bmc bioinformatics methodology article

Supplement 4. BMC Bioinformatics 0000004844 00000 n Found inside â Page 471Regulatory Toxicology and Pharmacology, 50(1), 37â49. McCall, M. N., Murakami, P. N., Lukk, M., Huber, W., & Irizarry, R. A. (2011). Assessing affymetrix genechip microarray quality. BMC Bioinformatics ... Found inside â Page 706Conditional variable importance for random forests. BMC Bioinformatics 9(307), URL http://www.biomedcentral.com/1471-2105/9/307 Stuart E. (2010). Matching methods for causal inference: A review and a look forward. 0000011517 00000 n Volume 22 Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. 0000034715 00000 n 6. 0000006025 00000 n First, we showed that the lists of cancer genes from some major data sources were ... terms of overlapping genes. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired. BMC Bioinformatics The genetic basis of phenotypic traits is highly variable and usually divided into mono-, oligo- and polygenic inheritance classes. BMC Bioinformatics Authors: Camila Riccio-Rengifo, Jorge Finke and Camilo Rocha, Citation: Supplement 5, Modelling p-value distributions to improve theme-driven survival analysis of cancer transcriptome datasets, Deep learning for cancer type classification and driver gene identification, Volume 22 L��&�W The recent advancement of scDNA sequencing technology sheds light upon addressing intratumor heterogeneity, detecting rare subclones, and reconstructing tumor evolution lineages at single-cell resolution. Authors: Younghoon Kim, Imhoi Koo, Byung Hwa Jung, Bong Chul Chung and Doheon Lee, Citation: 405 0 obj << /Linearized 1 /O 410 /H [ 3260 1190 ] /L 890953 /E 154159 /N 14 /T 882734 >> endobj xref 405 128 0000000016 00000 n 2021 7:481. Supplement 13. 22:553. Authors: Lauren Coombe, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, René L. Warren and Inanc Birol, Citation: 15(Suppl 10):P21, Authors: Duojiao Wu, Catherine M Rice and Xiangdong Wang, Citation: Terms and Conditions, 13(Suppl 6):S10, This article is part of a Supplement: Nat. 0000008523 00000 n Authors: Fabien Campagne and Lucy Skrabanek, Citation: BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. DNA methylation is an important epigenetic modification of the genome. 0000059839 00000 n 19:487. This text will equip both practitioners and theorists with the necessary background in testing hypothesis and decision theory to enable innumerable practical applications of statistics. 0000006944 00000 n Read papers from the ISCB. 2021 Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine (BIBM) 2016: systems biology Research. Search all BMC articles Search The "Cancer bioinformatics" thematic series focuses on the latest developments in the emerging field of systems clinical medicine in cancer which integrates systems biology, clinical science, omics-based technology, bioinformatics and computational science to improve diagnosis, therapies and prognosis of cancer. 16(Suppl 15):P14, Authors: Shruti S Sakhare, Gautam G Rao, Sammed N Mandape and Siddharth Pratap, Citation: Authors: Tao Jiang, Shiqi Liu, Shuqi Cao, Yadong Liu, Zhe Cui, Yadong Wang and Hongzhe Guo, Citation: 11:76. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. 2010 BMC Bioinformatics Recent development of single cell sequencing technologies has made it possible to identify genes with different expression (DE) levels at the cell type level between different groups of samples. Related Journals in Bioinformatics 0000081974 00000 n As a number of studies focus on DNA methylation... Citation: Mutational signatures proved to be a useful tool for identifying patterns of mutations in genomes, often providing valuable insights about mutagenic processes or normal DNA damage. BMC Bioinformatics With the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and spatial vocabularies is urgently needed to clarify PPI biological annotations. 0000026002 00000 n 0000026576 00000 n Volume 22 Found inside â Page 54SUPPLEMENTARY MATERIAL The Supplementary Material for this article can be found online at ... BMC Bioinformatics 7:56. doi:10.1186/1471-2105-7-56 Koh, C., Wu, F.-X., Selvaraj, G., and Kusalik, A. J. (2009). Using a state-space model and ... The book introduces the bioinformatics tools, databases and strategies for the translational research, focuses on the biomarker discovery based on integrative data analysis and systems biological network reconstruction. 0000011047 00000 n 0000008905 00000 n Authors: Marco Antonio Tangaro, Pietro Mandreoli, Matteo Chiara, Giacinto Donvito, Marica Antonacci, Antonio Parisi, Angelica Bianco, Angelo Romano, Daniela Manila Bianchi, Davide Cangelosi, Paolo Uva, Ivan Molineris, Vladimir Nosi, Raffaele A. Calogero, Luca Alessandri, Elena Pedrini…, Citation: 0000008811 00000 n BMC Bioinformatics Supplement 14. ƞkd��g�8�PQs�.