
- MacKay, Matthew;
- Sedlazeck, Fritz J.;
- Ivanov, Nikolay A.;
- Sierra, Maria;
- Pohle, Diana;
- Zietz, Michael;
- Gisladottir, Undina;
- Ramlall, Vijendra;
- Sholle, Evan T.;
- Schenck, Edward J.;
- Westover, Craig D.;
- Hassan, Ciaran
Publication type:
Article
Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.
Published in:
2021
By:
- Foox, Jonathan;
- Tighe, Scott W.;
- Nicolet, Charles M.;
- Zook, Justin M.;
- Byrska-Bishop, Marta;
- Clarke, Wayne E.;
- Khayat, Michael M.;
- Mahmoud, Medhat;
- Laaguiby, Phoebe K.;
- Herbert, Zachary T.;
- Warner, Derek;
- Grills, George S.;
- Jen, Jin;
- Levy, Shawn;
- Xiang, Jenny;
- Alonso, Alicia;
- Zhao, Xia;
- Zhang, Wenwei;
- Teng, Fei;
- Zhao, Yonggang
Publication type:
Correction Notice
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.
Published in:
Nature Biotechnology, 2021, v. 39, n. 9, p. 1129, doi. 10.1038/s41587-021-01049-5
By:
- Foox, Jonathan;
- Tighe, Scott W.;
- Nicolet, Charles M.;
- Zook, Justin M.;
- Byrska-Bishop, Marta;
- Clarke, Wayne E.;
- Khayat, Michael M.;
- Mahmoud, Medhat;
- Laaguiby, Phoebe K.;
- Herbert, Zachary T.;
- Warner, Derek;
- Grills, George S.;
- Jen, Jin;
- Levy, Shawn;
- Xiang, Jenny;
- Alonso, Alicia;
- Zhao, Xia;
- Zhang, Wenwei;
- Teng, Fei;
- Zhao, Yonggang
Publication type:
Article
Author Correction: The SEQC2 epigenomics quality control (EpiQC) study.
Published in:
2021
By:
- Foox, Jonathan;
- Nordlund, Jessica;
- Lalancette, Claudia;
- Gong, Ting;
- Lacey, Michelle;
- Lent, Samantha;
- Langhorst, Bradley W.;
- Ponnaluri, V. K. Chaithanya;
- Williams, Louise;
- Padmanabhan, Karthik Ramaswamy;
- Cavalcante, Raymond;
- Lundmark, Anders;
- Butler, Daniel;
- Mozsary, Christopher;
- Gurvitch, Justin;
- Greally, John M.;
- Suzuki, Masako;
- Menor, Mark;
- Nasu, Masaki;
- Alonso, Alicia
Publication type:
Correction Notice
The SEQC2 epigenomics quality control (EpiQC) study.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02529-2
By:
- Foox, Jonathan;
- Nordlund, Jessica;
- Lalancette, Claudia;
- Gong, Ting;
- Lacey, Michelle;
- Lent, Samantha;
- Langhorst, Bradley W.;
- Ponnaluri, V. K. Chaithanya;
- Williams, Louise;
- Padmanabhan, Karthik Ramaswamy;
- Cavalcante, Raymond;
- Lundmark, Anders;
- Butler, Daniel;
- Mozsary, Christopher;
- Gurvitch, Justin;
- Greally, John M.;
- Suzuki, Masako;
- Menor, Mark;
- Nasu, Masaki;
- Alonso, Alicia
Publication type:
Article
DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02510-z
By:
- Liu, Yang;
- Rosikiewicz, Wojciech;
- Pan, Ziwei;
- Jillette, Nathaniel;
- Wang, Ping;
- Taghbalout, Aziz;
- Foox, Jonathan;
- Mason, Christopher;
- Carroll, Martin;
- Cheng, Albert;
- Li, Sheng
Publication type:
Article
THE ROAD TO CNIDARIA: HISTORY OF PHYLOGENY OF THE MYXOZOA.
Published in:
Journal of Parasitology, 2015, v. 101, n. 3, p. 269, doi. 10.1645/14-671.1
By:
- Foox, Jonathan;
- Siddall, Mark E.
Publication type:
Article
Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.
Published in:
Nature Communications, 2016, v. 7, n. 2, p. 10164, doi. 10.1038/ncomms10164
By:
- Rosenfeld, Jeffrey A.;
- Reeves, Darryl;
- Brugler, Mercer R.;
- Narechania, Apurva;
- Simon, Sabrina;
- Durrett, Russell;
- Foox, Jonathan;
- Shianna, Kevin;
- Schatz, Michael C.;
- Gandara, Jorge;
- Afshinnekoo, Ebrahim;
- Lam, Ernest T.;
- Hastie, Alex R.;
- Chan, Saki;
- Cao, Han;
- Saghbini, Michael;
- Kentsis, Alex;
- Planet, Paul J.;
- Kholodovych, Vladyslav;
- Tessler, Michael
Publication type:
Article
Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight.
Published in:
Precision Clinical Medicine, 2024, v. 7, n. 1, p. 1, doi. 10.1093/pcmedi/pbae007
By:
- Garcia-Medina, J Sebastian;
- Sienkiewicz, Karolina;
- Narayanan, S Anand;
- Overbey, Eliah G;
- Grigorev, Kirill;
- Ryon, Krista A;
- Burke, Marissa;
- Proszynski, Jacqueline;
- Tierney, Braden;
- Schmidt, Caleb M;
- Mencia-Trinchant, Nuria;
- Klotz, Remi;
- Ortiz, Veronica;
- Foox, Jonathan;
- Chin, Christopher;
- Najjar, Deena;
- Matei, Irina;
- Chan, Irenaeus;
- Cruchaga, Carlos;
- Kleinman, Ashley
Publication type:
Article
Comparative Analysis of Single-Cell RNA Sequencing Platforms and Methods.
