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January 2018

Table of Contents - PeerJ (Biology Articles)

Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

Figure 4

January 10, 2018

Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

This article describes an improved treatment of membrane proteins and lipid-protein molecular interactions.

January 25, 2018

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

Tom O. Delmont, A. Murat Eren

https://doi.org/10.7717/peerj.4320 PubMed 29423345

January 31, 2018

Evidence for widespread dysregulation of circadian clock progression in human cancer

Jarrod Shilts, Guanhua Chen, Jacob J. Hughey

https://doi.org/10.7717/peerj.4327 PubMed 29404219

January 26, 2018

The oldest Archaeopteryx (Theropoda: Avialiae): a new specimen from the Kimmeridgian/Tithonian boundary of Schamhaupten, Bavaria

Oliver W.M. Rauhut, Christian Foth, Helmut Tischlinger

https://doi.org/10.7717/peerj.4191 PubMed 29383285

January 12, 2018

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data

Saima Sultana Tithi, Frank O. Aylward, Roderick V. Jensen, Liqing Zhang

https://doi.org/10.7717/peerj.4227 PubMed 29340239

January 3, 2018

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak

Jason C. Kwong, Courtney R. Lane, Finn Romanes, Anders Gonçalves da Silva, Marion Easton, Katie Cronin, Mary Jo Waters, Takehiro Tomita, Kerrie Stevens, Mark B. Schultz, Sarah L. Baines, Norelle L. Sherry, Glen P. Carter, Andre Mu, Michelle Sait, Susan A. Ballard, Torsten Seemann, Timothy P. Stinear, Benjamin P. Howden

https://doi.org/10.7717/peerj.4210 PubMed 29312831

January 19, 2018

CoMiniGut—a small volume in vitro colon model for the screening of gut microbial fermentation processes

Maria Wiese, Bekzod Khakimov, Sebastian Nielsen, Helena Sørensen, Frans van den Berg, Dennis Sandris Nielsen

https://doi.org/10.7717/peerj.4268 PubMed 29372119

January 24, 2018

Are pumas subordinate carnivores, and does it matter?

L. Mark Elbroch, Anna Kusler

https://doi.org/10.7717/peerj.4293 PubMed 29379688

January 31, 2018

A review of bottom-up vs. top-down control of sponges on Caribbean fore-reefs: what’s old, what’s new, and future directions

Joseph R. Pawlik, Tse-Lynn Loh, Steven E. McMurray

https://doi.org/10.7717/peerj.4343 PubMed 29404224

January 23, 2018

Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa

Nathaniel Evans

https://doi.org/10.7717/peerj.4260 PubMed 29379685

January 12, 2018

A revised cranial description of Massospondylus carinatus Owen (Dinosauria: Sauropodomorpha) based on computed tomographic scans and a review of cranial characters for basal Sauropodomorpha

Kimberley E.J. Chapelle, Jonah N. Choiniere

https://doi.org/10.7717/peerj.4224 PubMed 29340238

January 2, 2018

Satellite tagging highlights the importance of productive Mozambican coastal waters to the ecology and conservation of whale sharks

Christoph A. Rohner, Anthony J. Richardson, Fabrice R. A. Jaine, Michael B. Bennett, Scarla J. Weeks, Geremy Cliff, David P. Robinson, Katie E. Reeve-Arnold, Simon J. Pierce

https://doi.org/10.7717/peerj.4161 PubMed 29312815

January 3, 2018

Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice

Jose F. Garcia-Mazcorro, Nara N. Lage, Susanne Mertens-Talcott, Stephen Talcott, Boon Chew, Scot E. Dowd, Jorge R. Kawas, Giuliana D. Noratto

https://doi.org/10.7717/peerj.4195 PubMed 29312822

January 10, 2018

Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L. Gardy

https://doi.org/10.7717/peerj.4218 PubMed 29340235

January 8, 2018

Resounding failure to replicate links between developmental language disorder and cerebral lateralisation

Alexander C. Wilson, Dorothy V.M. Bishop

https://doi.org/10.7717/peerj.4217 PubMed 29333343

January 29, 2018

Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea

Shu-Xian Yu, Yun-Long Pang, Yin-Chu Wang, Jia-Lin Li, Song Qin

https://doi.org/10.7717/peerj.4272 PubMed 29404208

January 4, 2018

Domestic carnivore interactions with wildlife in the Cape Horn Biosphere Reserve, Chile: husbandry and perceptions of impact from a community perspective

Elke Schüttler, Lorena Saavedra-Aracena, Jaime E. Jiménez

https://doi.org/10.7717/peerj.4124 PubMed 29312813

January 12, 2018

Integrated genomic analyses of lung squamous cell carcinoma for identification of a possible competitive endogenous RNA network by means of TCGA datasets

Pengbo Ning, Zhongxing Wu, Aoxue Hu, Xuepeng Li, Jun He, Xiaocheng Gong, Yuqiong Xia, Yukui Shang, Huijie Bian

https://doi.org/10.7717/peerj.4254 PubMed 29340250

January 25, 2018

Tissue material properties and computational modelling of the human tibiofemoral joint: a critical review

Abby E. Peters, Riaz Akhtar, Eithne J. Comerford, Karl T. Bates

https://doi.org/10.7717/peerj.4298 PubMed 29379690

January 16, 2018

Sicegar: R package for sigmoidal and double-sigmoidal curve fitting

M. Umut Caglar, Ashley I. Teufel, Claus O. Wilke

https://doi.org/10.7717/peerj.4251 PubMed 29362694

January 11, 2018

A new small-bodied ornithopod (Dinosauria, Ornithischia) from a deep, high-energy Early Cretaceous river of the Australian–Antarctic rift system

Matthew C. Herne, Alan M. Tait, Vera Weisbecker, Michael Hall, Jay P. Nair, Michael Cleeland, Steven W. Salisbury

https://doi.org/10.7717/peerj.4113 PubMed 29340228

January 9, 2018

The old and the new plankton: ecological replacement of associations of mollusc plankton and giant filter feeders after the Cretaceous?

Amane Tajika, Alexander Nützel, Christian Klug

https://doi.org/10.7717/peerj.4219 PubMed 29333344

January 22, 2018

Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome

Alexandra H. Mandarano, Ludovic Giloteaux, Betsy A. Keller, Susan M. Levine, Maureen R. Hanson

https://doi.org/10.7717/peerj.4282 PubMed 29375937

January 18, 2018

The importance of local settings: within-year variability in seawater temperature at South Bay, Western Antarctic Peninsula

César A. Cárdenas, Marcelo González-Aravena, Pamela A. Santibañez

https://doi.org/10.7717/peerj.4289 PubMed 29372123

January 24, 2018

Historical baselines of coral cover on tropical reefs as estimated by expert opinion

Tyler D. Eddy, William W.L. Cheung, John F. Bruno

https://doi.org/10.7717/peerj.4308 PubMed 29379692

January 11, 2018

Stat-tracks and mediotypes: powerful tools for modern ichnology based on 3D models

Matteo Belvedere, Matthew R. Bennett, Daniel Marty, Marcin Budka, Sally C. Reynolds, Rashid Bakirov

https://doi.org/10.7717/peerj.4247 PubMed 29340246

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