Articles

Prioritizing candidate diseases-related metabolites based on literature and functional similarity

As the terminal products of cellular regulatory process, functional related metabolites have a close relationship with complex diseases, and are often associated with the same or similar diseases. Therefore, i...

Authors: Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang and Yadong Wang

ProbPFP: a multiple sequence alignment algorithm combining hidden Markov model optimized by particle swarm optimization with partition function

During procedures for conducting multiple sequence alignment, that is so essential to use the substitution score of pairwise alignment. To compute adaptive scores for alignment, researchers usually use Hidden ...

Authors: Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang and Yadong Wang

TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology

The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. Since the beginning of GO project, various tools have been developed to perform GO enrichment analys...

Authors: Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang and Xuequn Shang

Using deep reinforcement learning to speed up collective cell migration

Collective cell migration is a significant and complex phenomenon that affects many basic biological processes. The coordination between leader cell and follower cell affects the rate of collective cell migrat...

Authors: Hanxu Hou, Tian Gan, Yaodong Yang, Xianglei Zhu, Sen Liu, Weiming Guo and Jianye Hao

A novel algorithm based on bi-random walks to identify disease-related lncRNAs

There is evidence to suggest that lncRNAs are associated with distinct and diverse biological processes. The dysfunction or mutation of lncRNAs are implicated in a wide range of diseases. An accurate computati...

Authors: Jialu Hu, Yiqun Gao, Jing Li, Yan Zheng, Jingru Wang and Xuequn Shang

Identifying Cancer genes by combining two-rounds RWR based on multiple biological data

It’s a very urgent task to identify cancer genes that enables us to understand the mechanisms of biochemical processes at a biomolecular level and facilitates the development of bioinformatics. Although a larg...

Authors: Wenxiang Zhang, Xiujuan Lei (IEEE member) and Chen Bian

BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics

This preface introduces the content of the BioMed Central Bioinformatics journal Supplement related to the 15th annual meeting of the Bioinformatics Italian Society, BITS2018. The Conference was held in Torino...

Authors: Francesca Cordero, Raffaele A. Calogero and Michele Caselle

Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions....

Authors: Giovanni Spirito, Damiano Mangoni, Remo Sanges and Stefano Gustincich

Exploratory analysis of transposable elements expression in the C. elegans early embryo

Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is be...

Authors: Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich and Remo Sanges

metaSPARSim: a 16S rRNA gene sequencing count data simulator

In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable populari...

Authors: Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci and Barbara Di Camillo

Genes with human-specific features are primarily involved with brain, immune and metabolic evolution

Humans have adapted to widespread changes during the past 2 million years in both environmental and lifestyle factors. This is evident in overall body alterations such as average height and brain size. Althoug...

Authors: Mainá Bitar, Stefanie Kuiper, Elizabeth A. O’Brien and Guy Barry

Analyzing gene expression data for pediatric and adult cancer diagnosis using logic learning machine and standard supervised methods

Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules.

Authors: Damiano Verda, Stefano Parodi, Enrico Ferrari and Marco Muselli

MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage

Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it...

Authors: Jia Qian and Matteo Comin

TACITuS: transcriptomic data collector, integrator, and selector on big data platform

Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate d...

Authors: Salvatore Alaimo, Antonio Di Maria, Dennis Shasha, Alfredo Ferro and Alfredo Pulvirenti

STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST...

Authors: Mattia Dalsass, Margherita Bodini, Christophe Lambert, Marie-Cécile Mortier, Marco Romanelli, Duccio Medini, Alessandro Muzzi and Alessandro Brozzi

MiRNA therapeutics based on logic circuits of biological pathways

In silico experiments, with the aid of computer simulation, speed up the process of in vitro or in vivo experiments. Cancer therapy design is often based on signalling pathway. MicroRNAs (miRNA) are small non-...

Authors: Valeria Boscaino, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo and Alfonso Urso

ImaGene: a convolutional neural network to quantify natural selection from genomic data

The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic ass...

Authors: Luis Torada, Lucrezia Lorenzon, Alice Beddis, Ulas Isildak, Linda Pattini, Sara Mathieson and Matteo Fumagalli

Better quality score compression through sequence-based quality smoothing

Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity o...

Authors: Yoshihiro Shibuya and Matteo Comin

Identification of native protein structures captured by principal interactions

Evaluation of protein structure is based on trustworthy potential function. The total potential of a protein structure is approximated as the summation of all pair-wise interaction potentials. Knowledge-based ...

