Skip to content

Advertisement

Articles

Page 2 of 179

  1. Content type: Research

    Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They a...

    Authors: Francesco Bardozzo, Pietro Lió and Roberto Tagliaferri

    Citation: BMC Bioinformatics 2018 19(Suppl 7):194

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  2. Content type: Research

    A huge and continuous increase in the number of completely sequenced chloroplast genomes, available for evolutionary and functional studies in plants, has been observed during the past years. Consequently, it ...

    Authors: Régis Garnier, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Bashar Al-Nuaimi and Bassam AlKindy

    Citation: BMC Bioinformatics 2018 19(Suppl 7):218

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  3. Content type: Software

    Network controllability focuses on discovering combinations of external interventions that can drive a biological system to a desired configuration. In practice, this approach translates into finding a combine...

    Authors: Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler and Ion Petre

    Citation: BMC Bioinformatics 2018 19(Suppl 7):185

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  4. Content type: Research

    Determining the value of kinetic constants for a metabolic system in the exact physiological conditions is an extremely hard task. However, this kind of information is of pivotal relevance to effectively simul...

    Authors: Riccardo Colombo, Chiara Damiani, David Gilbert, Monika Heiner, Giancarlo Mauri and Dario Pescini

    Citation: BMC Bioinformatics 2018 19(Suppl 7):251

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  5. Content type: Research

    De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. G...

    Authors: Igor Saggese, Elisa Bona, Max Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini and Flavio Mignone

    Citation: BMC Bioinformatics 2018 19(Suppl 7):184

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  6. Content type: Methodology article

    Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each ...

    Authors: Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen and Lars Paulin

    Citation: BMC Bioinformatics 2018 19:257

    Published on:

  7. Content type: Correction

    Following publication of the original article [1], the authors reported that Figs. 1 and 3 were interchanged. The original article has been corrected.

    Authors: Maxwell Shapiro, Stephen Meier and Thomas MacCarthy

    Citation: BMC Bioinformatics 2018 19:256

    Published on:

    The original article was published in BMC Bioinformatics 2018 19:163

  8. Content type: Research Article

    Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encod...

    Authors: Henning Lenz, Anke Hein and Volker Knoop

    Citation: BMC Bioinformatics 2018 19:255

    Published on:

  9. Content type: Methodology article

    Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays...

    Authors: Stefano Beretta, Murray D. Patterson, Simone Zaccaria, Gianluca Della Vedova and Paola Bonizzoni

    Citation: BMC Bioinformatics 2018 19:252

    Published on:

  10. Content type: Software

    Computation of reaction similarity is a pre-requisite for several bioinformatics applications including enzyme identification for specific biochemical reactions, enzyme classification and mining for specific i...

    Authors: Tadi Venkata Sivakumar, Anirban Bhaduri, Rajasekhara Reddy Duvvuru Muni, Jin Hwan Park and Tae Yong Kim

    Citation: BMC Bioinformatics 2018 19:254

    Published on:

  11. Content type: Correction

    Following publication of the original article [1], the authors reported that there was an error in the spelling of the name of one of the authors.

    Authors: Makbule Gulcin Ozsoy, Tansel Özyer, Faruk Polat and Reda Alhajj

    Citation: BMC Bioinformatics 2018 19:250

    Published on:

    The original article was published in BMC Bioinformatics 2018 19:136

  12. Content type: Database

    For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers...

    Authors: John A. Bachman, Benjamin M. Gyori and Peter K. Sorger

    Citation: BMC Bioinformatics 2018 19:248

    Published on:

  13. Content type: Research article

    Circadian rhythms comprise oscillating molecular interactions, the disruption of the homeostasis of which would cause various disorders. To understand this phenomenon systematically, an accurate technique to i...

    Authors: Hitoshi Iuchi, Masahiro Sugimoto and Masaru Tomita

    Citation: BMC Bioinformatics 2018 19:249

    Published on:

  14. Content type: Software

    GenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirem...

    Authors: Georg Stricker, Mathilde Galinier and Julien Gagneur

    Citation: BMC Bioinformatics 2018 19:247

    Published on:

  15. Content type: Software

    Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionall...

