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  6. Content type: Software

    The biomedical literature is expanding at ever-increasing rates, and it has become extremely challenging for researchers to keep abreast of new data and discoveries even in their own domains of expertise. We i...

    Authors: Patricia Maraver, Rubén Armañanzas, Todd A. Gillette and Giorgio A. Ascoli

    Citation: BMC Bioinformatics 2019 20:50

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  7. Content type: Software

    Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days...

    Authors: Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi and Seyed Abolfazl Motahari

    Citation: BMC Bioinformatics 2019 20:51

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  9. Content type: Software

    With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI ...

    Authors: Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin and Alexander L. Greninger

    Citation: BMC Bioinformatics 2019 20:48

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  11. Content type: Research article

    Accurate prediction of anticancer drug responses in cell lines is a crucial step to accomplish the precision medicine in oncology. Although many popular computational models have been proposed towards this non...

    Authors: Dong Wei, Chuanying Liu, Xiaoqi Zheng and Yushuang Li

    Citation: BMC Bioinformatics 2019 20:44

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  12. Content type: Software

    Samples pooling is a method widely used in studies to reduce costs and labour. DNA sample pooling combined with massive parallel sequencing is a powerful tool for discovering DNA variants (polymorphisms) in la...

    Authors: Aleksandr Igorevich Zhernakov, Alexey Mikhailovich Afonin, Natalia Dmitrievna Gavriliuk, Olga Mikhailovna Moiseeva and Vladimir Aleksandrovich Zhukov

    Citation: BMC Bioinformatics 2019 20:45

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  13. Content type: Research article

    The development of sequencing techniques and statistical methods provides great opportunities for identifying the impact of rare genetic variation on complex traits. However, there is a lack of knowledge on th...

    Authors: Xinyuan Zhang, Anna O. Basile, Sarah A. Pendergrass and Marylyn D. Ritchie

    Citation: BMC Bioinformatics 2019 20:46

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  15. Content type: Software

    We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment.

    Authors: Christine P’ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Denise Y. F. Mak, Felix Lam, Marco A. Albuquerque, Ying Wu, Esther H. Jung, Maud H. W. Starmans, Michelle A. Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang…

    Citation: BMC Bioinformatics 2019 20:42

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  16. Content type: Research article

    The analysis of single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort ...

    Authors: Tianyu Wang, Boyang Li, Craig E. Nelson and Sheida Nabavi

    Citation: BMC Bioinformatics 2019 20:40

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  17. Content type: Methodology article

    Cryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, resear...

    Authors: Jingrong Zhang, Zihao Wang, Yu Chen, Renmin Han, Zhiyong Liu, Fei Sun and Fa Zhang

    Citation: BMC Bioinformatics 2019 20:41

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  18. Content type: Methodology article

    Image segmentation and quantification are essential steps in quantitative cellular analysis. In this work, we present a fast, customizable, and unsupervised cell segmentation method that is based solely on Fij...

    Authors: Mischa Schwendy, Ronald E. Unger, Mischa Bonn and Sapun H. Parekh

    Citation: BMC Bioinformatics 2019 20:39

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  19. Content type: Software

    Single-cell sequencing experiments use short DNA barcode ‘tags’ to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped bas...

    Authors: Akshay Tambe and Lior Pachter

    Citation: BMC Bioinformatics 2019 20:32

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  20. Content type: Software

    Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance...

    Authors: Charlotte Debus, Ralf Floca, Michael Ingrisch, Ina Kompan, Klaus Maier-Hein, Amir Abdollahi and Marco Nolden

    Citation: BMC Bioinformatics 2019 20:31

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  21. Content type: Software

    Simulation of genetic variants data is frequently required for the evaluation of statistical methods in the fields of human and animal genetics. Although a number of high-quality genetic simulators have been d...

    Authors: Apostolos Dimitromanolakis, Jingxiong Xu, Agnieszka Krol and Laurent Briollais

    Citation: BMC Bioinformatics 2019 20:26

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  22. Content type: Software

    Graphlets are useful for bioinformatics network analysis. Based on the structure of Hočevar and Demšar’s ORCA algorithm, we have created an orbit counting algorithm, named Jesse. This algorithm, like ORCA, use...

    Authors: Ine Melckenbeeck, Pieter Audenaert, Thomas Van Parys, Yves Van De Peer, Didier Colle and Mario Pickavet

    Citation: BMC Bioinformatics 2019 20:27

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  24. Content type: Methodology article

    The massive amounts of data from next generation sequencing (NGS) methods pose various challenges with respect to data security, storage and metadata management. While there is a broad range of data analysis p...

    Authors: Lech Nieroda, Lukas Maas, Scott Thiebes, Ulrich Lang, Ali Sunyaev, Viktor Achter and Martin Peifer

    Citation: BMC Bioinformatics 2019 20:29

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  25. Content type: Software

    Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological...

    Authors: Maarten W. Paul, H. Martijn de Gruiter, Zhanmin Lin, Willy M. Baarends, Wiggert A. van Cappellen, Adriaan B. Houtsmuller and Johan A. Slotman

    Citation: BMC Bioinformatics 2019 20:30

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  27. Content type: Methodology article

    Clustering molecular network is a typical method in system biology, which is effective in predicting protein complexes or functional modules. However, few studies have realized that biological molecules are sp...