� �� endstream endobj 532 0 obj 1048 endobj 410 0 obj << /Type /Page /Parent 402 0 R /Resources 469 0 R /Contents [ 496 0 R 503 0 R 505 0 R 507 0 R 514 0 R 516 0 R 518 0 R 529 0 R ] /CropBox [ 1 0 611 792 ] /Annots [ 447 0 R 448 0 R 449 0 R 450 0 R 451 0 R 452 0 R 453 0 R 454 0 R ] /B [ 455 0 R ] /Thumb 162 0 R /MediaBox [ 0 0 612 792 ] /Rotate 0 >> endobj 411 0 obj << /Count 17 /First 412 0 R /Last 413 0 R >> endobj 412 0 obj << /Title (Abstract) /Dest (G1007539) /Parent 411 0 R /Next 435 0 R /First 444 0 R /Last 445 0 R /Count 3 >> endobj 413 0 obj << /Title (References) /Dest (G1029583) /Parent 411 0 R /Prev 414 0 R >> endobj 414 0 obj << /Title (Acknowledgements) /Dest (G1029555) /Parent 411 0 R /Prev 415 0 R /Next 413 0 R >> endobj 415 0 obj << /Title (Methods) /Dest (G1024538) /Parent 411 0 R /Prev 416 0 R /Next 414 0 R /First 417 0 R /Last 418 0 R /Count 4 >> 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Citation: BMC Bioinformatics 2020 21 (Suppl 4) :248. Authors: Zexian Zeng, Chengsheng Mao, Andy Vo, Xiaoyu Li, Janna Ore Nugent, Seema A. Khan, Susan E. Clare and Yuan Luo, Citation: Authors: Ping-Nan Chen, Chia-Chiang Lee, Chang-Min Liang, Shu-I Pao, Ke-Hao Huang and Ke-Feng Lin, Citation: Epub 2003 Jan 13. 8:275. @MISC{Noto06bmcbioinformatics, author = {Keith Noto and Mark Craven}, title = {BMC Bioinformatics Methodology article}, year = {2006}} Share. H�dUT��a�YX��"��U�� 12(Suppl 11):A11, This article is part of a Supplement: Supplement 5, Thermal face recognition under different conditions, Artificial intelligence classification model for macular degeneration images: a robust optimization framework for residual neural networks, Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method, Epidemic prediction of dengue fever based on vector compartment model and Markov chain Monte Carlo method, Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning, A deep learning method for counting white blood cells in bone marrow images, Application of artificial intelligence ensemble learning model in early prediction of atrial fibrillation, Robust optimization of convolutional neural networks with a uniform experiment design method: a case of phonocardiogram testing in patients with heart diseases, General deep learning model for detecting diabetic retinopathy, Identifying stress responsive genes using overlapping communities in co-expression networks, MSA: reproducible mutational signature attribution with confidence based on simulations, Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia, SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and, PrognosiT: Pathway/gene set-based tumour volume prediction using multiple kernel learning, Development of a prognostic signature of patients with esophagus adenocarcinoma by using immune-related genes, FASTAFS: file system virtualisation of random access compressed FASTA files, LongStitch: high-quality genome assembly correction and scaffolding using long reads, Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph, A drug repositioning algorithm based on a deep autoencoder and adaptive fusion, Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data, isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data, End-to-end learning for compound activity prediction based on binding pocket information, Volume 22 For larger sample sizes, the methods combining a variance-stabilizing transformation with the 'limma' m … BMC Bioinformatics . Article within a journal (no page numbers) Rohrmann S, Overvad K, Bueno-de-Mesquita HB, Jakobsen MU, Egeberg R, Tjønneland A, et al. 2021 22:178. De novo extraction of signat... Citation: 2014 22(Suppl 3):521. 5. BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. Supplement 10, Computational analysis of genetic network involved in pancreatic cancer in human, Volume 12 0000008999 00000 n bmc bioinformatics methodology article parameter space reasonable amount polynomial equation semidefinite programming entire parameter set conventional approach good solution exists duality property inequality constraint posteriori step mass action kinetics complex biological system novel approach current approach single parameter set nonlinear . 0000036416 00000 n Authors: Xiangxin Zhang, Liu Yang, Ming Kong, Jian Ma and Yutao Wei, Citation: A Year in Bioinformatics. 0000011141 00000 n 13:12. Results: In this article, we propose a new computational method to predict interaction between a given pair of protein . Citation: Journal of Clinical Bioinformatics 2014 4 :3. 