FecalSeq: methylation-based enrichment for noninvasive population genomics from feces

FecalSeq: methylation-based enrichment for noninvasive population genomics from feces

Kenneth L Chiou, Christina M Bergey

Early farmers from across Europe directly descended from Neolithic Aegeans

Early farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanová, Susanne Kreutzer, Garrett Hellenthal, Christian Sell, Yoan Diekmann, David Díez del Molino, Lucy van Dorp, Saioa López, Athanasios Kousathanas, Vivian Link, Karola Kirsanow, Lara M Cassidy, Rui Martiniano, Melanie Strobel, Amelie Scheu, Kostas Kotsakis, Paul Halstead, Sevi Triantaphyllou, Nina Kyparissi-Apostolika, Dushanka-Christina Urem-Kotsou, Christina Ziota, Fotini Adaktylou, Shyamalika Gopalan, Dean M Bobo, Laura Winkelbach, Jens Blöcher, Martina Unterländer, Christoph Leuenberger, Çiler Çilingiroğlu, Barbara Horejs, Fokke Gerritsen, Stephen Shennan, Daniel G Bradley, Mathias Currat, Krishna Veeramah, Daniel Wegmann, Mark G Thomas, Christina Papageorgopoulou, Joachim Burger

Urbanization shapes the demographic history of a city-dwelling native rodent

Urbanization shapes the demographic history of a city-dwelling native rodent

Stephen E. Harris, Alexander T. Xue, Diego Alvarado-Serrano, Joel T. Boehm, Tyler Joseph, Michael J. Hickerson, Jason Munshi-South

A phylogenetically diverse class of blind type 1 opsins

A phylogenetically diverse class of blind type 1 opsins

Erin A Becker, Andrew I Yao, Phillip M Seitzer, Tobias Kind, Ting Wang, Rich Eigenheer, Katie S. Y. Shao, Vladimir Yarov-Yarovoy, Marc T Facciotti

AGOUTI: improving genome assembly and annotation using transcriptome data

AGOUTI: improving genome assembly and annotation using transcriptome data

Simo V Zhang, Luting Zhuo, Matthew W Hahn

Coevolution leaves a stronger imprint on interactions than on community structure

Coevolution leaves a stronger imprint on interactions than on community structure

Timothee Poisot, Daniel Stouffer

The role of deleterious substitutions in crop genomes

The role of deleterious substitutions in crop genomes

Thomas J Y Kono, Fengli Fu, Mohsen Mohammadi, Paul J Hoffman, Chaochih Liu, Robert M Stupar, Kevin P Smith, Peter Tiffin, Justin C Fay, Peter L Morrell

Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.

Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.

Nicolas Galtier

Efficient coalescent simulation and genealogical analysis for large sample sizes

Efficient coalescent simulation and genealogical analysis for large sample sizes

Jerome Kelleher, Gil McVean, Alison M Etheridge

Bayesian identification of bacterial strains from sequencing data

Bayesian identification of bacterial strains from sequencing data
Aravind Sankar, Brandon Malone, Sion Bayliss, Ben Pascoe, Guillaume Méric, Matthew D. Hitchings, Samuel K. Sheppard, Edward J. Feil, Jukka Corander, Antti Honkela

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel method for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at this https URL