Articles

Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection

Reproducibility of hits from independent CRISPR or siRNA screens is poor. This is partly due to data normalization primarily addressing technical variability within independent screens, and not the technical d...

Authors: Costa Bachas, Jasmina Hodzic, Johannes C. van der Mijn, Chantal Stoepker, Henk M. W. Verheul, Rob M. F. Wolthuis, Emanuela Felley-Bosco, Wessel N. van Wieringen, Victor W. van Beusechem, Ruud H. Brakenhoff and Renée X. de Menezes

Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries

Targeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical issue for research and applications using HT...

Authors: Felix Francis, Michael D. Dumas, Scott B. Davis and Randall J. Wisser

BALCONY: an R package for MSA and functional compartments of protein variability analysis

Here, we present an R package for entropy/variability analysis that facilitates prompt and convenient data extraction, manipulation and visualization of protein features from multiple sequence alignments. BALC...

Authors: Alicja Płuciennik, Michał Stolarczyk, Maria Bzówka, Agata Raczyńska, Tomasz Magdziarz and Artur Góra

DeepSort: deep convolutional networks for sorting haploid maize seeds

Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize ...

Authors: Balaji Veeramani, John W. Raymond and Pritam Chanda

Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture

Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms.

Authors: Shaoliang Peng, Minxia Cheng, Kaiwen Huang, YingBo Cui, Zhiqiang Zhang, Runxin Guo, Xiaoyu Zhang, Shunyun Yang, Xiangke Liao, Yutong Lu, Quan Zou and Benyun Shi

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation

Duplication-Transfer-Loss (DTL) reconciliation is a powerful and increasingly popular technique for studying the evolution of microbial gene families. DTL reconciliation requires the use of rooted gene trees t...

Authors: Soumya Kundu and Mukul S. Bansal

Multiple model species selection for transcriptomics analysis of non-model organisms

Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in gene functi...

Authors: Tun-Wen Pai, Kuan-Hung Li, Cing-Han Yang, Chin-Hwa Hu, Han-Jia Lin, Wen-Der Wang and Yet-Ran Chen

A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra

Top-down homogeneous multiplexed tandem mass (HomMTM) spectra are generated from modified proteoforms of the same protein with different post-translational modification patterns. They are frequently observed i...

Authors: Kaiyuan Zhu and Xiaowen Liu

Drug response prediction model using a hierarchical structural component modeling method

Component-based structural equation modeling methods are now widely used in science, business, education, and other fields. This method uses unobservable variables, i.e., “latent” variables, and structural equ...

Authors: Sungtae Kim, Sungkyoung Choi, Jung-Hwan Yoon, Youngsoo Kim, Seungyeoun Lee and Taesung Park

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Genome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and tr...

Authors: Dan Wang and Lusheng Wang

Predicting diabetic retinopathy and identifying interpretable biomedical features using machine learning algorithms

The risk factors of diabetic retinopathy (DR) were investigated extensively in the past studies, but it remains unknown which risk factors were more associated with the DR than others. If we can detect the DR ...

Authors: Hsin-Yi Tsao, Pei-Ying Chan and Emily Chia-Yu Su

BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion

Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are clo...

Authors: Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Jiang-Bo Cao and Siu-Ming Yiu

ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species

In bioinformatics, network alignment algorithms have been applied to protein-protein interaction (PPI) networks to discover evolutionary conserved substructures at the system level. However, most previous meth...

Authors: Jianliang Gao, Bo Song, Xiaohua Hu, Fengxia Yan and Jianxin Wang

Biomedical event extraction based on GRU integrating attention mechanism

Biomedical event extraction is a crucial task in biomedical text mining. As the primary forum for international evaluation of different biomedical event extraction technologies, BioNLP Shared Task represents a...

Authors: Lishuang Li, Jia Wan, Jieqiong Zheng and Jian Wang

Big data analysis for evaluating bioinvasion risk

Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area th...

Authors: Shengling Wang, Chenyu Wang, Shenling Wang and Liran Ma

REHUNT: a reliable and open source package for restriction enzyme hunting

Restriction enzymes are used frequently in biotechnology. However, manual mining of restriction enzymes is challenging. Furthermore, integrating available restriction enzymes into different bioinformatics syst...

