Search Results - computing algorithms and (((bioinformatics OR bioinformation) OR bioinformation) OR informatika)

classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes by Quinn, Gerard P., Sessler, Tamas, Ahmaderaghi, Baharak, Lambe, Shauna, VanSteenhouse, Harper, Lawler, Mark, Wappett, Mark, Seligmann, Bruce, Longley, Daniel B., McDade, Simon S.

“… However, assigning samples to these subtypes and other transcriptionally inferred predictions is time consuming and requires significant bioinformatics experience…”
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Using a stacked ensemble learning framework to predict modulators of protein–protein interactions by Gao, Mengyao, Zhao, Lingling, Zhang, Zitong, Wang, Junjie, Wang, Chunyu

“… In this study, we developed a stacking ensemble computational framework, SELPPI, based on a genetic algorithm and tree-based machine learning method for effectively predicting new modulators targeting protein…”
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A Novel Sequence-Based Method of Predicting Protein DNA-Binding Residues, Using a Machine Learning Approach by Cai, Yudong, Shanghai University, Shanghai, People's Republic of China, He, ZhiSong, Zhejiang University, ZheJiang, People's Republic of China, Shi, Xiaohe, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, People's Republic of China, Kong, Xiangying, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, People's Republic of China, Gu, Lei, Fraunhofer Institute for Algorithms and Scientific Computing, Germany, Xie, Lu, Shanghai Center for Bioinformation Technology, Shanghai, People's Republic of China

“…Protein-DNA interactions play an essential role in transcriptional regulation, DNA repair, and many vital biological processes. The mechanism of protein-DNA…”
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Accurate mass measurements in proteomics by Liu, Tao, Belov, Mikhail E, Jaitly, Navdeep, Qian, Wei-Jun, Smith, Richard D

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New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics by Mokhtari, Majid, Khoshbakht, Samane, Ziyaei, Kobra, Akbari, Mohammad Esmaeil, Moravveji, Sayyed Sajjad

“…Abstract Bioinformatics has revolutionized biology and medicine by using computational methods to analyze and interpret biological data…”
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Bioinformatics analysis of the epitope regions for norovirus capsid protein by Chen, Liping, Wu, Di, Ji, Lei, Wu, Xiaofang, Xu, Deshun, Cao, Zhiwei, Han, Jiankang

“… Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology…”
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Unipro UGENE: a unified bioinformatics toolkit by Okonechnikov, Konstantin, Golosova, Olga, Fursov, Mikhail

“…Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data…”
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Molecular Computing and Bioinformatics by Liang, Xin, Zhu, Wen, Lv, Zhibin, Zou, Quan

“…Molecular computing and bioinformatics are two important interdisciplinary sciences that study molecules and computers…”
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Quantum computing in bioinformatics: a systematic review mapping by Nałęcz-Charkiewicz, Katarzyna, Charkiewicz, Kamil, Nowak, Robert M

“… Bioinformatics is one such domain that is developing in terms of QC. This article offers a broad mapping review of methods and algorithms of QC in bioinformatics, marking the first of its kind…”
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Statistical advances in the biomedical sciences: clinical trials, epidemiology, survival analysis, and bioinformatics by Biswas, Atanu, Datta, Sujay, Fine, Jason P, Segal, Mark R

“… in computing, it has become essential for practitioners in the biomedical sciences to be fully educated on the role statistics plays in ensuring the accurate analysis of research findings…”
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Feature selection methods for big data bioinformatics: A survey from the search perspective by Wang, Lipo, Wang, Yaoli, Chang, Qing

“…This paper surveys main principles of feature selection and their recent applications in big data bioinformatic…”
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ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community by Castrignanò, Tiziana, Gioiosa, Silvia, Flati, Tiziano, Cestari, Mirko, Picardi, Ernesto, Chiara, Matteo, Fratelli, Maddalena, Amente, Stefano, Cirilli, Marco, Tangaro, Marco Antonio, Chillemi, Giovanni, Pesole, Graziano, Zambelli, Federico

“… Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the “Big Data” era…”
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SciPy 1.0: fundamental algorithms for scientific computing in Python by Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul

“…SciPy is an open-source scientific computing library for the Python programming language…”
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Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community by Krampis, Konstantinos, Booth, Tim, Chapman, Brad, Tiwari, Bela, Bicak, Mesude, Field, Dawn, Nelson, Karen E

“…Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still…”
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An integrated pharmacokinetics ontology and corpus for text mining by Wu, Heng-Yi, Karnik, Shreyas, Subhadarshini, Abhinita, Wang, Zhiping, Philips, Santosh, Han, Xu, Chiang, Chienwei, Liu, Lei, Boustani, Malaz, Rocha, Luis M, Quinney, Sara K, Flockhart, David, Li, Lang

“…Background Drug pharmacokinetics parameters, drug interaction parameters, and pharmacogenetics data have been unevenly collected in different databases and…”
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Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection by Flórez, Andrés F, Park, Daeui, Bhak, Jong, Kim, Byoung-Chul, Kuchinsky, Allan, Morris, John H, Espinosa, Jairo, Muskus, Carlos

“…Background Leishmaniasis is a virulent parasitic infection that causes a worldwide disease burden. Most treatments have toxic side-effects and efficacy has…”
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Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics by Baichoo, Shakuntala, Souilmi, Yassine, Panji, Sumir, Botha, Gerrit, Meintjes, Ayton, Hazelhurst, Scott, Bendou, Hocine, Beste, Eugene de, Mpangase, Phelelani T., Souiai, Oussema, Alghali, Mustafa, Yi, Long, O’Connor, Brian D., Crusoe, Michael, Armstrong, Don, Aron, Shaun, Joubert, Fourie, Ahmed, Azza E., Mbiyavanga, Mamana, Heusden, Peter van, Magosi, Lerato E., Zermeno, Jennie, Mainzer, Liudmila Sergeevna, Fadlelmola, Faisal M., Jongeneel, C. Victor, Mulder, Nicola

“… A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments…”
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Graphics processing units in bioinformatics, computational biology and systems biology by Nobile, Marco S, Cazzaniga, Paolo, Tangherloni, Andrea, Besozzi, Daniela

“…Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales…”
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The Carbon Footprint of Bioinformatics by Grealey, Jason, Lannelongue, Loïc, Saw, Woei-Yuh, Marten, Jonathan, Méric, Guillaume, Ruiz-Carmona, Sergio, Inouye, Michael

“…Abstract Bioinformatic research relies on large-scale computational infrastructures which have a nonzero carbon footprint but so far, no study has quantified the environmental costs of bioinformatic…”
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multiPhATE: bioinformatics pipeline for functional annotation of phage isolates by Ecale Zhou, Carol L, Malfatti, Stephanie, Kimbrel, Jeffrey, Philipson, Casandra, McNair, Katelyn, Hamilton, Theron, Edwards, Robert, Souza, Brian

“…) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric database…”
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