22(Suppl 5):314, This article is part of a Supplement: Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing. 22:555. 0000011705 00000 n In this study, we infer a colon cancer network from a large-scale gene expression ... the first study analyzing the genome-scale colon cancer network. BMC Bioinformatics is an open access, peer-reviewed journal that considers articles describing novel computational algorithms and software, models and tools, including statistical methods, machine learning and artificial intelligence, as well as systems biology. 0000007680 00000 n Supplement 6, Reconstructing cancer genomes from paired-end sequencing data, Volume 13 Supplement 8, Enabling proteomics-based identification of human cancer variations, Correction to: Computational approaches for cancer 2017 workshop overview, Large-scale integration of cancer microarray data identifies a robust common cancer signature, Predicting cancer involvement of genes from heterogeneous data, Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples, CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations, MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature, methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder, Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts, Volume 7 20:43, The Pangenome-wide association studies (e.g. Biomedical studies suggest that genomic measurements ... identify gene pathways with predictive power for breast cancer prognosis. Evaluations of wet-lab and bioinformatics approaches are needed to . BMC Bioinformatics 22:331. Host population structure is a key determinant of pathogen and infectious disease transmission patterns. This book contains information on how to tackle many important problems using a multiscale statistical approach. 14:323. It's been a year where our authors have looked at many different aspects of the bioinformatics field. 2013;11:63. 22(Suppl 5):148. 0000009442 00000 n 2004 0000040247 00000 n Authors: Rosa Barcelona-Cabeza, Walter Sanseverino and Riccardo Aiese Cigliano, Citation: Individual journals may differ in their peer review processes; for example, some journals operate an open and others a closed peer review system. Hajirasouliha I, Mahmoody A, Raphael BJ. Volume 12 Supplement 3. 0000035596 00000 n Found inside â Page 168BMC Bioinformatics . ... The journal publishes original peer - reviewed research articles and also methodology articles and articles that describe databases or software . ... Of interest to researchers in the bioinformatics field . BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. Volume 11 Supplement 3. This usually involves review by two independent peer reviewers. BMC Bioinformatics BMC Bioinformatics BMC Bioinformatics The central goal of the In the Light of Evolution (ILE) series is to promote the evolutionary sciences through state-of-the-art colloquia-in the series of Arthur M. Sackler colloquia sponsored by the National Academy of Sciences-and their ... Found inside â Page 21Our simulation study suggests that the methodology controls the overall false discovery rate while maintaining high power. ... BMC Bioinformatics 17:104. doi:10.1186/s12859-016-0937-5 Guo, W., Sarkar, S. K., and Peddada, S. D. (2010). BMC Bioinformatics 0000011329 00000 n Authors: Ali Ghanbari Sorkhi, Zahra Abbasi, Majid Iranpour Mobarakeh and Jamshid Pirgazi, Citation: Tutorial chapters by leaders in the field introduce state-of-the-art methods to handle information integration problems of omics data. Imaging mass cytometry (IMC) may be able to address all these questions by combining the power of MS-CyTOF and microscopy. �W)Exf� �V. 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA) BMC Bioinformatics BMC Bioinformatics 2021 California Privacy Statement, Ovarian cancer is a deadly female reproductive cancer. 2003 Jan 13;4:2. doi: 10.1186/1471-2105-4-2. Liver cancer is a common malignant tumor in China, with high mortality. Boltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. These methods can be applied to DNA, RNA or protein sequences. 15(Suppl 6):S6, This article is part of a Supplement: Authors: Athanasios D. Balomenos, Victoria Stefanou and Elias S. Manolakos, Citation: BMC Bioinformatics Raihan Ahmed, Hasin Rehana, Setu Chakraborty, Md. 2021 0000007479 00000 n Privacy Wearable devices enable monitoring and measurement of physiological parameters over a 24-h period, and some of which exhibit circadian rhythm characteristics. OpenURL . Authors: Ramkrishna Mitra, Jingchun Sun, Min Zhao and Zhongming Zhao, Citation: BMC Bioinformatics Cookies policy. 22:556. 10(Suppl 9):S17, This article is part of a Supplement:
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