Authors: Yu-Huei Cheng, Jiun-Jian Liaw and Che-Nan Kuo

miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set

The knowledge of miRNAs regulating the expression of sets of mRNAs has led to novel insights into numerous and diverse cellular mechanisms. While a single miRNA may regulate many genes, one gene can be regulat...

Authors: Luqman Hakim Abdul Hadi, Quy Xiao Xuan Lin, Tri Tran Minh, Marie Loh, Hong Kiat Ng, Agus Salim, Richie Soong and Touati Benoukraf

Multi-class segmentation of neuronal structures in electron microscopy images

Serial block face scanning electron microscopy (SBFEM) is becoming a popular technology in neuroscience. We have seen in the last years an increasing number of works addressing the problem of segmenting cellul...

Authors: Kendrick Cetina, José M. Buenaposada and Luis Baumela

PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly

Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it’s often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discove...

Authors: Renato Renison Moreira Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira and Ronnie Alves

BART: bioinformatics array research tool

Microarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and require...

Authors: Maria Luisa Amaral, Galina A. Erikson and Maxim N. Shokhirev

PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores

Polygenic risk scores (PRS) describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of variance in outcome than single nucleotide polymorphisms (SNPs) alone. Ho...

Authors: Lawrence M. Chen, Nelson Yao, Elika Garg, Yuecai Zhu, Thao T. T. Nguyen, Irina Pokhvisneva, Shantala A. Hari Dass, Eva Unternaehrer, Hélène Gaudreau, Marie Forest, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Celia M. T. Greenwood, Patricia P. Silveira, Michael J. Meaney…

Fusion of encoder-decoder deep networks improves delineation of multiple nuclear phenotypes

Nuclear segmentation is an important step for profiling aberrant regions of histology sections. If nuclear segmentation can be resolved, then new biomarkers of nuclear phenotypes and their organization can be ...

Authors: Mina Khoshdeli, Garrett Winkelmaier and Bahram Parvin

Prediction of 8-state protein secondary structures by a novel deep learning architecture

Protein secondary structure can be regarded as an information bridge that links the primary sequence and tertiary structure. Accurate 8-state secondary structure prediction can significantly give more precise ...

Authors: Buzhong Zhang, Jinyan Li and Qiang Lü

CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers

Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRN...

Authors: Shanliang Zhong, Jinyan Wang, Qian Zhang, Hanzi Xu and Jifeng Feng

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

Changes in spatial chromatin interactions are now emerging as a unifying mechanism orchestrating the regulation of gene expression. Hi-C sequencing technology allows insight into chromatin interactions on a ge...

Authors: John C. Stansfield, Kellen G. Cresswell, Vladimir I. Vladimirov and Mikhail G. Dozmorov

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases

Protein homology search is an important, yet time-consuming, step in everything from protein annotation to metagenomics. Its application, however, has become increasingly challenging, due to the exponential gr...

Authors: Alan Medlar and Liisa Holm

WISH-R– a fast and efficient tool for construction of epistatic networks for complex traits and diseases

Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this cont...

Authors: Victor A. O. Carmelo, Lisette J. A. Kogelman, Majbritt Busk Madsen and Haja N. Kadarmideen

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use case...

Authors: Stephen D. Shank, Steven Weaver and Sergei L. Kosakovsky Pond

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods

Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary “library size” by the sequencing depth of the assay, a...

Authors: Thomas P. Quinn, Tamsyn M. Crowley and Mark F. Richardson

De novo profile generation based on sequence context specificity with the long short-term memory network

Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, u...

Authors: Kazunori D. Yamada and Kengo Kinoshita

De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application

Many organisms, in particular bacteria, contain repetitive DNA fragments called tandem repeats. These structures are restored by DNA assemblers by mapping paired-end tags to unitigs, estimating the distance be...

Authors: Wiktor Kuśmirek and Robert Nowak

Random forest versus logistic regression: a large-scale benchmark experiment

The Random Forest (RF) algorithm for regression and classification has considerably gained popularity since its introduction in 2001. Meanwhile, it has grown to a standard classification approach competing wit...