Published in:
Journal of Biomolecular Techniques, 2021, v. 32, n. 4, p. 1, doi. 10.7171/3fc1f5fe.3eccea01
By:
- Ashton, John M.;
- Rehrauer, Hubert;
- Myers, Jason;
- Myers, Jacqueline;
- Zanche, Michelle;
- Balys, Malene;
- Foox, Jonathan;
- Mason, Chistopher E.;
- Steen, Robert;
- Kuentzel, Marcy;
- Aquino, Catharine;
- Garcia-Reyero, Natàlia;
- Chittur, Sridar V.
Publication type:
Article
Molecular Characterization of Increased Amplicon Lengths in SARS-CoV-2 Reverse Transcription Loop-Mediated Isothermal Amplification Assays.
Published in:
Journal of Biomolecular Techniques, 2021, v. 32, n. 3, p. 1, doi. 10.7171/jbt.21-3203-015
By:
- Tighe, Scott W.;
- Hayden, Andrew F.;
- Kuentzel, Marcy L.;
- Eckstrom, Korin M.;
- Foox, Jonathan;
- Vellone, Daniel L.;
- Finstad, Kristiaan H.;
- Laaguiby, Pheobe K.;
- Hoffman, Jessica J.;
- Chittur, Sridar V.
Publication type:
Article
Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).
Published in:
Journal of Biomolecular Techniques, 2017, v. 28, n. 1, p. 31, doi. 10.7171/jbt.17-2801-004
By:
- Tighe, Scott;
- Afshinnekoo, Ebrahim;
- Rock, Tara M.;
- McGrath, Ken;
- Alexander, Noah;
- McIntyre, Alexa;
- Ahsanuddin, Sofia;
- Bezdan, Daniela;
- Green, Stefan J.;
- Joye, Samantha;
- Johnson, Sarah Stewart;
- Baldwin, Don A.;
- Bivens, Nathan;
- Ajami, Nadim;
- Carmical, Joseph R.;
- Herriott, Ian Charold;
- Colwell, Rita;
- Donia, Mohamed;
- Foox, Jonathan;
- Greenfield, Nick
Publication type:
Article
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1299-7
By:
- McIntyre, Alexa B. R.;
- Ounit, Rachid;
- Afshinnekoo, Ebrahim;
- Prill, Robert J.;
- Hénaff, Elizabeth;
- Alexander, Noah;
- Minot, Samuel S.;
- Danko, David;
- Foox, Jonathan;
- Ahsanuddin, Sofia;
- Tighe, Scott;
- Hasan, Nur A.;
- Subramanian, Poorani;
- Moffat, Kelly;
- Levy, Shawn;
- Lonardi, Stefano;
- Greenfield, Nick;
- Colwell, Rita R.;
- Rosen, Gail L.;
- Mason, Christopher E.
Publication type:
Article
Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi , the First Novel Eukaryote Isolated from the International Space Station.
Published in:
Journal of Fungi, 2022, v. 8, n. 2, p. N.PAG, doi. 10.3390/jof8020165
By:
- Bijlani, Swati;
- Parker, Ceth;
- Singh, Nitin K.;
- Sierra, Maria A.;
- Foox, Jonathan;
- Wang, Clay C. C.;
- Mason, Christopher E.;
- Venkateswaran, Kasthuri
Publication type:
Article
Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts.
Published in:
Science Translational Medicine, 2023, v. 15, n. 708, p. 1, doi. 10.1126/scitranslmed.abq1533
By:
- Guarnieri, Joseph W.;
- Dybas, Joseph M.;
- Fazelinia, Hossein;
- Kim, Man S.;
- Frere, Justin;
- Zhang, Yuanchao;
- Soto Albrecht, Yentli;
- Murdock, Deborah G.;
- Angelin, Alessia;
- Singh, Larry N.;
- Weiss, Scott L.;
- Best, Sonja M.;
- Lott, Marie T.;
- Zhang, Shiping;
- Cope, Henry;
- Zaksas, Victoria;
- Saravia-Butler, Amanda;
- Meydan, Cem;
- Foox, Jonathan;
- Mozsary, Christopher
Publication type:
Article
Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
Published in:
2019
By:
- McIntyre, Alexa B. R.;
- Ounit, Rachid;
- Afshinnekoo, Ebrahim;
- Prill, Robert J.;
- Hénaff, Elizabeth;
- Alexander, Noah;
- Minot, Samuel S.;
- Danko, David;
- Foox, Jonathan;
- Ahsanuddin, Sofia;
- Tighe, Scott;
- Hasan, Nur A.;
- Subramanian, Poorani;
- Moffat, Kelly;
- Levy, Shawn;
- Lonardi, Stefano;
- Greenfield, Nick;
- Colwell, Rita R.;
- Rosen, Gail L.;
- Mason, Christopher E.
Publication type:
Correction Notice
In silico hybridization enables transcriptomic illumination of the nature and evolution of Myxozoa.
Published in:
BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2039-6
By:
- Foox, Jonathan;
- Ringuette, Maurice;
- Desser, Sherwin S.;
- Siddall, Mark E.
Publication type:
Article

Found: 19