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438 result(s) for 'Software' within Volume 20 of BMC Bioinformatics

Page 4 of 9

  1. The analysis of health and medical data is crucial for improving the diagnosis precision, treatments and prevention. In this field, machine learning techniques play a key role. However, the amount of health da...

    Authors: Josefa Díaz Álvarez, Jordi A. Matias-Guiu, María Nieves Cabrera-Martín, José L. Risco-Martín and José L. Ayala
    Citation: BMC Bioinformatics 2019 20:491
    Content type: Methodology Article Published on:

  2. 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
    Content type: Methodology article Published on:

  3. Here we propose DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach to identify bacteria, fungi and viruses genome contamination. Decon...

    Authors: Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind and Mario Rosario Guarracino
    Citation: BMC Bioinformatics 2019 20(Suppl 4):168
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  4. Untargeted metabolomics datasets contain large proportions of uninformative features that can impede subsequent statistical analysis such as biomarker discovery and metabolic pathway analysis. Thus, there is a...

    Authors: Courtney Schiffman, Lauren Petrick, Kelsi Perttula, Yukiko Yano, Henrik Carlsson, Todd Whitehead, Catherine Metayer, Josie Hayes, Stephen Rappaport and Sandrine Dudoit
    Citation: BMC Bioinformatics 2019 20:334
    Content type: Methodology article Published on:

  5. For large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential ...

    Authors: Wei Gu, Reha Yildirimman, Emmanuel Van der Stuyft, Denny Verbeeck, Sascha Herzinger, Venkata Satagopam, Adriano Barbosa-Silva, Reinhard Schneider, Bodo Lange, Hans Lehrach, Yike Guo, David Henderson and Anthony Rowe
    Citation: BMC Bioinformatics 2019 20:164
    Content type: Methodology article Published on:

  6. Studying structural and functional morphology of small organisms such as monogenean, is difficult due to the lack of visualization in three dimensions. One possible way to resolve this visualization issue is to c...

    Authors: Bee Guan Teo and Sarinder Kaur Dhillon
    Citation: BMC Bioinformatics 2019 20(Suppl 19):658
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 19

  8. Barrett’s esophagus (BE) is most commonly seen as the condition in which the normal squamous epithelium lining of the esophagus is replaced by goblet cells. Many studies show that BE is a predisposing factor f...

    Authors: Visanu Wanchai, Jing Jin, Emine Bircan, Charis Eng and Mohammed Orloff
    Citation: BMC Bioinformatics 2019 20(Suppl 2):98
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  11. Mathematical and computational models are widely used to study the transmission, pathogenicity, and propagation of infectious diseases. Unfortunately, complex mathematical models are difficult to define, reuse...

    Authors: Mai Anh BUI T., Nick Papoulias, Serge Stinckwich, Mikal Ziane and Benjamin Roche
    Citation: BMC Bioinformatics 2019 20:312
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:439

  12. To study cell biological phenomena which depend on diffusion, active transport processes, or the locations of species, modeling and simulation studies need to take space into account. To describe the system as...

    Authors: Till Köster, Philipp Henning and Adelinde M. Uhrmacher
    Citation: BMC Bioinformatics 2019 20:607
    Content type: Methodology Article Published on:

  13. 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 computationa...

    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
    Citation: BMC Bioinformatics 2019 20:557
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:722

  15. In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity ...

    Authors: Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci and Barbara Di Camillo
    Citation: BMC Bioinformatics 2019 20(Suppl 9):416
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  16. Group B streptococcus (GBS) is an important pathogen that is responsible for invasive infections, including sepsis and meningitis. GBS serotyping is an essential means for the investigation of possible infecti...

