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  1. Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data,...

    Authors: Antoine Buetti-Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Ran Friedman and Mark Dopson
    Citation: BMC Bioinformatics 2020 21:23
    Content type: Research Article Published on:

    The Data Descriptor to this article has been published in Scientific Data 2020 7:215

  2. Omics-profiling is a collection of increasingly prominent approaches that result in large-scale biological datasets, for instance capturing an organism’s behavior and response in an environment. It can be daun...

    Authors: Defne Surujon and Tim van Opijnen
    Citation: BMC Bioinformatics 2020 21:22
    Content type: Software Published on:

  3. Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analy...

    Authors: Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang and Xianming Shi
    Citation: BMC Bioinformatics 2020 21:20
    Content type: Software Published on:

  4. In order to improve the accuracy of constraint-based metabolic models, several approaches have been developed which intend to integrate additional biological information. Two of these methods, MOMENT and GECKO...

    Authors: Pavlos Stephanos Bekiaris and Steffen Klamt
    Citation: BMC Bioinformatics 2020 21:19
    Content type: Methodology article Published on:

  5. Integrating genome-wide gene expression patient profiles with regulatory knowledge is a challenging task because of the inherent heterogeneity, noise and incompleteness of biological data. From the computation...

    Authors: Maxime Folschette, Vincent Legagneux, Arnaud Poret, Lokmane Chebouba, Carito Guziolowski and Nathalie Théret
    Citation: BMC Bioinformatics 2020 21:18
    Content type: Research Article Published on:

  6. MicroRNAs (miRNAs) play important roles in a variety of biological processes by regulating gene expression at the post-transcriptional level. So, the discovery of new miRNAs has become a popular task in biolog...

    Authors: Xueming Zheng, Xingli Fu, Kaicheng Wang and Meng Wang
    Citation: BMC Bioinformatics 2020 21:17
    Content type: Methodology article Published on:

  7. Cell-type heterogeneity of tumors is a key factor in tumor progression and response to chemotherapy. Tumor cell-type heterogeneity, defined as the proportion of the various cell-types in a tumor, can be inferr...

    Authors: Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum and Magali Richard
    Citation: BMC Bioinformatics 2020 21:16
    Content type: Methodology article Published on:

    The Protocol to this article has been published in Nature Protocols 2020 15:s41596-020-0369-6

  8. Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints an...

    Authors: Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen and Rolf Backofen
    Citation: BMC Bioinformatics 2020 21:15
    Content type: Research Article Published on:

  10. The rapid growth of available knowledge on metabolic processes across thousands of species continues to expand the possibilities of producing chemicals by combining pathways found in different species. Several...

    Authors: Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett and Lydia E. Kavraki
    Citation: BMC Bioinformatics 2020 21:13
    Content type: Methodology Article Published on:

  15. Cell nuclei segmentation is a fundamental task in microscopy image analysis, based on which multiple biological related analysis can be performed. Although deep learning (DL) based techniques have achieved sta...

    Authors: Feixiao Long
    Citation: BMC Bioinformatics 2020 21:8
    Content type: Methodology Article Published on:

  20. The green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, thi...

    Authors: Melanie Fachet, Carina Witte, Robert J. Flassig, Liisa K. Rihko-Struckmann, Zaid McKie-Krisberg, Jürgen E. W. Polle and Kai Sundmacher
    Citation: BMC Bioinformatics 2020 21:1
    Content type: Research Article Published on:

  23. Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics suppo...

    Authors: Judit Kumuthini, Lyndon Zass, Sumir Panji, Samson P. Salifu, Jonathan K. Kayondo, Victoria Nembaware, Mamana Mbiyavanga, Ajayi Olabode, Ali Kishk, Gordon Wells and Nicola J. Mulder
    Citation: BMC Bioinformatics 2019 20:741
    Content type: Research article Published on:

  26. Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was de...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Franck Molina, Géraldine Lavigne, Claude Granier and Violaine Moreau
    Citation: BMC Bioinformatics 2019 20:738
    Content type: Methodology article Published on:

  27. Reactivation of the telomerase reverse transcriptase gene TERT is a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood.