    Authors: Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger Sutton and Derrick E. Fouts

    Citation: BMC Bioinformatics 2018 19:246

    Published on:

  16. Content type: Software

    The advent of next-generation sequencing (NGS) has made whole-genome sequencing of cohorts of individuals a reality. Primary datasets of raw or aligned reads of this sort can get very large. For scientific que...

    Authors: Kristiina Ausmees, Aji John, Salman Z. Toor, Andreas Hellander and Carl Nettelblad

    Citation: BMC Bioinformatics 2018 19:240

    Published on:

  17. Content type: Software

    High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters...

    Authors: Nikola Tom, Ondrej Tom, Jitka Malcikova, Sarka Pavlova, Blanka Kubesova, Tobias Rausch, Miroslav Kolarik, Vladimir Benes, Vojtech Bystry and Sarka Pospisilova

    Citation: BMC Bioinformatics 2018 19:243

    Published on:

  18. Content type: Research article

    The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule f...

    Authors: Dimitri Kagaris, Alireza Khamesipour and Constantin T. Yiannoutsos

    Citation: BMC Bioinformatics 2018 19:244

    Published on:

  19. Content type: Methodology article

    Asthma and allergies prevalence increased in recent decades, being a serious global health problem. They are complex diseases with strong contextual influence, so that the use of advanced machine learning tool...

    Authors: Rafael V. Veiga, Helio J. C. Barbosa, Heder S. Bernardino, João M. Freitas, Caroline A. Feitosa, Sheila M. A. Matos, Neuza M. Alcântara-Neves and Maurício L. Barreto

    Citation: BMC Bioinformatics 2018 19:245

    Published on:

  20. Content type: Research article

    Lysine succinylation is a new kind of post-translational modification which plays a key role in protein conformation regulation and cellular function control. To understand the mechanism of succinylation profo...

    Authors: Qiao Ning, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma and Xiaowei Zhao

    Citation: BMC Bioinformatics 2018 19:237

    Published on:

  21. Content type: Research article

    The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transpl...

    Authors: Maria Luisa Matey-Hernandez, Søren Brunak and Jose M. G. Izarzugaza

    Citation: BMC Bioinformatics 2018 19:239

    Published on:

  22. Content type: Research article

    In the rational drug design process, an ensemble of conformations obtained from a molecular dynamics simulation plays a crucial role in docking experiments. Some studies have found that Fully-Flexible Receptor...

    Authors: Renata De Paris, Christian Vahl Quevedo, Duncan D. Ruiz, Furia Gargano and Osmar Norberto de Souza

    Citation: BMC Bioinformatics 2018 19:235

    Published on:

  23. Content type: Methodology article

    Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

    Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts

    Citation: BMC Bioinformatics 2018 19:236

    Published on:

  24. Content type: Methodology article

    Spastic cerebral palsy (CP) is a leading cause of physical disability. Most people with spastic CP are born with it, but early diagnosis is challenging, and no current biomarker platform readily identifies aff...

    Authors: Erin L. Crowgey, Adam G. Marsh, Karyn G. Robinson, Stephanie K. Yeager and Robert E. Akins

    Citation: BMC Bioinformatics 2018 19:225

    Published on:

  25. Content type: Software

    The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assembli...

    Authors: Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanc Birol and René L. Warren

    Citation: BMC Bioinformatics 2018 19:234

    Published on:

  26. Content type: Research article

    Drug-disease associations provide important information for the drug discovery. Wet experiments that identify drug-disease associations are time-consuming and expensive. However, many drug-disease associations...

    Authors: Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang and Feng Liu

    Citation: BMC Bioinformatics 2018 19:233

    Published on:

  27. Content type: Research Article

    A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequ...

    Authors: Shuonan Chen and Jessica C. Mar

    Citation: BMC Bioinformatics 2018 19:232

    Published on:

  28. Content type: Research article

    Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with ...

    Authors: Qiang Yu, Dingbang Wei and Hongwei Huo

    Citation: BMC Bioinformatics 2018 19:228

    Published on:

  29. Content type: Research article

    Part of the missing heritability in Genome Wide Association Studies (GWAS) is expected to be explained by interactions between genetic variants, also called epistasis. Various statistical methods have been dev...

    Authors: Clément Chatelain, Guillermo Durand, Vincent Thuillier and Franck Augé

    Citation: BMC Bioinformatics 2018 19:231

    Published on:

  30. Content type: Methodology article

    With the reduction of gene sequencing cost and demand for emerging technologies such as precision medical treatment and deep learning in genome, it is an era of gene data outbreaks today. How to store, transmi...