    Authors: Hsin-Yao Wang, Wen-Chi Li, Kai-Yao Huang, Chia-Ru Chung, Jorng-Tzong Horng, Jen-Fu Hsu, Jang-Jih Lu and Tzong-Yi Lee
    Citation: BMC Bioinformatics 2019 20(Suppl 19):703
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 19

  17. With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic r...

    Authors: Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam and Eve Syrkin Wurtele
    Citation: BMC Bioinformatics 2019 20:440
    Content type: Software Published on:

  19. The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was “Methods, tools and platforms for Personalised Medicine in the Big Data Era”, bu...

    Authors: Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia and Alfonso Urso
    Citation: BMC Bioinformatics 2019 20(Suppl 4):125
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  21. Drug candidates often cause an unwanted blockage of the potassium ion channel of the human ether-a-go-go-related gene (hERG). The blockage leads to long QT syndrome (LQTS), which is a severe life-threatening c...

    Authors: Hyang-Mi Lee, Myeong-Sang Yu, Sayada Reemsha Kazmi, Seong Yun Oh, Ki-Hyeong Rhee, Myung-Ae Bae, Byung Ho Lee, Dae-Seop Shin, Kwang-Seok Oh, Hyithaek Ceong, Donghyun Lee and Dokyun Na
    Citation: BMC Bioinformatics 2019 20(Suppl 10):250
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  22. 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
    Content type: Software Published on:

  23. Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standa...

    Authors: Lucas M. Serra, William D. Duncan and Alexander D. Diehl
    Citation: BMC Bioinformatics 2019 20(Suppl 5):181
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  24. The advent of single cell RNA sequencing (scRNA-seq) enabled researchers to study transcriptomic activity within individual cells and identify inherent cell types in the sample. Although numerous computational...

    Authors: Douglas Abrams, Parveen Kumar, R. Krishna Murthy Karuturi and Joshy George
    Citation: BMC Bioinformatics 2019 20(Suppl 11):275
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  26. Cost-sensitive algorithm is an effective strategy to solve imbalanced classification problem. However, the misclassification costs are usually determined empirically based on user expertise, which leads to uns...

    Authors: Huijuan Lu, Yige Xu, Minchao Ye, Ke Yan, Zhigang Gao and Qun Jin
    Citation: BMC Bioinformatics 2019 20(Suppl 25):681
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  27. Topologically associating domains (TADs) are genomic regions with varying lengths. The interactions within TADs are more frequent than those between different TADs. TADs or sub-TADs are considered the structur...

    Authors: Tong Liu and Zheng Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 16):592
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  28. Modern molecular profiling techniques are yielding vast amounts of data from patient samples that could be utilized with machine learning methods to provide important biological insights and improvements in pa...

    Authors: Heinrich Roder, Carlos Oliveira, Lelia Net, Benjamin Linstid, Maxim Tsypin and Joanna Roder
    Citation: BMC Bioinformatics 2019 20:273
    Content type: Methodology article Published on:

  29. Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules.

    Authors: Damiano Verda, Stefano Parodi, Enrico Ferrari and Marco Muselli
    Citation: BMC Bioinformatics 2019 20(Suppl 9):390
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  31. Distributed approaches based on the MapReduce programming paradigm have started to be proposed in the Bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. ...

    Authors: Umberto Ferraro Petrillo, Mara Sorella, Giuseppe Cattaneo, Raffaele Giancarlo and Simona E. Rombo
    Citation: BMC Bioinformatics 2019 20(Suppl 4):138
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  32. Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast ...

    Authors: Tomas Vicar, Jan Balvan, Josef Jaros, Florian Jug, Radim Kolar, Michal Masarik and Jaromir Gumulec
    Citation: BMC Bioinformatics 2019 20:360
    Content type: Methodology article Published on:

  33. Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Current...

    Authors: Chi-Ching Lee, Po-Jung Huang, Yuan-Ming Yeh, Sin-You Chen, Cheng-Hsun Chiu, Wei-Hung Cheng and Petrus Tang
    Citation: BMC Bioinformatics 2019 20(Suppl 13):382
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  34. When designing an epigenome-wide association study (EWAS) to investigate the relationship between DNA methylation (DNAm) and some exposure(s) or phenotype(s), it is critically important to assess the sample si...