    Authors: Alexandra M. Poos, Theresa Kordaß, Amol Kolte, Volker Ast, Marcus Oswald, Karsten Rippe and Rainer König
    Citation: BMC Bioinformatics 2019 20:737
    Content type: Methodology article Published on:

  28. Portal vein system thrombosis (PVST) is potentially fatal for patients if the diagnosis is not timely or the treatment is not proper. There hasn’t been any available technique to detect clinic risk factors to ...

    Authors: Mingzhao Wang, Linglong Ding, Meng Xu, Juanying Xie, Shengli Wu, Shengquan Xu, Yingmin Yao and Qingguang Liu
    Citation: BMC Bioinformatics 2019 20(Suppl 22):720
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  29. Subcellular localization prediction of protein is an important component of bioinformatics, which has great importance for drug design and other applications. A multitude of computational tools for proteins su...

    Authors: Yu-hua Yao, Ya-ping Lv, Ling Li, Hui-min Xu, Bin-bin Ji, Jing Chen, Chun Li, Bo Liao and Xu-ying Nan
    Citation: BMC Bioinformatics 2019 20(Suppl 22):719
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  30. Identifying different types of cancer based on gene expression data has become hotspot in bioinformatics research. Clustering cancer gene expression data from multiple cancers to their own class is a significa...

    Authors: Juan Wang, Cong-Hai Lu, Jin-Xing Liu, Ling-Yun Dai and Xiang-Zhen Kong
    Citation: BMC Bioinformatics 2019 20(Suppl 22):718
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  31. Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, inclu...

    Authors: Guimin Qin, Luqiong Yang, Yuying Ma, Jiayan Liu and Qiuyan Huo
    Citation: BMC Bioinformatics 2019 20(Suppl 22):717
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  32. In recent years, identification of differentially expressed genes and sample clustering have become hot topics in bioinformatics. Principal Component Analysis (PCA) is a widely used method in gene expression d...

    Authors: Chun-Mei Feng, Yong Xu, Mi-Xiao Hou, Ling-Yun Dai and Jun-Liang Shang
    Citation: BMC Bioinformatics 2019 20(Suppl 22):716
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  33. The main goal of successful gene selection for microarray data is to find compact and predictive gene subsets which could improve the accuracy. Though a large pool of available methods exists, selecting the op...

    Authors: Ying Xiong, Qing-Hua Ling, Fei Han and Qing-Hua Liu
    Citation: BMC Bioinformatics 2019 20(Suppl 22):715
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  34. Tumor purity plays an important role in understanding the pathogenic mechanism of tumors. The purity of tumor samples is highly sensitive to tumor heterogeneity. Due to Intratumoral heterogeneity of genetic an...

    Authors: Shudong Wang, Lihua Wang, Yuanyuan Zhang, Shanchen Pang and Xinzeng Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 22):714
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  35. Variant calling and refinement from whole genome/exome sequencing data is a fundamental task for genomics studies. Due to the limited accuracy of NGS sequencing and variant callers, IGV-based manual review is ...

    Authors: Hang Zhang, Ke Wang, Juan Zhou, Jianhua Chen, Yizhou Xu, Dong Wang, Xiaoqi Li, Renliang Sun, Mancang Zhang, Zhuo Wang and Yongyong Shi
    Citation: BMC Bioinformatics 2019 20(Suppl 22):713
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 22

  37. With the global spread of multidrug resistance in pathogenic microbes, infectious diseases emerge as a key public health concern of the recent time. Identification of host genes associated with infectious dise...

    Authors: Ranjan Kumar Barman, Anirban Mukhopadhyay, Ujjwal Maulik and Santasabuj Das
    Citation: BMC Bioinformatics 2019 20:736
    Content type: Research article Published on:

  38. Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many i...

