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

Page 5 of 9

  1. Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, ...

    Authors: Vladimir A. Ivanisenko, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena L. Mishchenko and Olga V. Saik
    Citation: BMC Bioinformatics 2019 20(Suppl 1):34
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 1

  3. 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
    Content type: Software Published on:

  4. We develop a software, NCLcomparator, for systematically post-screening the...NCLscore) based on the variation in the number of supporting NCL junction reads identified by the tools examined. Of the input NCL eve...

    Authors: Chia-Ying Chen and Trees-Juen Chuang
    Citation: BMC Bioinformatics 2019 20:3
    Content type: Software Published on:

  5. First, we seek to mathematically characterize the quality of the profile by measuring changes in the signal with respect to amplicon size. Next, we examine the noise, allele, and stutter components of the signal ...

    Authors: Slim Karkar, Lauren E. Alfonse, Catherine M. Grgicak and Desmond S. Lun
    Citation: BMC Bioinformatics 2019 20(Suppl 16):584
    Content type: Research Published on:

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

  6. We suggest that our system can logically guide to select seed genes without additional prior knowledge that makes us free from the seed selection of network propagation issues. We showed that Venn-diaNet can r...

    Authors: Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee and Sun Kim
    Citation: BMC Bioinformatics 2019 20(Suppl 23):667
    Content type: Research Published on:

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

  7. An important task of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is the identification of single particles in micrographs (particle picking). Due to the necessity of human invo...

    Authors: Adil Al-Azzawi, Anes Ouadou, John J. Tanner and Jianlin Cheng
    Citation: BMC Bioinformatics 2019 20:326
    Content type: Methodology article Published on:

  9. 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

  11. Advances in medical technology have allowed for customized prognosis, diagnosis, and treatment regimens that utilize multiple heterogeneous data sources. Multiple kernel learning (MKL) is well suited for the i...

    Authors: Christopher M. Wilson, Kaiqiao Li, Xiaoqing Yu, Pei-Fen Kuan and Xuefeng Wang
    Citation: BMC Bioinformatics 2019 20:426
    Content type: Software Published on:

  15. Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequenc...

    Authors: Shintaro Katayama, Tiina Skoog, Cilla Söderhäll, Elisabet Einarsdottir, Kaarel Krjutškov and Juha Kere
    Citation: BMC Bioinformatics 2019 20:418
    Content type: Software Published on:

  16. Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studie...

    Authors: Franziska Schumann, Eric Blanc, Clemens Messerschmidt, Thomas Blankenstein, Antonia Busse and Dieter Beule
    Citation: BMC Bioinformatics 2019 20:450
    Content type: Software Published on:

  18. Deep learning techniques have been successfully applied to bioimaging problems; however, these methods are highly data demanding. An approach to deal with the lack of data and avoid overfitting is the applicat...

    Authors: Ángela Casado-García, César Domínguez, Manuel García-Domínguez, Jónathan Heras, Adrián Inés, Eloy Mata and Vico Pascual
    Citation: BMC Bioinformatics 2019 20:323
    Content type: Software Published on:

  19. 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

  20. Multiple Sclerosis (MS) is an immune-mediated inflammatory disease of the Central Nervous System (CNS) which damages the myelin sheath enveloping nerve cells thus causing severe physical disability in patients...

    Authors: Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Gianfranco Balbo, Marco Beccuti, Francesca Cordero and Raffaele A. Calogero
    Citation: BMC Bioinformatics 2019 20(Suppl 6):623
    Content type: Research Published on:

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

  22. Modern genomic and proteomic profiling methods produce large amounts of data from tissue and blood-based samples that are of potential utility for improving patient care. However, the design of precision medic...

    Authors: Joanna Roder, Carlos Oliveira, Lelia Net, Maxim Tsypin, Benjamin Linstid and Heinrich Roder
    Citation: BMC Bioinformatics 2019 20:325
    Content type: Methodology article Published on:

  23. Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and ...

    Authors: Ross Mawhorter and Ran Libeskind-Hadas
    Citation: BMC Bioinformatics 2019 20:612
    Content type: Methodology Article Published on:

  24. Biologically data-driven networks have become powerful analytical tools that handle massive, heterogeneous datasets generated from biomedical fields. Protein-protein interaction networks can identify the most ...

    Authors: Milagros Marín, Francisco J. Esteban, Hilario Ramírez-Rodrigo, Eduardo Ros and María José Sáez-Lara
    Citation: BMC Bioinformatics 2019 20:565
    Content type: Methodology article Published on:

  25. Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide app...

    Authors: Bruno M. S. Wanderley, Daniel S. A. Araújo, María V. Quiroga, André M. Amado, Adrião D. D. Neto, Hugo Sarmento, Sebastián D. Metz and Fernando Unrein
    Citation: BMC Bioinformatics 2019 20:274
    Content type: Methodology article Published on:

  26. For fair comparisons, we first set up experiments and verified the 28 fold times speedup on a single MIC against the original CPU-based implementation. We then execute the MCtandem for a very large dataset on an ...

