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Select item 66243081.

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

Alexander T. Dilthey, Chirag Jain, Sergey Koren, Adam M. Phillippy

Nat Commun. 2019; 10: 3066. Published online 2019 Jul 11. doi: 10.1038/s41467-019-10934-2

PMCID:: PMC6624308

Abstract Article PDF–1000K

Select item 51075712.

Genome-Wide Discovery of Putative sRNAs in Paracoccus denitrificans Expressed under Nitrous Oxide Emitting Conditions

Hannah Gaimster, Lisa Chalklen, Mark Alston, John T. Munnoch, David J. Richardson, Andrew J. Gates, Gary Rowley

Front Microbiol. 2016; 7: 1806. Published online 2016 Nov 14. doi: 10.3389/fmicb.2016.01806

PMCID:: PMC5107571

Abstract Article PDF–3.2M

Select item 47795613.

HGA: denovo genome assembly method for bacterial genomes using high coverage short sequencing reads

Anas A. Al-okaily

BMC Genomics. 2016; 17: 193. Published online 2016 Mar 5. doi: 10.1186/s12864-016-2515-7

PMCID:: PMC4779561

Abstract Article PDF–1.6M

Select item 47066504.

The mysterious orphans of Mycoplasmataceae

Tatiana V. Tatarinova, Inna Lysnyansky, Yuri V. Nikolsky, Alexander Bolshoy

Biol Direct. 2016; 11: 2. Published online 2016 Jan 8. doi: 10.1186/s13062-015-0104-3

PMCID:: PMC4706650

Abstract Article PDF–1.6M

Select item 46151795.

Thermodynamic matchers for the construction of the cuckoo RNA family

Jan Reinkensmeier, Robert Giegerich

RNA Biol. 2015 Feb; 12(2): 197–207. Published online 2015 Mar 16. doi: 10.1080/15476286.2015.1017206

PMCID:: PMC4615179

Abstract Article PDF–653K

Select item 44581276.

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs

Rebecca R. Murphy, Jared O’Connell, Anthony J. Cox, Ole Schulz-Trieglaff

PeerJ. 2015; 3: e996. Published online 2015 Jun 2. doi: 10.7717/peerj.996

PMCID:: PMC4458127

Abstract Article PDF–1.1M

Select item 44168547.

The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways

Patrick Scheerer, Fan Zhang, Jacqueline Kalms, David von Stetten, Norbert Krauß, Inga Oberpichler, Tilman Lamparter

J Biol Chem. 2015 May 1; 290(18): 11504–11514. Published online 2015 Mar 17. doi: 10.1074/jbc.M115.637868

PMCID:: PMC4416854

Abstract Article PDF–2.7M

Select item 39649388.

Network portal: a database for storage, analysis and visualization of biological networks

Serdar Turkarslan, Elisabeth J. Wurtmann, Wei-Ju Wu, Ning Jiang, J. Christopher Bare, Karen Foley, David J. Reiss, Pavel Novichkov, Nitin S. Baliga

Nucleic Acids Res. 2014 Jan 1; 42(Database issue): D184–D190. Published online 2013 Nov 23. doi: 10.1093/nar/gkt1190

PMCID:: PMC3964938

Abstract Article PDF–2.9M

Select item 39276079.

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

Arshan Nasir, Aisha Naeem, Muhammad Jawad Khan, Horacio D. Lopez-Nicora, Gustavo Caetano-Anollés

Genes (Basel) 2011 Dec; 2(4): 869–911. Published online 2011 Nov 8. doi: 10.3390/genes2040869

PMCID:: PMC3927607

Abstract Article PDF–2.0M

Select item 390900210.

Molecular Cloning, Overexpression and Characterization of a Novel Water Channel Protein from Rhodobacter sphaeroides

Mustafa Erbakan, Yue-xiao Shen, Mariusz Grzelakowski, Peter J. Butler, Manish Kumar, Wayne R. Curtis

PLoS One. 2014; 9(1): e86830. Published online 2014 Jan 31. doi: 10.1371/journal.pone.0086830

PMCID:: PMC3909002

Abstract Article PDF–934K

Select item 384714411.

Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme

Lorenzo Carretero-Paulet, Agnieszka Lipska, Jordi Pérez-Gil, Félix J Sangari, Victor A Albert, Manuel Rodríguez-Concepción

BMC Evol Biol. 2013; 13: 180. Published online 2013 Sep 3. doi: 10.1186/1471-2148-13-180

PMCID:: PMC3847144

Abstract Article PDF–1.9M

Select item 343997412.

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

Georgia Giannoukos, Dawn M Ciulla, Katherine Huang, Brian J Haas, Jacques Izard, Joshua Z Levin, Jonathan Livny, Ashlee M Earl, Dirk Gevers, Doyle V Ward, Chad Nusbaum, Bruce W Birren, Andreas Gnirke

Genome Biol. 2012; 13(3): r23. Published online 2012 Mar 28. doi: 10.1186/gb-2012-13-3-r23

PMCID:: PMC3439974

Abstract Article PDF–1.0M

Select item 342830213.

Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics

L. Safak Yilmaz, Alexander Loy, Erik S. Wright, Michael Wagner, Daniel R. Noguera

PLoS One. 2012; 7(8): e43862. Published online 2012 Aug 27. doi: 10.1371/journal.pone.0043862

PMCID:: PMC3428302

Abstract Article PDF–1.1M

Select item 342453914.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

Naama Wald, Maya Alroy, Maya Botzman, Hanah Margalit

Nucleic Acids Res. 2012 Aug; 40(15): 7074–7083. Published online 2012 May 11. doi: 10.1093/nar/gks348

PMCID:: PMC3424539

Abstract Article PDF–3.5M

Select item 337461315.

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

John Martin, Sean Sykes, Sarah Young, Karthik Kota, Ravi Sanka, Nihar Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva

PLoS One. 2012; 7(6): e36427. Published online 2012 Jun 13. doi: 10.1371/journal.pone.0036427

PMCID:: PMC3374613

Abstract Article PDF–3.3M

Select item 327883616.

Novel base triples in RNA structures revealed by graph theoretical searching methods

Mohd Firdaus-Raih, Anne-Marie Harrison, Peter Willett, Peter J Artymiuk

BMC Bioinformatics. 2011; 12(Suppl 13): S2. Published online 2011 Nov 30. doi: 10.1186/1471-2105-12-S13-S2

PMCID:: PMC3278836

Abstract Article PDF–1.3M

Select item 320497517.

A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster

Inga Oberpichler, Antonio J. Pierik, Janine Wesslowski, Richard Pokorny, Ran Rosen, Michal Vugman, Fan Zhang, Olivia Neubauer, Eliora Z. Ron, Alfred Batschauer, Tilman Lamparter

PLoS One. 2011; 6(10): e26775. Published online 2011 Oct 31. doi: 10.1371/journal.pone.0026775

PMCID:: PMC3204975

Abstract Article PDF–602K

Select item 316155118.

Adaptation of aerobic respiration to low O₂ environments

Huazhi Han, James Hemp, Laura A. Pace, Hanlin Ouyang, Krithika Ganesan, Jung Hyeob Roh, Fevzi Daldal, Steven R. Blanke, Robert B. Gennis

Proc Natl Acad Sci U S A. 2011 Aug 23; 108(34): 14109-14114. Published online 2011 Aug 15. doi: 10.1073/pnas.1018958108

Correction in:: Proc Natl Acad Sci U S A. 2012 May 15; 109(20): 7947.

PMCID:: PMC3161551

Abstract Article PDF–484K

Select item 313773519.

Tripping the Light Fantastic: Blue-Light Photoreceptors as Examples of Environmentally-Modulated Protein:Protein Interactions

Brian D. Zoltowski, Kevin H. Gardner

Biochemistry. Author manuscript; available in PMC 2012 Jun 14.

Published in final edited form as: Biochemistry. 2011 Jan 11; 50(1): 4–16. Published online 2010 Dec 14. doi: 10.1021/bi101665s

PMCID:: PMC3137735

Abstract Article PDF–2.6M

Select item 297464220.

Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments

Martin Barz, Christian Beimgraben, Torsten Staller, Frauke Germer, Friederike Opitz, Claudia Marquardt, Christoph Schwarz, Kirstin Gutekunst, Klaus Heinrich Vanselow, Ruth Schmitz, Julie LaRoche, Rüdiger Schulz, Jens Appel

PLoS One. 2010; 5(11): e13846. Published online 2010 Nov 5. doi: 10.1371/journal.pone.0013846