    Authors: Stefan Graw, Rosalyn Henn, Jeffrey A. Thompson and Devin C. Koestler
    Citation: BMC Bioinformatics 2019 20:218
    Content type: Software Published on:

  35. Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis. H...

    Authors: Daniel G. Piqué, Grasiella A. Andriani, Elaine Maggi, Samuel E. Zimmerman, John M. Greally, Cristina Montagna and Jessica C. Mar
    Citation: BMC Bioinformatics 2019 20:336
    Content type: Software Published on:

  36. RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and eve...

    Authors: Paula Pérez-Rubio, Claudio Lottaz and Julia C. Engelmann
    Citation: BMC Bioinformatics 2019 20:226
    Content type: Software Published on:

  37. Myocarditis is defined as the inflammation of the myocardium, i.e. the cardiac muscle. Among the reasons that lead to this disease, we may include infections caused by a virus, bacteria, protozoa, fungus, and ...

    Authors: Ruy Freitas Reis, Juliano Lara Fernandes, Thaiz Ruberti Schmal, Bernardo Martins Rocha, Rodrigo Weber dos Santos and Marcelo Lobosco
    Citation: BMC Bioinformatics 2019 20(Suppl 6):532
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  39. 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
    Content type: Software Published on:

  40. Atomic force microscopy (AFM) allows the mechanical characterization of single cells and live tissue by quantifying force-distance (FD) data in nano-indentation experiments. One of the main problems when deali...

    Authors: Paul Müller, Shada Abuhattum, Stephanie Möllmert, Elke Ulbricht, Anna V. Taubenberger and Jochen Guck
    Citation: BMC Bioinformatics 2019 20:465
    Content type: Methodology article Published on:

  41. Inexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems....

    Authors: Ousmane H. Cissé and Jason E. Stajich
    Citation: BMC Bioinformatics 2019 20:184
    Content type: Software Published on:

  42. Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is...

    Authors: Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li and Xinchun Lin
    Citation: BMC Bioinformatics 2019 20(Suppl 25):687
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  44. Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of m...

    Authors: Chen Li, Yiqi Jiang and Shuaicheng Li
    Citation: BMC Bioinformatics 2019 20(Suppl 23):702
    Content type: Research Published on:

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

  46. 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
    Citation: BMC Bioinformatics 2019 20:523
    Content type: Research article Published on:

  47. Principal components analysis (PCA) is often used to find characteristic patterns associated with certain diseases by reducing variable numbers before a predictive model is built, particularly when some variab...

    Authors: Ping Zhang, Nicholas P. West, Pin-Yen Chen, Mike W. C. Thang, Gareth Price, Allan W. Cripps and Amanda J. Cox
    Citation: BMC Bioinformatics 2019 20(Suppl 6):413
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  48. Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. ...

    Authors: Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri and József Tőzsér
    Citation: BMC Bioinformatics 2019 20:398
    Content type: Research article Published on:

  49. Tuberculosis (TB) represents a worldwide cause of mortality (it infects one third of the world’s population) affecting mostly developing countries, including India, and recently also developed ones due to the ...

    Authors: Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Angela Bonaccorso, Giuseppe Alessandro Parasiliti Palumbo, Epifanio Fichera, Dipendra Kumar Mitra, Kenneth B. Walker, Pere-Joan Cardona, Merce Amat, Marco Viceconti and Francesco Pappalardo
    Citation: BMC Bioinformatics 2019 20(Suppl 6):504
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  50. Set enrichment methods are commonly used to analyze high-dimensional molecular data and gain biological insight into molecular or clinical phenotypes. One important category of analysis methods employs an enri...

    Authors: Joanna Roder, Benjamin Linstid and Carlos Oliveira
    Citation: BMC Bioinformatics 2019 20:257
    Content type: Methodology article Published on:

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