A statistical framework for analyzing deep mutational scanning data

Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error est...

Authors: Alan F. Rubin, Hannah Gelman, Nathan Lucas, Sandra M. Bajjalieh, Anthony T. Papenfuss, Terence P. Speed and Douglas M. Fowler

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTran...

Authors: Nadia M. Davidson, Anthony D. K. Hawkins and Alicia Oshlack

Searching for cancer vulnerabilities amid genetic chaos

A meeting report on the Third European Association for Cancer Research Conference on Cancer Genomics, held at Churchill College, Cambridge, UK, 25–28 June 2017.

Authors: Michael R. Speicher

An interaction map of circulating metabolites, immune gene networks, and their genetic regulation

Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic ...

Authors: Artika P. Nath, Scott C. Ritchie, Sean G. Byars, Liam G. Fearnley, Aki S. Havulinna, Anni Joensuu, Antti J. Kangas, Pasi Soininen, Annika Wennerström, Lili Milani, Andres Metspalu, Satu Männistö, Peter Würtz, Johannes Kettunen, Emma Raitoharju, Mika Kähönen…

Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation

Using a powerful machine learning approach, a recent study of human genomes has revealed widespread footprints of recent positive selection on standing genetic variation.

Authors: Rajiv C. McCoy and Joshua M. Akey

The three-dimensional genome organization of Drosophila melanogaster through data integration

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate a...

Authors: Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo and Frank Alber

A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation

Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations as...

Authors: Nisha Patel, Arif O. Khan, Maher Al-Saif, Walid N. Moghrabi, Balsam M. AlMaarik, Niema Ibrahim, Firdous Abdulwahab, Mais Hashem, Tarfa Alshidi, Eman Alobeid, Rana A. Alomar, Saad Al-Harbi, Mohamed Abouelhoda, Khalid S. A. Khabar and Fowzan S. Alkuraya

Population and allelic variation of A-to-I RNA editing in human transcriptomes

A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism f...

Authors: Eddie Park, Jiguang Guo, Shihao Shen, Levon Demirdjian, Ying Nian Wu, Lan Lin and Yi Xing

ReMixT: clone-specific genomic structure estimation in cancer

Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...

Authors: Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp and Sohrab P. Shah

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence show...

Authors: Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...

Authors: Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin and Ekta Khurana

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of singl...

Authors: Joshua D. Welch, Alexander J. Hartemink and Jan F. Prins

Characterization of background noise in capture-based targeted sequencing data

Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are charact...

Authors: Gahee Park, Joo Kyung Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung K. D. Kim, Yeon Jeong Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Hyuck Lee, Dae-Soon Son, Woong-Yang Park and Donghyun Park

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...

Authors: Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan-Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck and Maike Stam

Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...

Authors: Catriona P. Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D. Bentley, Angela M. Kearns and Matthew T. G. Holden

Understanding the genetics behind complex human disease with large-scale iPSC collections

Three recent studies analyzing large-scale collections of human induced pluripotent stem cell lines provide valuable insight into how genetic regulatory variation affects cellular and molecular traits.

Authors: Amanda E. Yamasaki, Athanasia D. Panopoulos and Juan Carlos Izpisua Belmonte

Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding

Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanism...

Authors: Michael Thieme, Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze and Etienne Bucher

Canonical mRNA is the exception, rather than the rule

A report on the Second Aegean International Conference on the Long and the Short of Non-Coding RNAs, held in Heraklion, Greece, 9–14 June 2017.

Authors: Jun-An Chen and Simon Conn

MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity

Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we ...

Authors: David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling…

Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants

Authors: Claudia Köhler and Nathan Springer

Revisit linear regression-based deconvolution methods for tumor gene expression data

Authors: Bo Li, Jun S. Liu and X. Shirley Liu

Benchmarking: contexts and details matter

Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Bio...

Authors: Siyuan Zheng

Data normalization considerations for digital tumor dissection

In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...

Authors: Aaron M. Newman, Andrew J. Gentles, Chih Long Liu, Maximilian Diehn and Ash A. Alizadeh

Strong epistatic and additive effects of linked candidate SNPs for Drosophila pigmentation have implications for analysis of genome-wide association studies results

The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how ...

Authors: Jean-Michel Gibert, Jorge Blanco, Marlies Dolezal, Viola Nolte, Frédérique Peronnet and Christian Schlötterer

NicE-seq: high resolution open chromatin profiling

Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell...

Authors: V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf and Sriharsa Pradhan