Articles

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

A comparative study of topology-based pathway enrichment analysis methods

Pathway enrichment extensively used in the analysis of Omics data for gaining biological insights into the functional roles of pre-defined subsets of genes, proteins and metabolites. A large number of methods ...

Authors: Jing Ma, Ali Shojaie and George Michailidis

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis

miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable ...

Authors: Valerio Licursi, Federica Conte, Giulia Fiscon and Paola Paci

A binning tool to reconstruct viral haplotypes from assembled contigs

Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strateg...

Authors: Jiao Chen, Jiayu Shang, Jianrong Wang and Yanni Sun

Predictive modelling using pathway scores: robustness and significance of pathway collections

Transcriptomic data is often used to build statistical models which are predictive of a given phenotype, such as disease status. Genes work together in pathways and it is widely thought that pathway representa...

Authors: Marcelo P. Segura-Lepe, Hector C. Keun and Timothy M. D. Ebbels

Annot: a Django-based sample, reagent, and experiment metadata tracking system

In biological experiments, comprehensive experimental metadata tracking – which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies – remains a challen...

Authors: Elmar Bucher, Cheryl J. Claunch, Derrick Hee, Rebecca L. Smith, Kaylyn Devlin, Wallace Thompson, James E. Korkola and Laura M. Heiser

WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network

An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Infer...

Authors: Yahui Long and Jiawei Luo

Exploring effective approaches for haplotype block phasing

Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for d...

Authors: Ziad Al Bkhetan, Justin Zobel, Adam Kowalczyk, Karin Verspoor and Benjamin Goudey

SLR: a scaffolding algorithm based on long reads and contig classification

Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate result...

Authors: Junwei Luo, Mengna Lyu, Ranran Chen, Xiaohong Zhang, Huimin Luo and Chaokun Yan

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective in inferring inter-res...

Authors: Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu

Uncovering extensive post-translation regulation during human cell cycle progression by integrative multi-’omics analysis

Analysis of high-throughput multi-’omics interactions across the hierarchy of expression has wide interest in making inferences with regard to biological function and biomarker discovery. Expression levels acr...

Authors: Gregory M. Parkes and Mahesan Niranjan

PPR-SSM: personalized PageRank and semantic similarity measures for entity linking

Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomed...

Authors: Andre Lamurias, Pedro Ruas and Francisco M. Couto

RACS: rapid analysis of ChIP-Seq data for contig based genomes

Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA se...

Authors: Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah and Jeffrey Fillingham

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

High-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiment...

Authors: Jing Xie, Tieming Ji, Marco A. R. Ferreira, Yahan Li, Bhaumik N. Patel and Rocio M. Rivera

Computational prediction of MoRFs based on protein sequences and minimax probability machine

Molecular recognition features (MoRFs) are one important type of disordered segments that can promote specific protein-protein interactions. They are located within longer intrinsically disordered regions (IDR...

Authors: Hao He, Jiaxiang Zhao and Guiling Sun

CLINE: a web-tool for the comparison of biological dendrogram structures

When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes...

Authors: Rodolfo S. Allendes Osorio, Lokesh P. Tripathi and Kenji Mizuguchi

A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data

Cancer subtype classification attains the great importance for accurate diagnosis and personalized treatment of cancer. Latest developments in high-throughput sequencing technologies have rapidly produced mult...

Authors: Jing Xu, Peng Wu, Yuehui Chen, Qingfang Meng, Hussain Dawood and Hassan Dawood

Legofit: estimating population history from genetic data

Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these bias...

Authors: Alan R. Rogers

Network inference with ensembles of bi-clustering trees

Network inference is crucial for biomedicine and systems biology. Biological entities and their associations are often modeled as interaction networks. Examples include drug protein interaction or gene regulat...

Authors: Konstantinos Pliakos and Celine Vens

Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues

Stable isotope tracing can follow individual atoms through metabolic transformations through the detection of the incorporation of stable isotope within metabolites. This resulting data can be interpreted in t...

Authors: Huan Jin and Hunter N. B. Moseley

Domainoid: domain-oriented orthology inference

Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for it...

Authors: Emma Persson, Mateusz Kaduk, Sofia K. Forslund and Erik L. L. Sonnhammer

MIC_Locator: a novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy

Protein subcellular localization plays a crucial role in understanding cell function. Proteins need to be in the right place at the right time, and combine with the corresponding molecules to fulfill their fun...

Authors: Fan Yang, Yang Liu, Yanbin Wang, Zhijian Yin and Zhen Yang

Comprehensive ensemble in QSAR prediction for drug discovery

Quantitative structure-activity relationship (QSAR) is a computational modeling method for revealing relationships between structural properties of chemical compounds and biological activities. QSAR modeling i...

Authors: Sunyoung Kwon, Ho Bae, Jeonghee Jo and Sungroh Yoon

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

Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence a...

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

GenGraph: a python module for the simple generation and manipulation of genome graphs

As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is cl...

Authors: Jon Mitchell Ambler, Shandukani Mulaudzi and Nicola Mulder