Computational biology and bioinformatics

  • Article
    | Open Access

    Germline mutations in homologous recombination (HR) DNA repair genes are linked to breast and ovarian cancer. Here, the authors show that mutually exclusive bi-allelic inactivation of HR genes are present in other cancer types and associated with genomic features of HR deficiency, expanding the potential use of HR-directed therapies.

    • Nadeem Riaz
    • , Pedro Blecua
    •  & Jorge S. Reis-Filho
  • Article
    | Open Access

    Hepatocellular carcinoma is known to harbour numerous genomic and epigenomic aberrations, driving transcriptomic deregulation. Here, the authors integrate genomic, epigenomic, and expression data to reveal three prognostic subtypes, providing insight to the pathobiology of hepatocellular carcinoma.

    • Hyun Goo Woo
    • , Ji-Hye Choi
    •  & Yoon Jun Kim
  • Article
    | Open Access

    Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

    • Pedro H. Oliveira
    • , Marie Touchon
    •  & Eduardo P. C. Rocha
  • Article
    | Open Access

    Individual SNPs have small effects on anthropometric traits, yet the impact of CNVs has remained largely unknown. Here, Kutalik and co-workers perform a large-scale genome-wide meta-analysis of structural variation and find rare CNVs associated with height, weight and BMI with large effect sizes.

    • Aurélien Macé
    • , Marcus A. Tuke
    •  & Zoltán Kutalik
  • Article
    | Open Access

    Angiogenesis is a complex process that requires coordinated changes in endothelial cell behavior. Here the authors use Ribo-tag and RNA-Seq to determine temporal profiles of transcriptional activity during postnatal retinal angiogenesis, identifying transcriptional regulators of the process.

    • Hyun-Woo Jeong
    • , Benjamín Hernández-Rodríguez
    •  & Ralf H. Adams
  • Article
    | Open Access

    The structure and dynamics of microbial communities reflect trade-offs in the ability to use different resources. Here, Josephides and Swain incorporate metabolic trade-offs into an eco-evolutionary model to predict networks of mutational paths and the evolutionary outcomes for microbial communities.

    • Christos Josephides
    •  & Peter S. Swain
  • Article
    | Open Access

    The RNA Recognition Motif (RRM) is the most ubiquitous RNA binding domain. Here the authors combined NMR and molecular dynamics simulations and show that the RRM RNA binding surface exists in different states and that a conformational switch of aromatic side-chains fine-tunes sequence specific binding affinities.

    • Nana Diarra dit Konté
    • , Miroslav Krepl
    •  & Frédéric H.-T. Allain
  • Article
    | Open Access

    The pancreas arises from a small population of cells but how individual cells contribute to organ formation is unclear. Here, the authors deconstruct pancreas organogenesis into clonal units, showing that single progenitors give rise to heterogeneous multi-lineage and endocrinogenic single-lineage clones.

    • Hjalte List Larsen
    • , Laura Martín-Coll
    •  & Anne Grapin-Botton
  • Article
    | Open Access

    Network-based data integration for drug–target prediction is a promising avenue for drug repositioning, but performance is wanting. Here, the authors introduce DTINet, whose performance is enhanced in the face of noisy, incomplete and high-dimensional biological data by learning low-dimensional vector representations.

    • Yunan Luo
    • , Xinbin Zhao
    •  & Jianyang Zeng
  • Article
    | Open Access

    Although networks of interacting genes and metabolic reactions are interdependent, they have largely been treated as separate systems. Here the authors apply a statistical framework for interdependent networks to E. coli, and show that it is sensitive to gene and protein perturbations but robust against metabolic changes.

    • David F. Klosik
    • , Anne Grimbs
    •  & Marc-Thorsten Hütt
  • Article
    | Open Access

    Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.

    • Ben S. Wendel
    • , Chenfeng He
    •  & Ning Jiang
  • Article
    | Open Access

    So far no enzymatic activity has been attributed to flagellin, the major component of bacterial flagella. Here the authors use bioinformatic analysis and identify a metallopeptidase insertion in flagellins from 74 bacterial species and show that recombinant flagellin and flagellar filaments have proteolytic activity.

    • Ulrich Eckhard
    • , Hina Bandukwala
    •  & Andrew C. Doxey
  • Article
    | Open Access

    The interpretation of information-rich, high-throughput single-cell data is a challenge requiring sophisticated computational tools. Here the authors demonstrate a deep convolutional neural network that can classify cell cycle status on-the-fly.

    • Philipp Eulenberg
    • , Niklas Köhler
    •  & F. Alexander Wolf
  • Article
    | Open Access

    Exploiting synthetic lethality is a promising approach for cancer therapy. Here, the authors present an approach to identifying such interactions by finding genetic minimal cut sets (gMCSs) that block cancer proliferation, and apply it to study the lethality of RRM1 inhibition in multiple myeloma.