    Authors: Qiuming Luo, Chao Guo, Yi Jun Zhang, Ye Cai and Gang Liu

    Citation: BMC Bioinformatics 2018 19:230

    Published on:

  31. Content type: Research article

    Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact a...

    Authors: Jean-François Gibrat

    Citation: BMC Bioinformatics 2018 19:226

    Published on:

  32. Content type: Software

    Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic pac...

    Authors: Marcos Díaz-Gay, Maria Vila-Casadesús, Sebastià Franch-Expósito, Eva Hernández-Illán, Juan José Lozano and Sergi Castellví-Bel

    Citation: BMC Bioinformatics 2018 19:224

    Published on:

  33. Content type: Research

    Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific...

    Authors: Yousang Jo, Sanghyeon Kim and Doheon Lee

    Citation: BMC Bioinformatics 2018 19(Suppl 8):213

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  34. Content type: Research

    Deep Neural Networks (DNN), in particular, Convolutional Neural Networks (CNN), has recently achieved state-of-art results for the task of Drug-Drug Interaction (DDI) extraction. Most CNN architectures incorpo...

    Authors: Víctor Suárez-Paniagua and Isabel Segura-Bedmar

    Citation: BMC Bioinformatics 2018 19(Suppl 8):209

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  35. Content type: Research

    Systems biology is an important field for understanding whole biological mechanisms composed of interactions between biological components. One approach for understanding complex and diverse mechanisms is to a...

    Authors: Munui Kim, Seung Han Baek and Min Song

    Citation: BMC Bioinformatics 2018 19(Suppl 8):206

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  36. Content type: Research

    Suicide is an alarming public health problem accounting for a considerable number of deaths each year worldwide. Many more individuals contemplate suicide. Understanding the attributes, characteristics, and ex...

    Authors: Reilly N. Grant, David Kucher, Ana M. León, Jonathan F. Gemmell, Daniela S. Raicu and Samah J. Fodeh

    Citation: BMC Bioinformatics 2018 19(Suppl 8):211

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  37. Content type: Research

    Administered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. Ho...

    Authors: Myeong-Sang Yu, Hyang-Mi Lee, Aaron Park, Chungoo Park, Hyithaek Ceong, Ki-Hyeong Rhee and Dokyun Na

    Citation: BMC Bioinformatics 2018 19(Suppl 8):207

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  38. Content type: Research

    Natural products have been widely investigated in the drug development field. Their traditional use cases as medicinal agents and their resemblance of our endogenous compounds show the possibility of new drug ...

    Authors: Kyungrin Noh, Sunyong Yoo and Doheon Lee

    Citation: BMC Bioinformatics 2018 19(Suppl 8):205

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  39. Content type: Research

    As Twitter has become an active data source for health surveillance research, it is important that efficient and effective methods are developed to identify tweets related to personal health experience. Conven...

    Authors: Keyuan Jiang, Shichao Feng, Qunhao Song, Ricardo A. Calix, Matrika Gupta and Gordon R. Bernard

    Citation: BMC Bioinformatics 2018 19(Suppl 8):210

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  40. Content type: Research

    Social media is a useful platform to share health-related information due to its vast reach. This makes it a good candidate for public-health monitoring tasks, specifically for pharmacovigilance. We study the ...

    Authors: Shashank Gupta, Sachin Pawar, Nitin Ramrakhiyani, Girish Keshav Palshikar and Vasudeva Varma

    Citation: BMC Bioinformatics 2018 19(Suppl 8):212

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  41. Content type: Research

    Identification of drug-target interactions acts as a key role in drug discovery. However, identifying drug-target interactions via in-vitro, in-vivo experiments are very laborious, time-consuming. Thus, predic...

    Authors: Ingoo Lee and Hojung Nam

    Citation: BMC Bioinformatics 2018 19(Suppl 8):208

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  42. Content type: Methodology article

    Discovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. Howe...

    Authors: Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, Hélène Touzet and Martin Figeac

    Citation: BMC Bioinformatics 2018 19:223

    Published on:

Featured videos

View featured videos from across the BMC-series journals

2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

Advertisement