Authors: Mehdi Mirzaie

Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described ...

Authors: Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard E. Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti and Thomas R. Ioerger

SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models

S-sulphenylation is a ubiquitous protein post-translational modification (PTM) where an S-hydroxyl (−SOH) bond is formed via the reversible oxidation on the Sulfhydryl group of cysteine (C). Recent experimenta...

Authors: Xiaochuan Wang, Chen Li, Fuyi Li, Varun S. Sharma, Jiangning Song and Geoffrey I. Webb

Multiplatform biomarker identification using a data-driven approach enables single-sample classification

High-throughput gene expression profiles have allowed discovery of potential biomarkers enabling early diagnosis, prognosis and developing individualized treatment. However, it remains a challenge to identify ...

Authors: Ling Zhang, Ishwor Thapa, Christian Haas and Dhundy Bastola

Correction to: CompNet: a GUI based tool for comparison of multiple biological interaction networks

Following publication of the original article [1], the authors requested to update a link in the article. There was a server update and the hosted applications needed to move to a new web location.

Authors: Bhusan K. Kuntal, Anirban Dutta and Sharmila S. Mande

Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging

Cellular aging is best studied in the budding yeast Saccharomyces cerevisiae. As an example of a pleiotropic trait, yeast lifespan is influenced by hundreds of interconnected genes. However, no quantitative metho...

Authors: Hong Qin

Correction to: GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data

Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below.

Authors: Nauman Ahmed, Jonathan Lévy, Shanshan Ren, Hamid Mushtaq, Koen Bertels and Zaid Al-Ars

A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons

Researchers commonly analyze lists of differentially expressed entities (DEEs), such as differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and differentially methylated positions/...

Authors: Stanislav A. Listopad and Trina M. Norden-Krichmar

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks

To increase the accuracy of microbiome data analysis, solving the technical limitations of the existing sequencing machines is required. Quality trimming is suggested to reduce the effect of the progressive de...

Authors: Attayeb Mohsen, Jonguk Park, Yi-An Chen, Hitoshi Kawashima and Kenji Mizuguchi

omicplotR: visualizing omic datasets as compositions

Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each us...

Authors: Daniel J. Giguere, Jean M. Macklaim, Brandon Y. Lieng and Gregory B. Gloor

MLW-gcForest: a multi-weighted gcForest model towards the staging of lung adenocarcinoma based on multi-modal genetic data

Lung cancer is one of the most common types of cancer, among which lung adenocarcinoma accounts for the largest proportion. Currently, accurate staging is a prerequisite for effective diagnosis and treatment o...

Authors: Yunyun Dong, Wenkai Yang, Jiawen Wang, Juanjuan Zhao, Yan Qiang, Zijuan Zhao, Ntikurako Guy Fernand Kazihise, Yanfen Cui, Xiaotong Yang and Siyuan Liu

The assessment of efficient representation of drug features using deep learning for drug repositioning

De novo drug discovery is a time-consuming and expensive process. Nowadays, drug repositioning is utilized as a common strategy to discover a new drug indication for existing drugs. This strategy is mostly use...

Authors: Mahroo Moridi, Marzieh Ghadirinia, Ali Sharifi-Zarchi and Fatemeh Zare-Mirakabad

The translational network for metabolic disease – from protein interaction to disease co-occurrence

The recent advances in human disease network have provided insights into establishing the relationships between the genotypes and phenotypes of diseases. In spite of the great progress, it yet remains as only a m...

Authors: Yonghyun Nam, Dong-gi Lee, Sunjoo Bang, Ju Han Kim, Jae-Hoon Kim and Hyunjung Shin

SCOPIT: sample size calculations for single-cell sequencing experiments

In single cell DNA and RNA sequencing experiments, the number of cells to sequence must be decided before running an experiment, and afterwards, it is necessary to decide whether sufficient cells were sampled....

Authors: Alexander Davis, Ruli Gao and Nicholas E. Navin

An integrative methodology based on protein-protein interaction networks for identification and functional annotation of disease-relevant genes applied to channelopathies

Biologically data-driven networks have become powerful analytical tools that handle massive, heterogeneous datasets generated from biomedical fields. Protein-protein interaction networks can identify the most ...

