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Items: 9

1.

MetaCarvel: linking assembly graph motifs to biological variants.

Ghurye J, Treangen T, Fedarko M, Hervey WJ 4th, Pop M.

Genome Biol. 2019 Aug 26;20(1):174. doi: 10.1186/s13059-019-1791-3.

2.

Integrating Hi-C links with assembly graphs for chromosome-scale assembly.

Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S.

PLoS Comput Biol. 2019 Aug 21;15(8):e1007273. doi: 10.1371/journal.pcbi.1007273. eCollection 2019 Aug.

3.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL.

Genome Biol. 2019 Aug 2;20(1):153. doi: 10.1186/s13059-019-1760-x.

4.

Modern technologies and algorithms for scaffolding assembled genomes.

Ghurye J, Pop M.

PLoS Comput Biol. 2019 Jun 5;15(6):e1006994. doi: 10.1371/journal.pcbi.1006994. eCollection 2019 Jun. Review.

5.

A chromosome-scale assembly of the major African malaria vector Anopheles funestus.

Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ.

Gigascience. 2019 Jun 1;8(6). pii: giz063. doi: 10.1093/gigascience/giz063.

6.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ.

Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5.

7.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M.

Brief Bioinform. 2017 Aug 7. doi: 10.1093/bib/bbx098. [Epub ahead of print]

PMID:
28968737
8.

Scaffolding of long read assemblies using long range contact information.

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.

BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z.

9.

Metagenomic Assembly: Overview, Challenges and Applications.

Ghurye JS, Cepeda-Espinoza V, Pop M.

Yale J Biol Med. 2016 Sep 30;89(3):353-362. eCollection 2016 Sep. Review.

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