Treangen, Todd: search on Z-Library

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1

Repetitive DNA and next-generation sequencing: computational challenges and solutions

Treangen, Todd J., Salzberg, Steven L.

Journal:

Nature Reviews Genetics

Year:

2011

Language:

english

File:

PDF, 771 KB

english, 2011

2

Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications

Chopyk, Jessica, Nasko, Daniel J., Allard, Sarah, Bui, Anthony, Treangen, Todd, Pop, Mihai, Mongodin, Emmanuel F., Sapkota, Amy R.

Journal:

Year:

2019

Language:

english

File:

PDF, 1.65 MB

english, 2019

3

M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

Todd J Treangen, Xavier Messeguer

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.15 MB

english, 2006

4

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

Treangen, Todd J., Rocha, Eduardo P. C., Moran, Nancy A.

Journal:

Year:

2011

Language:

english

File:

PDF, 760 KB

english, 2011

5

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

Davison, Michelle, Treangen, Todd J., Koren, Sergey, Pop, Mihai, Bhaya, Devaki, Schuch, Raymond

Journal:

Year:

2016

Language:

english

File:

PDF, 2.77 MB

english, 2016

6

ScaffViz: visualizing metagenome assemblies

Sergey Koren, Todd Treangen, Mihai Pop

Journal:

Year:

2011

Language:

english

File:

PDF, 333 KB

english, 2011

7

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS

Treangen, Todd J, Koren, Sergey, Astrovskaya, Irina, Sommer, Dan, Liu, Bo, Pop, Mihai

Journal:

Year:

2011

Language:

english

File:

PDF, 373 KB

english, 2011

8

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

Olson, Nathan D., Treangen, Todd J., Hill, Christopher M., Cepeda-Espinoza, Victoria, Ghurye, Jay, Koren, Sergey, Pop, Mihai

Journal:

Briefings in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 459 KB

english, 2017

9

Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone

Todd J Treangen, Adam M Phillippy

Journal:

Year:

2012

Language:

english

File:

PDF, 90 KB

english, 2012

10

Automated ensemble assembly and validation of microbial genomes

Koren, Sergey, Treangen, Todd J, Hill, Christopher M, Pop, Mihai, Phillippy, Adam M

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 876 KB

english, 2014

11

Genesis, effects and fates of repeats in prokaryotic genomes

Todd J. Treangen, Anne-Laure Abraham, Marie Touchon, Eduardo P.C. Rocha

Journal:

FEMS Microbiology Reviews

Year:

2009

Language:

english

File:

PDF, 559 KB

english, 2009

12

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop

Journal:

Year:

2011

Language:

english

File:

PDF, 333 KB

english, 2011

13

MetaCarvel: linking assembly graph motifs to biological variants

Ghurye, Jay, Treangen, Todd, Fedarko, Marcus, Hervey, W. Judson, Pop, Mihai

Journal:

Year:

2019

Language:

english

File:

PDF, 1.25 MB

english, 2019

14

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya…

Journal:

Year:

2013

Language:

english

File:

PDF, 1.02 MB

english, 2013

15

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop

Journal:

Year:

2011

Language:

english

File:

PDF, 373 KB

english, 2011

16

[IEEE 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - San Diego, CA, USA (2019.11.18-2019.11.21)] 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest

Albin, Dreycey, Muthu, Pravin, Godbold, Gene, Lindvall, Mikael, Diep, Madeline, Porter, Adam, Pop, Mihai, Ternus, Krista, Treangen, Todd J., Nasko, Dan, Elworth, R. A. Leo, Lu, Jacob, Balaji, Advait,

Year:

2019

File:

PDF, 3.61 MB

2019

17

Repetitive DNA and next-generation sequencing: computational challenges and solutions

Treangen, Todd J., Salzberg, Steven L.

Journal:

Nature Reviews Genetics

Year:

2012

File:

PDF, 41 KB

2012

18

[IEEE 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Shanghai, China (2013.12.18-2013.12.21)] 2013 IEEE International Conference on Bioinformatics and Biomedicine - De novo likelihood-based measures for comparing metagenomic assemblies

Hill, Christopher M., Astrovskaya, Irina, Huang, Howard, Koren, Sergey, Memon, Atif, Treangen, Todd J., Pop, Mihai

Year:

2013

Language:

english

File:

PDF, 141 KB

english, 2013

19

Mash: fast genome and metagenome distance estimation using MinHash

Ondov, Brian D., Treangen, Todd J., Melsted, Páll, Mallonee, Adam B., Bergman, Nicholas H., Koren, Sergey, Phillippy, Adam M.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.12 MB

english, 2016

20

MetAMOS: a metagenomic assembly and analysis pipeline for AMOS

Todd J Treangen, Sergey Koren, Irina Astrovskaya, Dan Sommer, Bo Liu…

Journal:

Year:

2011

Language:

english

File:

PDF, 333 KB

english, 2011

21

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

Treangen, Todd J, Ondov, Brian D, Koren, Sergey, Phillippy, Adam M

Journal:

Year:

2014

Language:

english

File:

PDF, 2.01 MB

english, 2014

22

Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides

Elworth, R. A. Leo, Diaz, Christian, Yang, Jing, de Figueiredo, Paul, Ternus, Krista, Treangen, Todd, Mehle, Andrew

Journal:

Year:

2020

File:

PDF, 599 KB

2020

23

You can't always sequence your way out of a tight spot

Treangen, Todd J, Pop, Mihai

Journal:

Year:

2018

Language:

english

File:

PDF, 389 KB

english, 2018

24

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop

Journal:

Year:

2011

Language:

english

File:

PDF, 1.76 MB

english, 2011

25

ScaffViz: visualizing metagenome assemblies

Sergey Koren, Todd Treangen, Mihai Pop

Journal:

Year:

2011

Language:

english

File:

PDF, 373 KB

english, 2011

26

[ACM Press the 7th ACM International Conference - Seattle, WA, USA (2016.10.02-2016.10.05)] Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16 - Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection

Bateman, Amelia, Treangen, Todd J., Pop, Mihai

Year:

2016

Language:

english

File:

PDF, 692 KB

english, 2016

27

The impact of the neisserial DNA uptake sequences on genome evolution and stability

Todd J Treangen, Ole Herman Ambur, Tone Tonjum, Eduardo PC Rocha

Journal:

Year:

2008

Language:

english

File:

PDF, 652 KB

english, 2008

28

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

Nasko, Daniel J., Koren, Sergey, Phillippy, Adam M., Treangen, Todd J.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.00 MB

english, 2018

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