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Select item 79860431.

Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species

Silvia Madritsch, Agnes Burg, Eva M. Sehr

BMC Bioinformatics. 2021; 22: 146. Published online 2021 Mar 22. doi: 10.1186/s12859-021-04078-8

PMCID:: PMC7986043

Abstract Article PDF–1.0M

Select item 47105002.

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline

Mark Davids, Floor Hugenholtz, Vitor Martins dos Santos, Hauke Smidt, Michiel Kleerebezem, Peter J. Schaap

PLoS One. 2016; 11(1): e0146423. Published online 2016 Jan 12. doi: 10.1371/journal.pone.0146423

PMCID:: PMC4710500

Abstract Article PDF–2.3M

Select item 57313473.

From word models to executable models of signaling networks using automated assembly

Benjamin M Gyori, John A Bachman, Kartik Subramanian, Jeremy L Muhlich, Lucian Galescu, Peter K Sorger

Mol Syst Biol. 2017 Nov; 13(11): 954. Published online 2017 Nov 24. doi: 10.15252/msb.20177651

PMCID:: PMC5731347

Abstract Article PDF–4.3M

Select item 76483914.

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

Lei Liu, Yulin Wang, You Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Chunmiao Zheng, Tong Zhang

Microbiome. 2020; 8: 155. Published online 2020 Nov 6. doi: 10.1186/s40168-020-00937-3

PMCID:: PMC7648391

Abstract Article PDF–1.2M

Select item 89522635.

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Weihong Qi, Yi-Wen Lim, Andrea Patrignani, Pascal Schläpfer, Anna Bratus-Neuenschwander, Simon Grüter, Christelle Chanez, Nathalie Rodde, Elisa Prat, Sonia Vautrin, Margaux-Alison Fustier, Diogo Pratas, Ralph Schlapbach, Wilhelm Gruissem

Gigascience. 2022; 11: giac028. Published online 2022 Mar 24. doi: 10.1093/gigascience/giac028

PMCID:: PMC8952263

Abstract Article PDF–6.7M

Select item 73601086.

A Summary of the Fourth Annual Virology Education HIV Microbiome Workshop

Brett Williams, Mimi Ghosh, Charles Boucher, Frederic Bushman, Stacy Carrington-Lawrence, Ronald G. Collman, Satya Dandekar, Que Dang, Angela Malaspina, Roger Paredes, Cara Wilson, Sandra Pinto Cardoso, Laurel Lagenaur, Jessica Santos, Christopher Joy, Alan Landay

AIDS Res Hum Retroviruses. May 2020; 36(5): 349–356. Published online 2020 Apr 30. doi: 10.1089/aid.2019.0197

PMCID:: PMC7360108

Abstract Article PDF–180K

Select item 55699217.

Kronos: a workflow assembler for genome analytics and informatics

M. Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M. Grande, Radhouane Aniba, Jasleen Grewal, Paul C. Boutros, Ryan D. Morin, Ali Bashashati, Sohrab P. Shah

Gigascience. 2017 Jul; 6(7): 1–10. Published online 2017 Jun 26. doi: 10.1093/gigascience/gix042

PMCID:: PMC5569921

Abstract Article PDF–2.0M

Select item 31898838.

SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery

Davide Bedognetti, James M Balwit, Ena Wang, Mary L Disis, Cedrik M Britten, Lucia G Delogu, Sara Tomei, Bernard A Fox, Thomas F Gajewski, Francesco M Marincola, Lisa H Butterfield

J Transl Med. 2011; 9: 155. Published online 2011 Sep 19. doi: 10.1186/1479-5876-9-155

PMCID:: PMC3189883

Abstract Article PDF–766K

Select item 31268509.

Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

Francisco Prosdocimi, Daniela Bittencourt, Felipe Rodrigues da Silva, Matias Kirst, Paulo C. Motta, Elibio L. Rech

PLoS One. 2011; 6(6): e21634. Published online 2011 Jun 29. doi: 10.1371/journal.pone.0021634

PMCID:: PMC3126850

Abstract Article PDF–1.0M

Select item 986563210.

Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica

Frédéric Bigey, Emilie Pasteur, Xymena Połomska, Stéphane Thomas, Anne-Marie Crutz-Le Coq, Hugo Devillers, Cécile Neuvéglise

J Fungi (Basel) 2023 Jan; 9(1): 76. Published online 2023 Jan 4. doi: 10.3390/jof9010076

PMCID:: PMC9865632

Abstract Article PDF–28M

Select item 791324011.

Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome

O. Ufuk Nalbantoglu

Entropy (Basel) 2021 Feb; 23(2): 187. Published online 2021 Feb 2. doi: 10.3390/e23020187

PMCID:: PMC7913240

Abstract Article PDF–1.9M

Select item 959326312.

BOA: A partitioned view of genome assembly

Xiaojing An, Priyanka Ghosh, Patrick Keppler, Sureyya Emre Kurt, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam, Ümit V. Çatalyürek, Ananth Kalyanaraman

iScience. 2022 Nov 18; 25(11): 105273. Published online 2022 Oct 8. doi: 10.1016/j.isci.2022.105273

PMCID:: PMC9593263

Abstract Article PDF–1.5M

Select item 793586813.

Engineered yeast genomes accurately assembled from pure and mixed samples

Joseph H. Collins, Kevin W. Keating, Trent R. Jones, Shravani Balaji, Celeste B. Marsan, Marina Çomo, Zachary J. Newlon, Tom Mitchell, Bryan Bartley, Aaron Adler, Nicholas Roehner, Eric M. Young

Nat Commun. 2021; 12: 1485. Published online 2021 Mar 5. doi: 10.1038/s41467-021-21656-9

PMCID:: PMC7935868

Abstract Article PDF–1.7M

Select item 784201514.

Telomere length de novo assembly of all 7 chromosomes and mitogenome sequencing of the model entomopathogenic fungus, Metarhizium brunneum, by means of a novel assembly pipeline

Zack Saud, Alexandra M. Kortsinoglou, Vassili N. Kouvelis, Tariq M. Butt

BMC Genomics. 2021; 22: 87. Published online 2021 Jan 28. doi: 10.1186/s12864-021-07390-y

PMCID:: PMC7842015

Abstract Article PDF–1.6M

Select item 600344115.

FEMPAR: An Object-Oriented Parallel Finite Element Framework

Santiago Badia, Alberto F. Martín, Javier Principe

Arch Comput Methods Eng. 2018; 25(2): 195–271. Published online 2017 Oct 11. doi: 10.1007/s11831-017-9244-1

PMCID:: PMC6003441

Abstract Article PDF–12M

Select item 765753916.

A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA

Hans Vasquez-Gross, Sukhwinder Kaur, Lynn Epstein, Jorge Dubcovsky

PLoS One. 2020; 15(11): e0238611. Published online 2020 Nov 11. doi: 10.1371/journal.pone.0238611

PMCID:: PMC7657539

Abstract Article PDF–1.8M

Select item 1095588817.

Self-replicating hierarchical modular robotic swarms

Amira Abdel-Rahman, Christopher Cameron, Benjamin Jenett, Miana Smith, Neil Gershenfeld

Commun Eng. 2022; 1: 35. Published online 2022 Nov 22. doi: 10.1038/s44172-022-00034-3

PMCID:: PMC10955888

Abstract Article PDF–2.5M

Select item 670733118.

Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet

R. Dean Astumian

Nat Commun. 2019; 10: 3837. Published online 2019 Aug 23. doi: 10.1038/s41467-019-11402-7

PMCID:: PMC6707331

Abstract Article PDF–1.1M

Select item 290554719.

A computational genomics pipeline for prokaryotic sequencing projects

Andrey O. Kislyuk, Lee S. Katz, Sonia Agrawal, Matthew S. Hagen, Andrew B. Conley, Pushkala Jayaraman, Viswateja Nelakuditi, Jay C. Humphrey, Scott A. Sammons, Dhwani Govil, Raydel D. Mair, Kathleen M. Tatti, Maria L. Tondella, Brian H. Harcourt, Leonard W. Mayer, I. King Jordan

Bioinformatics. 2010 Aug 1; 26(15): 1819–1826. Published online 2010 Jun 2. doi: 10.1093/bioinformatics/btq284