    Authors: Lixin Cheng, Pengfei Liu, Dong Wang and Kwong-Sak Leung

    Citation: BMC Bioinformatics 2019 20:23

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  28. Content type: Software

    Around 1% of human proteins are predicted to contain a disordered and low complexity prion-like domain (PrLD). Mutations in PrLDs have been shown promote a transition towards an aggregation-prone state in seve...

    Authors: Valentin Iglesias, Oscar Conchillo-Sole, Cristina Batlle and Salvador Ventura

    Citation: BMC Bioinformatics 2019 20:24

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  30. Content type: Software

    Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications. This remarkable progress poses a challe...

    Authors: Harald Marx and Joshua J. Coon

    Citation: BMC Bioinformatics 2019 20:21

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  32. Content type: Methodology article

    In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways an...

    Authors: Alexandra Zaharia, Bernard Labedan, Christine Froidevaux and Alain Denise

    Citation: BMC Bioinformatics 2019 20:19

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  33. Content type: Research article

    Random-effects (RE) models are commonly applied to account for heterogeneity in effect sizes in gene expression meta-analysis. The degree of heterogeneity may differ due to inconsistencies in sample quality. H...

    Authors: Uma Siangphoe, Kellie J. Archer and Nitai D. Mukhopadhyay

    Citation: BMC Bioinformatics 2019 20:18

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  34. Content type: Software

    Translational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the m...

    Authors: Morteza H. Chalabi, Vasileios Tsiamis, Lukas Käll, Fabio Vandin and Veit Schwämmle

    Citation: BMC Bioinformatics 2019 20:17

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  36. Content type: Research article

    Long non-coding RNA (lncRNA) studies play an important role in the development, invasion, and metastasis of the tumor. The analysis and screening of the differential expression of lncRNAs in cancer and corresp...

    Authors: Rong Zhu, Guangshun Li, Jin-Xing Liu, Ling-Yun Dai and Ying Guo

    Citation: BMC Bioinformatics 2019 20:16

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  37. Content type: Research article

    Previous cancer genomics studies focused on searching for novel oncogenes and tumor suppressor genes whose abundance is positively or negatively correlated with end-point observation, such as survival or tumor...

    Authors: Minzhe Zhang, Tao Wang, Rosa Sirianni, Philip W. Shaul and Yang Xie

    Citation: BMC Bioinformatics 2019 20:13

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  38. Content type: Methodology article

    Hypothetical proteins [HP] are those that are predicted to be expressed in an organism, but no evidence of their existence is known. In the recent past, annotation and curation efforts have helped overcome the...

    Authors: Johny Ijaq, Girik Malik, Anuj Kumar, Partha Sarathi Das, Narendra Meena, Neeraja Bethi, Vijayaraghava Seshadri Sundararajan and Prashanth Suravajhala

    Citation: BMC Bioinformatics 2019 20:14

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  39. Content type: Software

    The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genot...

    Authors: Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton, Derrick E. Fouts and Karen E. Nelson

    Citation: BMC Bioinformatics 2019 20:8

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  40. Content type: Methodology article

    Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked dise...

    Authors: Peng Wang, Yu Zhang, Bei-Qi Wang, Jian-Long Li, Yi-Xin Wang, Dongdong Pan, Xian-Bo Wu, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Bioinformatics 2019 20:11

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  41. Content type: Research article

    Recent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific res...

    Authors: Andre Lamurias, Diana Sousa, Luka A. Clarke and Francisco M. Couto

    Citation: BMC Bioinformatics 2019 20:10

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  42. Content type: Software

    Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorith...

    Authors: Minzhe Zhang, Qiwei Li, Donghyeon Yu, Bo Yao, Wei Guo, Yang Xie and Guanghua Xiao

    Citation: BMC Bioinformatics 2019 20:12

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  43. Content type: Software

    Traditional Map based Cloning approaches, used for the identification of desirable alleles, are extremely labour intensive and years can elapse between the mutagenesis and the detection of the polymorphism. Hi...

    Authors: Ghanasyam Rallapalli, Pilar Corredor-Moreno, Edward Chalstrey, Martin Page and Daniel MacLean

    Citation: BMC Bioinformatics 2019 20:9

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  44. Content type: Methodology article

    To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their relianc...

    Authors: Kevin Michael Boehm, Bhavneet Bhinder, Vijay Joseph Raja, Noah Dephoure and Olivier Elemento

    Citation: BMC Bioinformatics 2019 20:7

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  46. Content type: Methodology article

    Predicting drug-disease interactions (DDIs) is time-consuming and expensive. Improving the accuracy of prediction results is necessary, and it is crucial to develop a novel computing technology to predict new ...

    Authors: Zhen Cui, Ying-Lian Gao, Jin-Xing Liu, Juan Wang, Junliang Shang and Ling-Yun Dai

    Citation: BMC Bioinformatics 2019 20:5

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  47. Content type: Software

    Non-co-linear (NCL) transcripts consist of exonic sequences that are topologically inconsistent with the reference genome in an intragenic fashion (circular or intragenic trans-spliced RNAs) or in an intergenic f...

    Authors: Chia-Ying Chen and Trees-Juen Chuang

    Citation: BMC Bioinformatics 2019 20:3

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  48. Content type: Research article

    Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemb...

    Authors: Marco Seeland, Michael Rzanny, David Boho, Jana Wäldchen and Patrick Mäder

    Citation: BMC Bioinformatics 2019 20:4

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