    Authors: A. B. M. Shamim Ul Hasan, Hiroyuki Kurata and Sebastian Pechmann
    Citation: BMC Bioinformatics 2019 20:734
    Content type: Research article Published on:

  39. The protein ki67 (pki67) is a marker of tumor aggressiveness, and its expression has been proven to be useful in the prognostic and predictive evaluation of several types of tumors. To numerically quantify the...

    Authors: Barbara Rita Barricelli, Elena Casiraghi, Jessica Gliozzo, Veronica Huber, Biagio Eugenio Leone, Alessandro Rizzi and Barbara Vergani
    Citation: BMC Bioinformatics 2019 20:733
    Content type: Methodology article Published on:

  40. Genome-wide Association Studies (GWAS) have contributed to unraveling associations between genetic variants in the human genome and complex traits for more than a decade. While many works have been invented as...

    Authors: Haohan Wang, Tianwei Yue, Jingkang Yang, Wei Wu and Eric P. Xing
    Citation: BMC Bioinformatics 2019 20(Suppl 23):656
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  41. Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites ...

    Authors: Ruohan Wang, Zishuai Wang, Jianping Wang and Shuaicheng Li
    Citation: BMC Bioinformatics 2019 20(Suppl 23):652
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  42. Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden...

    Authors: Cheng Yan, Guihua Duan, Fang-Xiang Wu and Jianxin Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 23):651
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  43. How small, fast-growing bacteria ensure tight cell-size distributions remains elusive. High-throughput measurement techniques have propelled efforts to build modeling tools that help to shed light on the relat...

    Authors: Cesar Augusto Nieto-Acuna, Cesar Augusto Vargas-Garcia, Abhyudai Singh and Juan Manuel Pedraza
    Citation: BMC Bioinformatics 2019 20(Suppl 23):647
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  44. There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional annotation of a new miRNA is to classify it into charact...

    Authors: Xubo Tang and Yanni Sun
    Citation: BMC Bioinformatics 2019 20(Suppl 23):646
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  45. Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a ch...

    Authors: Binh P. Nguyen, Quang H. Nguyen, Giang-Nam Doan-Ngoc, Thanh-Hoang Nguyen-Vo and Susanto Rahardja
    Citation: BMC Bioinformatics 2019 20(Suppl 23):634
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  46. Modern flow cytometry technology has enabled the simultaneous analysis of multiple cell markers at the single-cell level, and it is widely used in a broad field of research. The detection of cell populations i...

    Authors: Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura
    Citation: BMC Bioinformatics 2019 20(Suppl 23):633
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  47. Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to...

    Authors: Mehwish Noureen, Ipputa Tada, Takeshi Kawashima and Masanori Arita
    Citation: BMC Bioinformatics 2019 20(Suppl 23):631
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  48. Current Hi-C technologies for chromosome conformation capture allow to understand a broad spectrum of functional interactions between genome elements. Although significant progress has been made into analysis ...

    Authors: Juris Viksna, Gatis Melkus, Edgars Celms, Kārlis Čerāns, Karlis Freivalds, Paulis Kikusts, Lelde Lace, Mārtiņš Opmanis, Darta Rituma and Peteris Rucevskis
    Citation: BMC Bioinformatics 2019 20(Suppl 23):618
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  49. Removing duplicates might be considered as a well-resolved problem in next-generation sequencing (NGS) data processing domain. However, as NGS technology gains more recognition in clinical application, researc...

    Authors: Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li and Jia Gu
    Citation: BMC Bioinformatics 2019 20(Suppl 23):606
    Content type: Software Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  50. Detection of new drug-target interactions by computational algorithms is of crucial value to both old drug repositioning and new drug discovery. Existing machine-learning methods rely only on experimentally va...

    Authors: Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao and Jinyan Li
    Citation: BMC Bioinformatics 2019 20(Suppl 23):605
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

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