Epigenetic supersimilarity of monozygotic twin pairs

Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to...

Authors: Timothy E. Van Baak, Cristian Coarfa, Pierre-Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S. Baker, Noah J. Kessler, Jianrong Dong, Jack D. Duryea, Matt J. Silver, Ayden Saffari, Andrew M. Prentice, Sophie E. Moore, Akram Ghantous, Michael N. Routledge, Yun Yun Gong…

RNA virus interference via CRISPR/Cas13a system in plants

CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleav...

Authors: Rashid Aman, Zahir Ali, Haroon Butt, Ahmed Mahas, Fatimah Aljedaani, Muhammad Zuhaib Khan, Shouwei Ding and Magdy Mahfouz

DotAligner: identification and clustering of RNA structure motifs

The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable natu...

Authors: Martin A. Smith, Stefan E. Seemann, Xiu Cheng Quek and John S. Mattick

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

The iCLIP and eCLIP techniques facilitate the detection of protein–RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the...

Authors: Sabrina Krakau, Hugues Richard and Annalisa Marsico

Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers

Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhanc...

Authors: Robert S. Young, Yatendra Kumar, Wendy A. Bickmore and Martin S. Taylor

Intergenic disease-associated regions are abundant in novel transcripts

Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS...

Authors: N. Bartonicek, M. B. Clark, X. C. Quek, J. R. Torpy, A. L. Pritchard, J. L. V. Maag, B. S. Gloss, J. Crawford, R. J. Taft, N. K. Hayward, G. W. Montgomery, J. S. Mattick, T. R. Mercer and M. E. Dinger

Adaptation of Arabidopsis thaliana to the Yangtze River basin

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms a...

Authors: Yu-Pan Zou, Xing-Hui Hou, Qiong Wu, Jia-Fu Chen, Zi-Wen Li, Ting-Shen Han, Xiao-Min Niu, Li Yang, Yong-Chao Xu, Jie Zhang, Fu-Min Zhang, Dunyan Tan, Zhixi Tian, Hongya Gu and Ya-Long Guo

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with ...

Authors: Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes and Daniel Gautheret

From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence

Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts...

Authors: Athina Vidaki and Manfred Kayser

Single-cell RNA-seq study determines the ontogeny of macrophages in glioblastomas

A large-scale single-cell RNA-seq analysis of tumor-associated macrophages in gliomas has unveiled a new aspect of the complex tumor microenvironment and new biomarkers.

Authors: Chenghang (Chuck) Zong

Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development

Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylatio...

Authors: Yuting Chen, Martin Widschwendter and Andrew E. Teschendorff

The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex

Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and n...

Authors: Lorena Verduci, Maria Ferraiuolo, Andrea Sacconi, Federica Ganci, Jlenia Vitale, Teresa Colombo, Paola Paci, Sabrina Strano, Giuseppe Macino, Nikolaus Rajewsky and Giovanni Blandino

Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment

Tumor-associated macrophages (TAMs) are abundant in gliomas and immunosuppressive TAMs are a barrier to emerging immunotherapies. It is unknown to what extent macrophages derived from peripheral blood adopt th...

Authors: Sören Müller, Gary Kohanbash, S. John Liu, Beatriz Alvarado, Diego Carrera, Aparna Bhaduri, Payal B. Watchmaker, Garima Yagnik, Elizabeth Di Lullo, Martina Malatesta, Nduka M. Amankulor, Arnold R. Kriegstein, Daniel A. Lim, Manish Aghi, Hideho Okada and Aaron Diaz

MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline,...

Authors: Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert and David Hot

Stranger in a strange land: the experiences of immigrant researchers

Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three researchers on their experiences as immigrants.

Authors: Sophien Kamoun, Rosa Lozano-Durán and Luay Nakhleh

Balancing selection and trans-specific polymorphisms

Balancing selection maintains variation for evolution. A recent study investigated the extent of balancing selection in two Brassicaceae species and highlighted its importance for adaptation.

Authors: Baosheng Wang and Thomas Mitchell-Olds

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, a...

Authors: Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, Yvonne Y. Y. Lai, Iris K. Pang, Grace Tin-Yun Chung, Angel C. Y. Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J. K. Wu, Ernest T. Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu…

Experimental design and quantitative analysis of microbial community multiomics

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the res...

Authors: Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan and Curtis Huttenhower

Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species

Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3′-sequencing data in this species precludes comprehensive ...

Authors: Piero Sanfilippo, Jiayu Wen and Eric C. Lai

RNAs: dynamic and mutable

Authors: Mihaela Zavolan and Brenton R. Graveley

The 3′ end of the story: deciphering combinatorial interactions that control mRNA fate

A new study investigates how microRNAs affect the binding of proteins to RNA.

Authors: Jeremy R. Sanford and Luiz O. F. Penalva

Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

The American College of Medical Genetics and American College of Pathologists (ACMG/AMP) variant classification guidelines for clinical reporting are widely used in diagnostic laboratories for variant interpre...

Authors: Rajarshi Ghosh, Ninad Oak and Sharon E. Plon

CRISPR/Cas9-mediated targeted chromosome elimination

The CRISPR/Cas9 system has become an efficient gene editing method for generating cells carrying precise gene mutations, including the rearrangement and deletion of chromosomal segments. However, whether an en...

Authors: Erwei Zuo, Xiaona Huo, Xuan Yao, Xinde Hu, Yidi Sun, Jianhang Yin, Bingbing He, Xing Wang, Linyu Shi, Jie Ping, Yu Wei, Wenqin Ying, Wei Wei, Wenjia Liu, Cheng Tang, Yixue Li…

Computational biologists: moving to the driver's seat

The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by ...

Authors: Itai Yanai and Eva Chmielnicki

Functional assessment of human enhancer activities using whole-genome STARR-sequencing

Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, be...

Authors: Yuwen Liu, Shan Yu, Vineet K. Dhiman, Tonya Brunetti, Heather Eckart and Kevin P. White