    • Iñigo Apaolaza
    • , Edurne San José-Eneriz
    •  & Francisco J. Planes
  • Article
    | Open Access

    Inflammation mediated by microglia plays a key role in brain injury associated with preterm birth, but little is known about the microglial response in preterm infants. Here, the authors integrate molecular and imaging data from animal models and preterm infants, and find that microglial expression of DLG4 plays a role.

    • Michelle L. Krishnan
    • , Juliette Van Steenwinckel
    •  & Pierre Gressens
  • Article
    | Open Access

    Stromal cells contribute to tumor development but the mechanisms regulating this process are still unclear. Here the authors analyze gene expression profiles in the prostate and show that stromal gene signature changes ahead of the epithelial gene signature as prostate cancer initiates and progresses.

    • Svitlana Tyekucheva
    • , Michaela Bowden
    •  & Massimo Loda
  • Article
    | Open Access

    As the experimental discovery of microRNAs (miRNAs) is cumbersome, computational tools have been developed for the prediction of pre-miRNAs. Here the authors develop a framework to assess the performance of existing and novel pre-miRNA prediction tools and provide guidelines for selecting an appropriate approach for a given data set.

    • Müşerref Duygu Saçar Demirci
    • , Jan Baumbach
    •  & Jens Allmer
  • Article
    | Open Access

    Protein stability modulation by E3 ubiquitin ligases is an important layer of functional regulation, but screening for E3 ligase-substrate interactions is time-consuming and costly. Here, the authors take an in silico naïve Bayesian classifier approach to integrate multiple lines of evidence for E3-substrate prediction, enabling prediction of the proteome-wide human E3 ligase interaction network.

    • Yang Li
    • , Ping Xie
    •  & Fuchu He
  • Article
    | Open Access

    Estimates of human mutation rates differ substantially based on the approach. Here, the authors present a multi-generational estimate from the autozygous segment in a non-European population that gives insight into the contribution of post-zygotic mutations and population-specific mutational processes.

    • Vagheesh M. Narasimhan
    • , Raheleh Rahbari
    •  & Richard Durbin
  • Article
    | Open Access

    Early molecules of life likely served both as templates and catalysts, raising the question of how functionally distinct genomes and enzymes arose. Here, the authors show that conflict between evolution at the molecular and cellular levels can drive functional differentiation of the two strands of self-replicating molecules and lead to copy number differences between the two.

    • Nobuto Takeuchi
    • , Paulien Hogeweg
    •  & Kunihiko Kaneko
  • Article
    | Open Access

    While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

    • Sahar Gelfman
    • , Quanli Wang
    •  & David B. Goldstein
  • Article
    | Open Access

    Deregulation of E2F family transcription factors is associated with cancer progression and metastasis. Here, the authors construct a map of the regulatory network around the E2F family, and using gene expression profiles, identify tumour type-specific regulatory cores and receptor expression signatures associated with epithelial-mesenchymal transition in bladder and breast cancer.

    • Faiz M. Khan
    • , Stephan Marquardt
    •  & Brigitte M. Pützer
  • Article
    | Open Access

    Cells in the connective tissue are surrounded by a heterogeneous network of biopolymers. Here, the authors investigate how such heterogeneity affects cellular mechanosensing by simulating the deformation response of experimental and modelled biopolymer networks to locally applied forces.

    • Farzan Beroz
    • , Louise M. Jawerth
    •  & Ned S. Wingreen
  • Article
    | Open Access

    The emergence of novel catalytic functions in ancient proteins likely played a role in the evolution of modern enzymes. Here, the authors use protein sequences from Precambrian beta-lactamases and demonstrate that a single hydrophobic-to-ionizable amino acid mutation can lead to substantial Kemp eliminase activity.

    • Valeria A. Risso
    • , Sergio Martinez-Rodriguez
    •  & Jose M. Sanchez-Ruiz
  • Article
    | Open Access

    Increased availability of large-scale molecular profiling has enabled system-level monitoring of molecular effects of candidate therapeutics. Here, the authors take advantage of such data to show that the ability of a drug to reverse cancer-associated gene expression changes is indicative of itsin vitroanti-proliferative efficacy, allowing them to identify novel compounds against liver cancer.

    • Bin Chen
    • , Li Ma
    •  & Atul J. Butte
  • Article
    | Open Access

    Parasitemia has been considered the main determinant of visceral leishmaniasis transmission. By combining imaging, qPCR and experimental xenodiagnoses with mathematical models, Doehl et al. argue that the patchy landscape of parasites in the skin is necessary to explain infectiousness.

    • Johannes S. P. Doehl
    • , Zoe Bright
    •  & Paul M. Kaye
  • Article
    | Open Access

    Coupling of growth and product synthesis is an important principle in metabolic engineering, but its range of applicability is unclear. Here, the authors use a dedicated computational framework to study the feasibility of coupling the production of metabolites to growth in the genome-scale metabolic models of five production organisms, and show that coupling can be achieved for most metabolites.

