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Lawrence Berkeley National Laboratory's Articles

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Page 7 of 39

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

Authors: Marcus D. Hanwell, Wibe A. de Jong and Christopher J. Harris

Citation: Journal of Cheminformatics 2017 9:55

Content type: Research article

Published on: 30 October 2017
Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts

Authors: Junko Yaegashi, James Kirby, Masakazu Ito, Jian Sun, Tanmoy Dutta, Mona Mirsiaghi, Eric R. Sundstrom, Alberto Rodriguez, Edward Baidoo, Deepti Tanjore, Todd Pray, Kenneth Sale, Seema Singh, Jay D. Keasling, Blake A. Simmons, Steven W. Singer…

Citation: Biotechnology for Biofuels 2017 10:241

Content type: Research

Published on: 23 October 2017
Towards a balanced view of the bacterial tree of life

Authors: Frederik Schulz, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides and Tanja Woyke

Citation: Microbiome 2017 5:140

Content type: Short report

Published on: 17 October 2017

The Correction to this article has been published in Microbiome 2017 5:149
Draft genome sequence of Dethiobacter alkaliphilus strain AHT1^T, a gram-positive sulfidogenic polyextremophile

Authors: Emily Denise Melton, Dimitry Y. Sorokin, Lex Overmars, Alla L. Lapidus, Manoj Pillay, Natalia Ivanova, Tijana Glavina del Rio, Nikos C. Kyrpides, Tanja Woyke and Gerard Muyzer

Citation: Standards in Genomic Sciences 2017 12:57

Content type: Extended genome report

Published on: 21 September 2017
Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

Authors: Joanne B. Emerson, Rachel I. Adams, Clarisse M. Betancourt Román, Brandon Brooks, David A. Coil, Katherine Dahlhausen, Holly H. Ganz, Erica M. Hartmann, Tiffany Hsu, Nicholas B. Justice, Ivan G. Paulino-Lima, Julia C. Luongo, Despoina S. Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk…

Citation: Microbiome 2017 5:86

Content type: Review

Published on: 16 August 2017
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

Authors: Janine Kamke, Priya Soni, Yang Li, Siva Ganesh, William J. Kelly, Sinead C. Leahy, Weibing Shi, Jeff Froula, Edward M. Rubin and Graeme T. Attwood

Citation: BMC Research Notes 2017 10:367

Content type: Research article

Published on: 8 August 2017
NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks

Authors: Theodosios Theodosiou, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C. Kyrpides, Pantelis G. Bagos, Ioannis Iliopoulos and Georgios A. Pavlopoulos

Citation: BMC Research Notes 2017 10:278

Content type: Research note

Published on: 14 July 2017
Control of lupus nephritis by changes of gut microbiota

Authors: Qinghui Mu, Husen Zhang, Xiaofeng Liao, Kaisen Lin, Hualan Liu, Michael R. Edwards, S. Ansar Ahmed, Ruoxi Yuan, Liwu Li, Thomas E. Cecere, David B. Branson, Jay L. Kirby, Poorna Goswami, Caroline M. Leeth, Kaitlin A. Read, Kenneth J. Oestreich…

Citation: Microbiome 2017 5:73

Content type: Research

Published on: 11 July 2017
Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects

Authors: Athel Cornish-Bowden, Athel Cornish-Bowden, David Rasnick, Henry H. Heng, Steven Horne, Batoul Abdallah, Guo Liu, Christine J. Ye, Mathew Bloomfield, Mark D. Vincent, C. Marcelo Aldaz, Jenny Karlsson, Anders Valind, Caroline Jansson, David Gisselsson, Jennifer A. Marshall Graves…

Citation: Molecular Cytogenetics 2017 10(Suppl 2):21

Content type: Meeting abstracts

Published on: 22 June 2017

This article is part of a Supplement: Volume 10 Supplement 2
Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation

Authors: Jian Sun, Jian Shi, N. V. S. N. Murthy Konda, Dan Campos, Dajiang Liu, Stuart Nemser, Julia Shamshina, Tanmoy Dutta, Paula Berton, Gabriela Gurau, Robin D. Rogers, Blake A. Simmons and Seema Singh

Citation: Biotechnology for Biofuels 2017 10:154

Content type: Research

Published on: 15 June 2017
The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa

Authors: Nils Thieme, Vincent W. Wu, Axel Dietschmann, Asaf A. Salamov, Mei Wang, Jenifer Johnson, Vasanth R. Singan, Igor V. Grigoriev, N. Louise Glass, Chris R. Somerville and J. Philipp Benz

Citation: Biotechnology for Biofuels 2017 10:149

Content type: Research

Published on: 12 June 2017
Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions

Authors: Sugeerth Murugesan, Kristofer Bouchard, Edward Chang, Max Dougherty, Bernd Hamann and Gunther H. Weber

Citation: BMC Bioinformatics 2017 18(Suppl 6):236

Content type: Research

Published on: 6 June 2017

This article is part of a Supplement: Volume 18 Supplement 6
Dead simple OWL design patterns

Authors: David Osumi-Sutherland, Melanie Courtot, James P. Balhoff and Christopher Mungall

Citation: Journal of Biomedical Semantics 2017 8:18

Content type: Software

Published on: 5 June 2017
Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space

Authors: Junyu Zhang, Qun Gao, Qiuting Zhang, Tengxu Wang, Haowei Yue, Linwei Wu, Jason Shi, Ziyan Qin, Jizhong Zhou, Jiane Zuo and Yunfeng Yang

Citation: Microbiome 2017 5:57

Content type: Research

Published on: 31 May 2017
Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar

Authors: Kwang Ho Kim, Tanmoy Dutta, John Ralph, Shawn D. Mansfield, Blake A. Simmons and Seema Singh

Citation: Biotechnology for Biofuels 2017 10:101

Content type: Research

Published on: 20 April 2017
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Authors: Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling and Héctor García Martín

Citation: BMC Bioinformatics 2017 18:219

Content type: Erratum

Published on: 18 April 2017

The original article was published in BMC Bioinformatics 2017 18:205
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Authors: Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling and Héctor García Martín

Citation: BMC Bioinformatics 2017 18:205

Content type: Software

Published on: 5 April 2017

The Erratum to this article has been published in BMC Bioinformatics 2017 18:219
Ternary ionic liquid–water pretreatment systems of an agave bagasse and municipal solid waste blend

Authors: Jose A. Perez-Pimienta, Noppadon Sathitsuksanoh, Vicki S. Thompson, Kim Tran, Teresa Ponce-Noyola, Vitalie Stavila, Seema Singh and Blake A. Simmons

Citation: Biotechnology for Biofuels 2017 10:72

Content type: Research

Published on: 21 March 2017
Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

Authors: Emil D. Jensen, Raphael Ferreira, Tadas Jakočiūnas, Dushica Arsovska, Jie Zhang, Ling Ding, Justin D. Smith, Florian David, Jens Nielsen, Michael K. Jensen and Jay D. Keasling

Citation: Microbial Cell Factories 2017 16:46

Content type: Research

Published on: 15 March 2017
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Authors: Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A. Braus-Stromeyer, Camila Caldana, David Cánovas…

Citation: Genome Biology 2017 18:28

Content type: Research

Published on: 14 February 2017

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Lawrence Berkeley National Laboratory

Lawrence Berkeley National Laboratory's Articles

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts

Towards a balanced view of the bacterial tree of life

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1^T, a gram-positive sulfidogenic polyextremophile

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks

Control of lupus nephritis by changes of gut microbiota

Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects

Efficient dehydration and recovery of ionic liquid after lignocellulosic processing using pervaporation

The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa

Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions

Dead simple OWL design patterns

Bacteriophage–prokaryote dynamics and interaction within anaerobic digestion processes across time and space

Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar

Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Ternary ionic liquid–water pretreatment systems of an agave bagasse and municipal solid waste blend

Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus