Articles

Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life

It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial ...

Authors: Zhengqiao Zhao, Alexandru Cristian and Gail Rosen

PAWER: protein array web exploreR

Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while exis...

Authors: Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo and Hedi Peterson

A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network

Drug-target interaction prediction is of great significance for narrowing down the scope of candidate medications, and thus is a vital step in drug discovery. Because of the particularity of biochemical experi...

Authors: Jiajie Peng, Jingyi Li and Xuequn Shang

Model-based clustering for flow and mass cytometry data with clinical information

High-dimensional flow cytometry and mass cytometry allow systemic-level characterization of more than 10 protein profiles at single-cell resolution and provide a much broader landscape in many biological appli...

Authors: Ko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura

EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes

In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the...

Authors: Xiaoyang Chen, Shengquan Chen and Rui Jiang

Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation

Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the...

Authors: Yongchun Lü, Xiangrui Zeng, Xinhui Tian, Xiao Shi, Hui Wang, Xiaohui Zheng, Xiaodong Liu, Xiaofang Zhao, Xin Gao and Min Xu

MAIRA- real-time taxonomic and functional analysis of long reads on a laptop

Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually desig...

Authors: Benjamin Albrecht, Caner Bağcı and Daniel H. Huson

Multi-omics profiling reveals microRNA-mediated insulin signaling networks

MicroRNAs (miRNAs) play a key role in mediating the action of insulin on cell growth and the development of diabetes. However, few studies have been conducted to provide a comprehensive overview of the miRNA-m...

Authors: Yang-Chi-Dung Lin, Hsi-Yuan Huang, Sirjana Shrestha, Chih-Hung Chou, Yen-Hua Chen, Chi-Ru Chen, Hsiao-Chin Hong, Jing Li, Yi-An Chang, Men-Yee Chiew, Ya-Rong Huang, Siang-Jyun Tu, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng and Hsien-Da Huang

GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads

In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo asse...

Authors: Nauman Ahmed, Tong Dong Qiu, Koen Bertels and Zaid Al-Ars

NEDD: a network embedding based method for predicting drug-disease associations

Drug discovery is known for the large amount of money and time it consumes and the high risk it takes. Drug repositioning has, therefore, become a popular approach to save time and cost by finding novel indica...

Authors: Renyi Zhou, Zhangli Lu, Huimin Luo, Ju Xiang, Min Zeng and Min Li

A consensus multi-view multi-objective gene selection approach for improved sample classification

In the field of computational biology, analyzing complex data helps to extract relevant biological information. Sample classification of gene expression data is one such popular bio-data analysis technique. Ho...

Authors: Sudipta Acharya, Laizhong Cui and Yi Pan

Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks

Network alignment is an efficient computational framework in the prediction of protein function and phylogenetic relationships in systems biology. However, most of existing alignment methods focus on aligning ...

Authors: Yuanke Zhong, Jing Li, Junhao He, Yiqun Gao, Jie Liu, Jingru Wang, Xuequn Shang and Jialu Hu

Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach

Protein-DNA interaction governs a large number of cellular processes, and it can be altered by a small fraction of interface residues, i.e., the so-called hot spots, which account for most of the interface bindin...

Authors: Yuliang Pan, Shuigeng Zhou and Jihong Guan

Developing the novel bioinformatics algorithms to systematically investigate the connections among survival time, key genes and proteins for Glioblastoma multiforme

Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors and its average survival time is less than 1 year after diagnosis.

Authors: Yujie You, Xufang Ru, Wanjing Lei, Tingting Li, Ming Xiao, Huiru Zheng, Yujie Chen and Le Zhang

Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan

Introducing deep learning approach to medical images has rendered a large amount of un-decoded information into usage in clinical research. But mostly, it has been focusing on the performance of the prediction...

Authors: Sangwoo Lee, Eun Kyung Choe, So Yeon Kim, Hua Sun Kim, Kyu Joo Park and Dokyoon Kim

Prediction of hot spots in protein–DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting

Identification of hot spots in protein-DNA interfaces provides crucial information for the research on protein-DNA interaction and drug design. As experimental methods for determining hot spots are time-consum...