    Authors: Chuang Li, Kenli Li, Keqin Li and Feng Lin
    Citation: BMC Bioinformatics 2019 20:397
    Content type: Research article Published on:

  27. The interplay between metabolic processes and signalling pathways remains poorly understood. Global, detailed and comprehensive reconstructions of human metabolism and signalling pathways exist in the form of ...

    Authors: Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Zinovyev and Inna Kuperstein
    Citation: BMC Bioinformatics 2019 20(Suppl 4):140
    Content type: Research Published on:

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

  28. Advances in next-generation sequencing (NGS) of antibody repertoires have led to an explosion in B cell receptor sequence data from donors with many different disease states. These data have the potential to d...

    Authors: Alexander M. Sevy, Cinque Soto, Robin G. Bombardi, Jens Meiler and James E. Crowe Jr
    Citation: BMC Bioinformatics 2019 20:629
    Content type: Methodology article Published on:

  29. Bacterial surfaces are complex systems, constructed from membranes, peptidoglycan and, importantly, proteins. The proteins play crucial roles as critical regulators of how the bacterium interacts with and surv...

    Authors: Hamed Khakzad, Johan Malmström and Lars Malmström
    Citation: BMC Bioinformatics 2019 20(Suppl 4):141
    Content type: Research Published on:

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

  30. We have developed a novel software, reactIDR, for the prediction of stem/...https://​github.​com/​carushi/​reactIDR.

    Authors: Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri and Jun Sese
    Citation: BMC Bioinformatics 2019 20(Suppl 3):130
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  31. Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretati...

    Authors: Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres and Philipp Rescheneder
    Citation: BMC Bioinformatics 2019 20:258
    Content type: Research article Published on:

  32. A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine des...

    Authors: Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach and Amjad Ali
    Citation: BMC Bioinformatics 2019 20:123
    Content type: Software Published on:

  33. RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free s...

    Authors: Michela Quadrini, Luca Tesei and Emanuela Merelli
    Citation: BMC Bioinformatics 2019 20(Suppl 4):161
    Content type: Methodology Published on:

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

  34. Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For...

    Authors: Zhiguo Li, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew Allen and Kouros Owzar
    Citation: BMC Bioinformatics 2019 20:269
    Content type: Software Published on:

  35. MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing compl...

    Authors: Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo and Claudia Coronnello
    Citation: BMC Bioinformatics 2019 20(Suppl 4):120
    Content type: Research Published on:

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

  36. Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases,...

    Authors: Alan R. Rogers
    Citation: BMC Bioinformatics 2019 20:526
    Content type: Software Published on:

  37. MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a ...

    Authors: Nathan LaPierre, Rob Egan, Wei Wang and Zhong Wang
    Citation: BMC Bioinformatics 2019 20:552
    Content type: Software Published on:

  38. Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Al...

    Authors: Minoo Ashtiani, Payman Nickchi, Soheil Jahangiri-Tazehkand, Abdollah Safari, Mehdi Mirzaie and Mohieddin Jafari
    Citation: BMC Bioinformatics 2019 20:73
    Content type: Software Published on:

  40. Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast...

    Authors: Carlos J. Rivera-Rivera and Juan I. Montoya-Burgos
    Citation: BMC Bioinformatics 2019 20:420
    Content type: Software Published on:

  41. Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two base...

    Authors: Jianghui Wen, Yeshu Liu, Yu Shi, Haoran Huang, Bing Deng and Xinping Xiao
    Citation: BMC Bioinformatics 2019 20:469
    Content type: Methodology article Published on:

  42. 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:

  43. 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
    Content type: Methodology article Published on:

  44. Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It...

    Authors: Garrett Jenkinson, Jordi Abante, Michael A. Koldobskiy, Andrew P. Feinberg and John Goutsias
    Citation: BMC Bioinformatics 2019 20:175
    Content type: Methodology article Published on:

  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. The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts...

    Authors: Tao-Chuan Shih, Li-Ping Ho, Jen-Leih Wu, Hsin-Yiu Chou and Tun-Wen Pai
    Citation: BMC Bioinformatics 2019 20(Suppl 7):192
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  48. Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such m...

    Authors: Dewan M. Sarwar, Reza Kalbasi, John H. Gennari, Brian E. Carlson, Maxwell L. Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter and David P. Nickerson
    Citation: BMC Bioinformatics 2019 20:457
    Content type: Methodology article Published on:

  49. Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant chal...

    Authors: A. Iacoangeli, A. Al Khleifat, W. Sproviero, A. Shatunov, A. R. Jones, S. L. Morgan, A. Pittman, R. J. Dobson, S. J. Newhouse and A. Al-Chalabi
    Citation: BMC Bioinformatics 2019 20:213
    Content type: Methodology article Published on:

  50. An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with respect to a chosen taxonomic level, which delimits the position of t...

    Authors: Davide Heller, Damian Szklarczyk and Christian von Mering
    Citation: BMC Bioinformatics 2019 20:228
    Content type: Methodology article Published on:

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