Authors: Milagros Marín, Francisco J. Esteban, Hilario Ramírez-Rodrigo, Eduardo Ros and María José Sáez-Lara

PyBDA: a command line tool for automated analysis of big biological data sets

Analysing large and high-dimensional biological data sets poses significant computational difficulties for bioinformaticians due to lack of accessible tools that scale to hundreds of millions of data points.

Authors: Simon Dirmeier, Mario Emmenlauer, Christoph Dehio and Niko Beerenwinkel

ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data

Data from discovery proteomic and phosphoproteomic experiments typically include missing values that correspond to proteins that have not been identified in the analyzed sample. Replacing the missing values wi...

Authors: Matúš Medo, Daniel M. Aebersold and Michaela Medová

The MG-RAST API explorer: an on-ramp for RESTful query composition

The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs...

Authors: Tobias Paczian, William L. Trimble, Wolfgang Gerlach, Travis Harrison, Andreas Wilke and Folker Meyer

PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets

With the growth of available sequenced datasets, analysis of heterogeneous processed data can answer increasingly relevant biological and clinical questions. Scientists are challenged in performing efficient a...

Authors: Luca Nanni, Pietro Pinoli, Arif Canakoglu and Stefano Ceri

MiPepid: MicroPeptide identification tool using machine learning

Micropeptides are small proteins with length < = 100 amino acids. Short open reading frames that could produces micropeptides were traditionally ignored due to technical difficulties, as few small peptides had...

Authors: Mengmeng Zhu and Michael Gribskov

VARUS: sampling complementary RNA reads from the sequence read archive

Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation o...

Authors: Mario Stanke, Willy Bruhn, Felix Becker and Katharina J. Hoff

Recommendations for performance optimizations when using GATK3.8 and GATK4

Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the toolkit has been rapidly evolving. Significant computati...

Authors: Jacob R Heldenbrand, Saurabh Baheti, Matthew A Bockol, Travis M Drucker, Steven N Hart, Matthew E Hudson, Ravishankar K Iyer, Michael T Kalmbach, Katherine I Kendig, Eric W Klee, Nathan R Mattson, Eric D Wieben, Mathieu Wiepert, Derek E Wildman and Liudmila S Mainzer

Optimal sequencing depth design for whole genome re-sequencing in pigs

As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological ...

Authors: Yifan Jiang, Yao Jiang, Sheng Wang, Qin Zhang and Xiangdong Ding

An EM algorithm to improve the estimation of the probability of clonal relatedness of pairs of tumors in cancer patients

We previously introduced a random-effects model to analyze a set of patients, each of which has two distinct tumors. The goal is to estimate the proportion of patients for which one of the tumors is a metastas...

Authors: Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya and Colin B. Begg

OmicsARules: a R package for integration of multi-omics datasets via association rules mining

The improvements of high throughput technologies have produced large amounts of multi-omics experiments datasets. Initial analysis of these data has revealed many concurrent gene alterations within single data...

Authors: Danze Chen, Fan Zhang, Qianqian Zhao and Jianzhen Xu

Third international conference “Bioinformatics: from Algorithms to Applications” (BiATA 2019)

Authors:

Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), ...

Authors: Fang-Dong Li, Wei Tong, En-Hua Xia and Chao-Ling Wei

De novo Nanopore read quality improvement using deep learning

Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error ...

Authors: Nathan LaPierre, Rob Egan, Wei Wang and Zhong Wang

Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Kluyveromyces marxianus is a thermotolerant yeast with multiple biotechnological potentials for industrial applications, which can metabolize a broad range of carbon sources, including less conventional sugars li...

Authors: Simonas Marcišauskas, Boyang Ji and Jens Nielsen

Topology Consistency of Disease-specific Differential Co-regulatory Networks

Sets of differentially expressed genes often contain driver genes that induce disease processes. However, various methods for identifying differentially expressed genes yield quite different results. Thus, we ...

Authors: Maryam Nazarieh, Hema Sekhar Reddy Rajula and Volkhard Helms

Quality control of imbalanced mass spectra from isotopic labeling experiments

Mass spectra are usually acquired from the Liquid Chromatography-Mass Spectrometry (LC-MS) analysis for isotope labeled proteomics experiments. In such experiments, the mass profiles of labeled (heavy) and unl...

Authors: Tianjun Li, Long Chen and Min Gan

MoMI-G: modular multi-scale integrated genome graph browser

Genome graph is an emerging approach for representing structural variants on genomes with branches. For example, representing structural variants of cancer genomes as a genome graph is more natural than repres...

Authors: Toshiyuki T. Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki and Masahiro Kasahara