Authors: Ke Li, Sijia Zhang, Di Yan, Yannan Bin and Junfeng Xia

Biomedical document triage using a hierarchical attention-based capsule network

Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine. Recently, some neural networks-based methods have been proposed to classify biomedic...

Authors: Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang and YiJia Zhang

Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks

Protein phosphorylation networks play an important role in cell signaling. In these networks, phosphorylation of a protein kinase usually leads to its activation, which in turn will phosphorylate its downstrea...

Authors: Jinling Liu, Xiaojun Ma, Gregory F. Cooper and Xinghua Lu

MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates

Motif enrichment analysis (MEA) identifies over-represented transcription factor binding (TF) motifs in the DNA sequence of regulatory regions, enabling researchers to infer which transcription factors can reg...

Authors: Nathaniel P. Delos Santos, Lorane Texari and Christopher Benner

Correction to: FastMM: an efficient toolbox for personalized constraint-based metabolic modeling

An amendment to this paper has been published and can be accessed via the original article.

Authors: Gong-Hua Li, Shaoxing Dai, Feifei Han, Wenxing Li, Jingfei Huang and Wenzhong Xiao

BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics

The 16th Annual Meeting of the Bioinformatics Italian Society was held in Palermo, Italy, on June 26-28, 2019. More than 80 scientific contributions were presented, including 4 keynote lectures, 31 oral commun...

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

A computational framework for modeling and studying pertussis epidemiology and vaccination

Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context...

Authors: Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno and Marco Beccuti

CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification

Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, includ...

Authors: Domenico Amato, Giosue’ Lo Bosco and Riccardo Rizzo

A preliminary PET radiomics study of brain metastases using a fully automatic segmentation method

Positron Emission Tomography (PET) is increasingly utilized in radiomics studies for treatment evaluation purposes. Nevertheless, lesion volume identification in PET images is a critical and still challenging ...

Authors: Alessandro Stefano, Albert Comelli, Valentina Bravatà, Stefano Barone, Igor Daskalovski, Gaetano Savoca, Maria Gabriella Sabini, Massimo Ippolito and Giorgio Russo

Convolutional architectures for virtual screening

A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false...

Authors: Isabella Mendolia, Salvatore Contino, Ugo Perricone, Edoardo Ardizzone and Roberto Pirrone

Metagenomic analysis through the extended Burrows-Wheeler transform

The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxon...

Authors: Veronica Guerrini, Felipe A. Louza and Giovanna Rosone

Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito

The prediction of protein subcellular localization is a key step of the big effort towards protein functional annotation. Many computational methods exist to identify high-level protein subcellular compartment...

Authors: Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari and Rita Casadio

The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses

Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind d...

Authors: Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo and Romina Oliva

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly im...

Authors: Nicola Prezza, Nadia Pisanti, Marinella Sciortino and Giovanna Rosone

An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs

MicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs. MicroRNA regulation activity depends on the recognition of binding sites located on mRNA molecul...

Authors: Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello and Claudia Coronnello

miRTissue _ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions

Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interac...

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

Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent

Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalization approaches are often the methods of choic...

Authors: Jan Klosa, Noah Simon, Pål Olof Westermark, Volkmar Liebscher and Dörte Wittenburg

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optima...

Authors: Muaaz G. Awan, Jack Deslippe, Aydin Buluc, Oguz Selvitopi, Steven Hofmeyr, Leonid Oliker and Katherine Yelick

Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields

De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, seque...

Authors: Aranka Steyaert, Pieter Audenaert and Jan Fostier

Bioinformatics research at SBB-2019

Authors: Yuriy L. Orlov, Elvira R. Galieva and Tatiana V. Tatarinova

The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion

The alignment of character sequences is important in bioinformatics. The quality of this procedure is determined by the substitution matrix and parameters of the insertion-deletion penalty function. These matr...

Authors: Valery Polyanovsky, Alexander Lifanov, Natalia Esipova and Vladimir Tumanyan

A novel approach for predicting protein S-glutathionylation

S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in ...