Authors: Raphael Couronné, Philipp Probst and Anne-Laure Boulesteix

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple cancers, and ...

Authors: Saurabh Baheti, Xiaojia Tang, Daniel R. O’Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher and Krishna R. Kalari

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data

Data generated by RNA sequencing (RNA-Seq) is now accumulating in vast amounts in public repositories, especially for human and mouse genomes. Reanalyzing these data has emerged as a promising approach to iden...

Authors: Yasunobu Okamura and Kengo Kinoshita

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links

Netpredictor is an R package for prediction of missing links in any given unipartite or bipartite network. The package provides utilities to compute missing links in a bipartite and well as unipartite networks...

Authors: Abhik Seal and David J. Wild

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and ...

Authors: Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen and Lachlan Coin

Discovering themes in biomedical literature using a projection-based algorithm

The need to organize any large document collection in a manner that facilitates human comprehension has become crucial with the increasing volume of information available. Two common approaches to provide a br...

Authors: Lana Yeganova, Sun Kim, Grigory Balasanov and W. John Wilbur

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata

Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associate...

Authors: Syed Ahmad Chan Bukhari, Marcos Martínez-Romero, Martin J. O’ Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung and Steven H. Kleinstein

An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease

There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predic...

Authors: Ryohei Eguchi, Mohammand Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya and Md. Altaf-Ul-Amin

npInv: accurate detection and genotyping of inversions using long read sub-alignment

Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombinat...

Authors: Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive J. Hoggart and Lachlan J. M. Coin

Effective automated pipeline for 3D reconstruction of synapses based on deep learning

The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accura...

Authors: Chi Xiao, Weifu Li, Hao Deng, Xi Chen, Yang Yang, Qiwei Xie and Hua Han

trumpet: transcriptome-guided quality assessment of m⁶A-seq data

Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m⁶A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic pr...

Authors: Teng Zhang, Shao-Wu Zhang, Lin Zhang and Jia Meng

Alternative empirical Bayes models for adjusting for batch effects in genomic studies

Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or require the sequential generation of data. How...

Authors: Yuqing Zhang, David F. Jenkins, Solaiappan Manimaran and W. Evan Johnson

INBIA: a boosting methodology for proteomic network inference

The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, ...

Authors: Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti and Rosalba Giugno

Effect of the number of removed lymph nodes on prostate cancer recurrence and survival: evidence from an observational study

The aim of this article is to analyze the effect on biochemical recurrence and on overall survival of removing an extensive number of pelvic lymph nodes during prostate cancer surgery. The lack of evidence fro...

Authors: Chiara Gigliarano, Alessandro Nonis, Alberto Briganti, Marco Bonetti and Clelia Di Serio

Beyond the one-way ANOVA for ’omics data

With ever increasing accessibility to high throughput technologies, more complex treatment structures can be assessed in a variety of ’omics applications. This adds an extra layer of complexity to the analysis...

Authors: Kirsty L. Hassall and Andrew Mead

Mendelian randomisation analysis of clustered causal effects of body mass on cardiometabolic biomarkers

Recent advances in data analysis methods based on principles of Mendelian Randomisation, such as Egger regression and the weighted median estimator, add to the researcher’s ability to infer cause-effect links ...

Authors: Susana Conde, Xiaoguang Xu, Hui Guo, Markus Perola, Teresa Fazia, Luisa Bernardinelli and Carlo Berzuini

Deep learning models for bacteria taxonomic classification of metagenomic data

An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered ...

Authors: Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosue’ Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio and Alfonso Urso

Modeling the covariates effects on the hazard function by piecewise exponential artificial neural networks: an application to a controlled clinical trial on renal carcinoma

In exploring the time course of a disease to support or generate biological hypotheses, the shape of the hazard function provides relevant information. For long follow-ups the shape of hazard function may be c...

Authors: Marco Fornili, Patrizia Boracchi, Federico Ambrogi and Elia Biganzoli

Preface to the BMC-CIBB 2015-16 special issue

Authors: Claudia Angelini, Andrea Bracciali, David Gilbert and Riccardo Rizzo