Another good collection of recommended papers from Pubchase

Got my weekly "Recommended papers" from Pubchase today.  I wrote about this here: Pubchase recommended papers to read system pretty good ... Below is the email I got: many of direct relevance to my work.  Thanks Pubchase.  Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. Jan 23, 2014 Journal Of Clinical Microbiology Lim YW, Evangelista JS, Schmieder R, Bailey B, Haynes M, Furlan M, Maughan H, Edwards R, Rohwer F, Conrad D, Forbes BA

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Jan 17, 2014 GigaScience Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF

Diet rapidly and reproducibly alters the human gut microbiome. Jan 23, 2014 Nature David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ

Sequencing depth and coverage: key considerations in genomic analyses. Jan 17, 2014 Nature Reviews. Genetics Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP

Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis. Jan 21, 2014 The ISME Journal Blasiak LC, Zinder SH, Buckley DH, Hill RT

Networks of lexical borrowing and lateral gene transfer in language and genome evolution. Jan 15, 2014 BioEssays : News And Reviews In Molecular, Cellular And Developmental Biology List JM, Nelson-Sathi S, Geisler H, Martin W

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. Jan 21, 2014 The ISME Journal Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L

New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis. Jan 22, 2014 MBio Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM, Bajaksouzian S, Benard MF, Jacobs MR, Bonomo RA, Adams MD

Cultivation and preservation of members of the family Halobacteriaceae. Jan 15, 2014 World Journal Of Microbiology & Biotechnology Tindall BJ

Muc5b is required for airway defence. Jan 16, 2014 Nature Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition. Jan 17, 2014 Applied And Environmental Microbiology Porras-Alfaro A, Liu KL, Kuske CR, Xie G

A genetic inventory of spacecraft and associated surfaces. Jan 17, 2014 Astrobiology La Duc MT, Venkateswaran K, Conley CA

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Jan 17, 2014 Molecular Ecology Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA

Molecular analysis of point-of-use municipal drinking water microbiology. Jan 20, 2014 Water Research Holinger EP, Ross KA, Robertson CE, Stevens MJ, Harris JK, Pace NR

The Pine Bark Adelgid, Pineus strobi, Contains Two Novel Bacteriocyte-Associated Gammaproteobacterial Symbionts. Jan 17, 2014 Applied And Environmental Microbiology Toenshoff ER, Szabó G, Gruber D, Horn M

First detection of Toscana virus in Corsica, France. Jan 15, 2014 Clinical Microbiology And Infection : The Official Publication Of The European Society Of Clinical Microbiology And Infectious Diseases Bichaud L, Izri A, de Lamballerie X, Moureau G, Charrel RN

Deposition of Extreme-Tolerant Bacterial Strains Isolated during Different Phases of Phoenix Spacecraft Assembly in a Public Culture Collection. Jan 17, 2014 Astrobiology Venkateswaran K, Vaishampayan P, Benardini JN, Rooney AP, Spry JA

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Jan 16, 2014 Bioinformatics (Oxford, England) Matias Rodrigues JF, von Mering C

Clinical and epidemiologic phenotypes of childhood asthma. Jan 16, 2014 American Journal Of Respiratory And Critical Care Medicine Depner M, Fuchs O, Genuneit J, Karvonen AM, Hyvärinen A, Kaulek V, Roduit C, Weber J, Schaub B, Lauener R, Kabesch M, Pfefferle PI, Frey U, Pekkanen J, Dalphin JC, Riedler J, Braun-Fahrländer C, von Mutius E, Ege MJ, PASTURE Study Group

Genome degeneration and adaptation in a nascent stage of symbiosis. Jan 17, 2014 Genome Biology And Evolution Oakeson KF, Gil R, Clayton AL, Dunn DM, von Niederhausern AC, Hamil C, Aoyagi A, Duval B, Baca A, Silva FJ, Vallier A, Jackson DG, Latorre A, Weiss RB, Heddi A, Moya A, Dale C

Heavy rainfall events and diarrhea incidence: the role of social and environmental factors. Jan 20, 2014 American Journal Of Epidemiology Carlton EJ, Eisenberg JN, Goldstick J, Cevallos W, Trostle J, Levy K

Implementing planetary protection measures on the Mars science laboratory. Jan 17, 2014 Astrobiology Benardini JN, La Duc MT, Beaudet RA, Koukol R

Implementing planetary protection on the atlas v fairing and ground systems used to launch the Mars science laboratory. Jan 17, 2014 Astrobiology Benardini JN, La Duc MT, Ballou D, Koukol R

Observation time scale, free-energy landscapes, and molecular symmetry. Jan 15, 2014 Proceedings Of The National Academy Of Sciences Of The United States Of America Wales DJ, Salamon P

Characterization of Escherichia coli Isolates from Hospital Inpatients or Outpatients with Urinary Tract Infection. Jan 23, 2014 Journal Of Clinical Microbiology Toval F, Köhler CD, Vogel U, Wagenlehner F, Mellmann A, Fruth A, Schmidt MA, Karch H, Bielaszewska M, Dobrindt U, Forbes BA

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. Jan 24, 2014 Omics : A Journal Of Integrative Biology Kolker E, Ozdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G

Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Jan 17, 2014 Molecular Phylogenetics And Evolution Smith DR, Arrigo KR, Alderkamp AC, Allen AE

Meiosis and Haploid Gametes in the Pathogen Trypanosoma brucei. Jan 24, 2014 Current Biology : CB Peacock L, Bailey M, Carrington M, Gibson W

Recruiting human microbiome shotgun data to site-specific reference genomes. Jan 23, 2014 PloS One Xie G, Lo CC, Scholz M, Chain PS

Metadata Checklist for the Integrated Personal OMICS Study: Proteomics and Metabolomics Experiments. Jan 24, 2014 Omics : A Journal Of Integrative Biology Snyder M, Mias G, Stanberry L, Kolker E

Ready to put metadata on the post-2015 development agenda? Linking data publications to responsible innovation and science diplomacy. Jan 24, 2014 Omics : A Journal Of Integrative Biology Ozdemir V, Kolker E, Hotez PJ, Mohin S, Prainsack B, Wynne B, Vayena E, Coşkun Y, Dereli T, Huzair F, Borda-Rodriguez A, Bragazzi NL, Faris J, Ramesar R, Wonkam A, Dandara C, Nair B, Llerena A, Kılıç K, Jain R, Reddy PJ, Gollapalli K, Srivastava S, Kickbusch I

Vibrio mimicus are the reservoirs of the heat-stable enterotoxin gene (nag-st) among species of the genus Vibrio. Jan 14, 2014 World Journal Of Microbiology & Biotechnology Yuan P, Ogawa A, Ramamurthy T, Nair GB, Shimada T, Shinoda S, Takeda T

[Two peaks of plastidial DNA-synthesis with different light-dependency in the cell cycle of Euglena gracilis]. Jan 17, 2014 Planta Brandt P

[Regulation of the synthesis of plastid proteins in Euglena gracilis]. Jan 15, 2014 Planta Brandt P

Multi-scale modelling of bioreactor-separator system for wastewater treatment with two-dimensional activated sludge floc dynamics. Jan 21, 2014 Water Research Ofiţeru ID, Bellucci M, Picioreanu C, Lavric V, Curtis TP