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Terabase-scale metagenome coassembly with MetaHipMer.
Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K. Hofmeyr S, et al. Among authors: clum a. Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5. Sci Rep. 2020. PMID: 32612216 Free PMC article.
One bacterial cell, one complete genome.
Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF. Woyke T, et al. Among authors: clum a. PLoS One. 2010 Apr 23;5(4):e10314. doi: 10.1371/journal.pone.0010314. PLoS One. 2010. PMID: 20428247 Free PMC article.
Generation of long insert pairs using a Cre-LoxP Inverse PCR approach.
Peng Z, Zhao Z, Nath N, Froula JL, Clum A, Zhang T, Cheng JF, Copeland AC, Pennacchio LA, Chen F. Peng Z, et al. Among authors: clum a. PLoS One. 2012;7(1):e29437. doi: 10.1371/journal.pone.0029437. Epub 2012 Jan 9. PLoS One. 2012. PMID: 22253722 Free PMC article.
Next generation sequencing data of a defined microbial mock community.
Singer E, Andreopoulos B, Bowers RM, Lee J, Deshpande S, Chiniquy J, Ciobanu D, Klenk HP, Zane M, Daum C, Clum A, Cheng JF, Copeland A, Woyke T. Singer E, et al. Among authors: clum a. Sci Data. 2016 Sep 27;3:160081. doi: 10.1038/sdata.2016.81. Sci Data. 2016. PMID: 27673566 Free PMC article.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium; Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Among authors: clum a. Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Nat Biotechnol. 2017. PMID: 28787424 Free PMC article.
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom.
Nowinski B, Smith CB, Thomas CM, Esson K, Marin R 3rd, Preston CM, Birch JM, Scholin CA, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Glavina Del Rio T, Whitman WB, Kiene RP, Eloe-Fadrosh EA, Moran MA. Nowinski B, et al. Among authors: clum a. Sci Data. 2019 Jul 22;6(1):129. doi: 10.1038/s41597-019-0132-4. Sci Data. 2019. PMID: 31332186 Free PMC article.
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot.
Camargo AP, de Souza RSC, de Britto Costa P, Gerhardt IR, Dante RA, Teodoro GS, Abrahão A, Lambers H, Carazzolle MF, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Pennacchio C, Eloe-Fadrosh EA, Arruda P, Oliveira RS. Camargo AP, et al. Among authors: clum a. Sci Data. 2019 Jul 31;6(1):140. doi: 10.1038/s41597-019-0141-3. Sci Data. 2019. PMID: 31366912 Free PMC article.
Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.
Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, Brambilla D, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IA, Ivanova NN, Kyrpides NC, Harmon-Smith M, Eloe-Fadrosh EA, Lundin D, Engblom S, Dopson M. Högfors-Rönnholm E, et al. Among authors: clum a. Sci Data. 2019 Oct 16;6(1):207. doi: 10.1038/s41597-019-0222-3. Sci Data. 2019. PMID: 31619684 Free PMC article.
Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.
Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T. Sevim V, et al. Among authors: clum a. Sci Data. 2019 Nov 26;6(1):285. doi: 10.1038/s41597-019-0287-z. Sci Data. 2019. PMID: 31772173 Free PMC article.
113 results