Authors: Anastasia A. Anashkina, Yuri M. Poluektov, Vladimir A. Dmitriev, Eugene N. Kuznetsov, Vladimir A. Mitkevich, Alexander A. Makarov and Irina Yu. Petrushanko

Review of medical image recognition technologies to detect melanomas using neural networks

Melanoma is one of the most aggressive types of cancer that has become a world-class problem. According to the World Health Organization estimates, 132,000 cases of the disease and 66,000 deaths from malignant...

Authors: Mila Efimenko, Alexander Ignatev and Konstantin Koshechkin

On the dynamical aspects of local translation at the activated synapse

The key role in the dynamic regulation of synaptic protein turnover belongs to the Fragile X Mental Retardation Protein, which regulates the efficiency of dendritic mRNA translation in response to stimulation ...

Authors: Tamara M. Khlebodarova, Vladislav V. Kogai and Vitaly A. Likhoshvai

Limit cycles in models of circular gene networks regulated by negative feedback loops

The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal r...

Authors: Vitaly A. Likhoshvai, Vladimir P. Golubyatnikov and Tamara M. Khlebodarova

ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature

The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMe...

Authors: Timofey V. Ivanisenko, Olga V. Saik, Pavel S. Demenkov, Nikita V. Ivanisenko, Alexander N. Savostianov and Vladimir A. Ivanisenko

NEMPD: a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information

As an important non-coding RNA, microRNA (miRNA) plays a significant role in a series of life processes and is closely associated with a variety of Human diseases. Hence, identification of potential miRNA-disease...

Authors: Bo-Ya Ji, Zhu-Hong You, Zhan-Heng Chen, Leon Wong and Hai-Cheng Yi

Comprehensive host-pathogen protein-protein interaction network analysis

Infectious diseases are a cruel assassin with millions of victims around the world each year. Understanding infectious mechanism of viruses is indispensable for their inhibition. One of the best ways of unveil...

Authors: Babak Khorsand, Abdorreza Savadi and Mahmoud Naghibzadeh

A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation

Cryo-electron tomography is an important and powerful technique to explore the structure, abundance, and location of ultrastructure in a near-native state. It contains detailed information of all macromolecula...

Authors: Sinuo Liu, Xiaojuan Ban, Xiangrui Zeng, Fengnian Zhao, Yuan Gao, Wenjie Wu, Hongpan Zhang, Feiyang Chen, Thomas Hall, Xin Gao and Min Xu

Automated classification of protein subcellular localization in immunohistochemistry images to reveal biomarkers in colon cancer

Protein biomarkers play important roles in cancer diagnosis. Many efforts have been made on measuring abnormal expression intensity in biological samples to identity cancer types and stages. However, the chang...

Authors: Zhen-Zhen Xue, Yanxia Wu, Qing-Zu Gao, Liang Zhao and Ying-Ying Xu

IonCRAM: a reference-based compression tool for ion torrent sequence files

Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers...

Authors: Moustafa Shokrof and Mohamed Abouelhoda

A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path

MicroRNAs are a class of important small noncoding RNAs, which have been reported to be involved in the processes of tumorigenesis and development by targeting a few genes. Existing studies show that the imbal...

Authors: Peng Xu, Qian Wu, Deyang Lu, Jian Yu, Yongsheng Rao, Zheng Kou, Gang Fang, Wenbin Liu and Henry Han

Skeleton optimization of neuronal morphology based on three-dimensional shape restrictions

Neurons are the basic structural unit of the brain, and their morphology is a key determinant of their classification. The morphology of a neuronal circuit is a fundamental component in neuron modeling. Recent...

Authors: Siqi Jiang, Zhengyu Pan, Zhao Feng, Yue Guan, Miao Ren, Zhangheng Ding, Shangbin Chen, Hui Gong, Qingming Luo and Anan Li

“METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI’s sequence read archive”

The improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximiz...

Authors: Mariam Quiñones, David T. Liou, Conrad Shyu, Wongyu Kim, Ivan Vujkovic-Cvijin, Yasmine Belkaid and Darrell E. Hurt

LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting

A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can...

Authors: Yuan Zhang, Fei Ye, Dapeng Xiong and Xieping Gao