Javascript is disabled in your browser. Please enable Javascript to view PeerJ.

July 2018

Table of Contents - PeerJ (Biology Articles)

Investigating parental care behaviour in same-sex pairing of zoo greater flamingo

Greater flamingos at Kutch

July 18, 2018

Investigating parental care behaviour in same-sex pairing of zoo greater flamingo

Same-sex pair bonding is an understudied area of research interest. In an early, small sample study, researchers have observed similar behavior in female-female parenting as with heterosexual pairs in the zoo greater flamingo (Phoenicopterus roseus). These early results could be illuminating with regard to the evolution of flamingo social behavior, same-sex pair bonds, and why pair bonds form in general. Image credit: Dhaval Vargiya, CC SA 4.0.

- read article

July 2, 2018

Identification of hub genes and potential molecular mechanisms in gastric cancer by integrated bioinformatics analysis

Ling Cao, Yan Chen, Miao Zhang, De-quan Xu, Yan Liu, Tonglin Liu, Shi-xin Liu, Ping Wang

https://doi.org/10.7717/peerj.5180 PubMed 30002985

July 12, 2018

Staphylococcus aureus viewed from the perspective of 40,000+ genomes

Robert A. Petit, Timothy D. Read

https://doi.org/10.7717/peerj.5261 PubMed 30013858

July 13, 2018

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

Tobias Andermann, Ángela Cano, Alexander Zizka, Christine Bacon, Alexandre Antonelli

https://doi.org/10.7717/peerj.5175 PubMed 30023140

July 17, 2018

Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato

Elham Ashrafi-Dehkordi, Abbas Alemzadeh, Nobukazu Tanaka, Hooman Razi

https://doi.org/10.7717/peerj.4631 PubMed 30038850

July 12, 2018

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome

Jun Miyoshi, Vanessa Leone, Kentaro Nobutani, Mark W. Musch, Kristina Martinez-Guryn, Yunwei Wang, Sawako Miyoshi, Alexandria M. Bobe, A. Murat Eren, Eugene B. Chang

https://doi.org/10.7717/peerj.5166 PubMed 30013837

July 31, 2018

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

Alexandre Coudray, Anna M. Battenhouse, Philipp Bucher, Vishwanath R. Iyer

https://doi.org/10.7717/peerj.5362 PubMed 30083469

July 17, 2018

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Bruno A. S. de Medeiros, Brian D. Farrell

https://doi.org/10.7717/peerj.5089 PubMed 30038852

July 16, 2018

Time series clustering of mRNA and lncRNA expression during osteogenic differentiation of periodontal ligament stem cells

Yunfei Zheng, Xiaobei Li, Yiping Huang, Lingfei Jia, Weiran Li

https://doi.org/10.7717/peerj.5214 PubMed 30038865

July 25, 2018

Integrative machine learning analysis of multiple gene expression profiles in cervical cancer

Mei Sze Tan, Siow-Wee Chang, Phaik Leng Cheah, Hwa Jen Yap

https://doi.org/10.7717/peerj.5285 PubMed 30065881

July 30, 2018

Genome-wide analysis reveals four key transcription factors associated with cadmium stress in creeping bentgrass (Agrostis stolonifera L.)

Jianbo Yuan, Yuqing Bai, Yuehui Chao, Xinbo Sun, Chunyan He, Xiaohong Liang, Lijuan Xie, Liebao Han

https://doi.org/10.7717/peerj.5191 PubMed 30083437

July 31, 2018

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

Andrew J. Page, Jacqueline A. Keane

https://doi.org/10.7717/peerj.5233 PubMed 30083440

July 25, 2018

Performance comparison of machine learning techniques in sleep scoring based on wavelet features and neighboring component analysis

Behrouz Alizadeh Savareh, Azadeh Bashiri, Ali Behmanesh, Gholam Hossein Meftahi, Boshra Hatef

https://doi.org/10.7717/peerj.5247 PubMed 30065866

July 31, 2018

Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data

Jason Macrander, Jyothirmayi Panda, Daniel Janies, Marymegan Daly, Adam M. Reitzel

https://doi.org/10.7717/peerj.5361 PubMed 30083468

July 3, 2018

Local and relaxed clocks: the best of both worlds

Mathieu Fourment, Aaron E. Darling

https://doi.org/10.7717/peerj.5140 PubMed 30002973

July 10, 2018

Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments

Keri Ann Lydon, Erin K. Lipp

https://doi.org/10.7717/peerj.5248 PubMed 30018864

July 4, 2018

Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses

Camilla A. Santos, Sónia C.S. Andrade, Patrícia D. Freitas

https://doi.org/10.7717/peerj.5154 PubMed 30013834

July 11, 2018

MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis

Rahim Rajwani, Sheeba Shehzad, Gilman Kit Hang Siu

https://doi.org/10.7717/peerj.5090 PubMed 30018852

July 20, 2018

In silico-guided sequence modifications of K-ras epitopes improve immunological outcome against G12V and G13D mutant KRAS antigens

Allan Wee Ren Ng, Pei Jun Tan, Winfrey Pui Yee Hoo, Dek Shen Liew, Michelle Yee Mun Teo, Pui Yan Siak, Sze Man Ng, Ee Wern Tan, Raha Abdul Rahim, Renee Lay Hong Lim, Adelene Ai Lian Song, Lionel Lian Aun In

https://doi.org/10.7717/peerj.5056 PubMed 30042874

July 17, 2018

Integrated analysis of differentially expressed profiles and construction of a competing endogenous long non-coding RNA network in renal cell carcinoma

Qianwei Xing, Yeqing Huang, You Wu, Limin Ma, Bo Cai

https://doi.org/10.7717/peerj.5124 PubMed 30038853

July 3, 2018

AnnotationBustR: an R package to extract subsequences from GenBank annotations

Samuel R. Borstein, Brian C. O’Meara

https://doi.org/10.7717/peerj.5179 PubMed 30002984

July 6, 2018

Revisiting historical beech and oak forests in Indiana using a GIS method to recover information from bar charts

Brice Hanberry