    • Axel von Kamp
    •  & Steffen Klamt
  • Article
    | Open Access

    In single-cell RNA sequencing data of heterogeneous cell populations, cell cycle stage of individual cells would often be informative. Here, the authors introduce a computational model to reconstruct a pseudo-time series from single cell transcriptome data, identify the cell cycle stages, identify candidate cell cycle-regulated genes and recover the methylome changes during the cell cycle.

    • Zehua Liu
    • , Huazhe Lou
    •  & Ting Chen
  • Article
    | Open Access

    Accurate quantification of bioimaging data is often confounded by uneven illumination (shading) in space and background variation in time. Here the authors present BaSiC, a Fiji plugin solving both issues. It requires fewer input images and is more robust to artefacts than existing shading correction tools.

    • Tingying Peng
    • , Kurt Thorn
    •  & Nassir Navab
  • Article
    | Open Access

    V2 neurons exhibit complex and diverse selectivity for visual features. Here the authors use a statistical analytical framework to model V2 responses to natural stimuli and find three organizing principles, chief among them is the cross-orientation suppression that increases response selectivity.

    • Ryan J. Rowekamp
    •  & Tatyana O. Sharpee
  • Article
    | Open Access

    Some cancers with DNA mismatch repair deficiency display microsatellite instability. Here the authors analyse twenty three cancer types at the exome and whole-genome level, and identify loci with recurrent microsatellite instability that could be used to identify patients who would benefit from immunotherapy.

    • Isidro Cortes-Ciriano
    • , Sejoon Lee
    •  & Peter J. Park
  • Article
    | Open Access

    Maximum Intensity Projection is a common tool to represent 3D biological imaging data in a 2D space, but it creates artefacts. Here the authors develop Smooth Manifold Extraction, an ImageJ/Fiji plugin, to preserve local spatial relationships when extracting the content of a 3D volume to a 2D space.

    • Asm Shihavuddin
    • , Sreetama Basu
    •  & Auguste Genovesio
  • Article
    | Open Access

    There are no robust methods for systematically identifying mutation-specific synthetic lethal (SL) partners in cancer. Here, the authors develop a computational algorithm that uses pan-cancer data to detect mutation-andcancer-specific SL partners and they validate a novel SL interaction between mutant IDH and loss of ACACA in leukaemia.

    • Subarna Sinha
    • , Daniel Thomas
    •  & David L. Dill
  • Article
    | Open Access

    Tumour expression profiling is currently used for prognostic and predictive purposes without taking into account the intra patient heterogeneity. Here the authors show that cancer cell specific signatures overcome the tumour heterogeneity effect and result in better classification of colorectal cancer patients.

    • Philip D. Dunne
    • , Matthew Alderdice
    •  & Mark Lawler
  • Article
    | Open Access

    Growth-coupled designs for chemical production are limited by native metabolic networks’ optimality for growth. Here, the authors introduce pathway orthogonality as a measure of the independence of biomass and chemical production pathways, identify metabolic valves that allow substrate utilization to be switched between the two, and demonstrate advantages of orthogonal designs.

    • Aditya Vikram Pandit
    • , Shyam Srinivasan
    •  & Radhakrishnan Mahadevan
  • Article
    | Open Access

    There are few methods available that can quantify relationships between cell types in tissue images. Here the authors present a quantitative method to evaluate cellular organization, validated in the mouse thymus and spinal cord, called Multitaper Circularly Averaged Spectral Analysis (MiCASA).

    • Andrew Sornborger
    • , Jie Li
    •  & Nancy R. Manley
  • Article
    | Open Access

    Analysis of molecular quantitative trait loci (molQTL) can help interpret genome-wide association studies and requires efficient approaches to correct for multiple testing. This study describes a bioinformatics toolkit called QTLtool that can handle large data sets and quickly perform multiple types of molQTL analyses.

    • Olivier Delaneau
    • , Halit Ongen
    •  & Emmanouil T. Dermitzakis
  • Article
    | Open Access

    Outsourcing computation for genomic data processing offers the ability to allocate massive computing power and storage on demand. Here, Popic and Batzoglou develop a hybrid cloud aligner for sequence read mapping that preserves privacy with competitive accuracy and speed.

    • Victoria Popic
    •  & Serafim Batzoglou
  • Article
    | Open Access

    Biomphalaria glabrata is a fresh water snail that acts as a host for trematode Schistosoma mansoni that causes intestinal infection in human. This work describes the genome and transcriptome analyses from 12 different tissues of B glabrata, and identify genes for snail behavior and evolution.

    • Coen M. Adema
    • , LaDeana W. Hillier
    •  & Richard K. Wilson