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1

Lomberk, Gwen. "Bioinformatics tools." Pancreatology 5, no. 4-5 (2005): 314–15. http://dx.doi.org/10.1159/000086531.

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Moreews, François, Olivier Sallou, Hervé Ménager, et al. "BioShaDock: a community driven bioinformatics shared Docker-based tools registry." F1000Research 4 (December 14, 2015): 1443. http://dx.doi.org/10.12688/f1000research.7536.1.

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Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docke
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3

Grisham, William, Natalie A. Schottler, Joanne Valli-Marill, Lisa Beck, and Jackson Beatty. "Teaching Bioinformatics and Neuroinformatics by Using Free Web-based Tools." CBE—Life Sciences Education 9, no. 2 (2010): 98–107. http://dx.doi.org/10.1187/cbe.09-11-0079.

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This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and th
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Zhang, Xiaorong. "Teaching Botany Using Bioinformatics Tools." Creative Education 10, no. 10 (2019): 2137–46. http://dx.doi.org/10.4236/ce.2019.1010155.

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5

Cantó‐Pastor, Alex, G. Alex Mason, Siobhan M. Brady, and Nicholas J. Provart. "Arabidopsis bioinformatics: tools and strategies." Plant Journal 108, no. 6 (2021): 1585–96. http://dx.doi.org/10.1111/tpj.15547.

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6

Skuse, Gary R., and Chunguang Du. "Bioinformatics Tools for Plant Genomics." International Journal of Plant Genomics 2008 (June 11, 2008): 1–2. http://dx.doi.org/10.1155/2008/910474.

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7

Arndt, Timothy. "Visual software tools for bioinformatics." Journal of Visual Languages & Computing 19, no. 2 (2008): 291–301. http://dx.doi.org/10.1016/j.jvlc.2007.06.001.

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8

Margolis, David J., Nandita Mitra, Bradley Wubbenhorst, and Katherine L. Nathanson. "Filaggrin sequencing and bioinformatics tools." Archives of Dermatological Research 312, no. 2 (2019): 155–58. http://dx.doi.org/10.1007/s00403-019-01956-3.

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9

Arora, Pankaj Kumar, and Wenxin Shi. "Tools of bioinformatics in biodegradation." Reviews in Environmental Science and Bio/Technology 9, no. 3 (2010): 211–13. http://dx.doi.org/10.1007/s11157-010-9211-x.

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10

Lomberk, Gwen. "Educational Websites — Bioinformatics Tools II." Pancreatology 9, no. 1-2 (2009): 4–5. http://dx.doi.org/10.1159/000178767.

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11

Iwakiri, Junichi, Michiaki Hamada, and Kiyoshi Asai. "Bioinformatics tools for lncRNA research." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1859, no. 1 (2016): 23–30. http://dx.doi.org/10.1016/j.bbagrm.2015.07.014.

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12

Caccia, Dario, Matteo Dugo, Maurizio Callari, and Italia Bongarzone. "Bioinformatics tools for secretome analysis." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1834, no. 11 (2013): 2442–53. http://dx.doi.org/10.1016/j.bbapap.2013.01.039.

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13

Blekherman, Grigoriy, Reinhard Laubenbacher, Diego F. Cortes, et al. "Bioinformatics tools for cancer metabolomics." Metabolomics 7, no. 3 (2011): 329–43. http://dx.doi.org/10.1007/s11306-010-0270-3.

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14

Mullany, Lila E., Roger K. Wolff, and Martha L. Slattery. "Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression." Cancer Informatics 14 (January 2015): CIN.S32716. http://dx.doi.org/10.4137/cin.s32716.

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MiRNAs are small, nonprotein-coding RNA molecules involved in gene regulation. While bioinformatics help guide miRNA research, it is less clear how they perform when studying biological pathways. We used 13 criteria to evaluate effectiveness and usability of existing bioinformatics tools. We evaluated the performance of six bioinformatics tools with a cluster of 12 differentially expressed miRNAs in colorectal tumors and three additional sets of 12 miRNAs that are not part of a known cluster. MiRPath performed the best of all the tools in linking miRNAs, with 92% of all miRNAs linked as well a
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Mazola, Yuliet, Glay Chinea, and Alexis Musacchio. "Integrating Bioinformatics Tools to Handle Glycosylation." PLoS Computational Biology 7, no. 12 (2011): e1002285. http://dx.doi.org/10.1371/journal.pcbi.1002285.

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16

Fernandez-Pozo, N., A. Gómez-Ollé, A. Bullones, L. A. Mueller, and J. I. Hormaza. "MangoBase: bioinformatics tools for mango research." Acta Horticulturae, no. 1415 (January 2025): 229–36. https://doi.org/10.17660/actahortic.2025.1415.27.

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17

Debes, Jose D., and Raul Urrutia. "Bioinformatics tools to understand human diseases." Surgery 135, no. 6 (2004): 579–85. http://dx.doi.org/10.1016/j.surg.2003.11.010.

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18

Prilusky, Jaime, and Joel L. Sussman. "Guest Editorial: Databases and Bioinformatics Tools." Israel Journal of Chemistry 53, no. 3-4 (2013): 143. http://dx.doi.org/10.1002/ijch.201310004.

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19

Vitorino, Rui. "Special Issue: “Bioinformatics and Omics Tools”." International Journal of Molecular Sciences 24, no. 14 (2023): 11625. http://dx.doi.org/10.3390/ijms241411625.

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With the rapid introduction of high-throughput omics approaches such as genomics, transcriptomics, proteomics and metabolomics, the generation of large amounts of data has become a fundamental aspect of modern biological research [...]
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20

Luna Buitrago, Diana, Ruth C. Lovering, and Andrea Caporali. "Insights into Online microRNA Bioinformatics Tools." Non-Coding RNA 9, no. 2 (2023): 18. http://dx.doi.org/10.3390/ncrna9020018.

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MicroRNAs (miRNAs) are members of the small non-coding RNA family regulating gene expression at the post-transcriptional level. MiRNAs have been found to have critical roles in various biological and pathological processes. Research in this field has significantly progressed, with increased recognition of the importance of miRNA regulation. As a result of the vast data and information available regarding miRNAs, numerous online tools have emerged to address various biological questions related to their function and influence across essential cellular processes. This review includes a brief int
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21

Esteban, David J., Melissa Da Silva, and Chris Upton. "New bioinformatics tools for viral genome analyses at Viral Bioinformatics – Canada." Pharmacogenomics 6, no. 3 (2005): 271–80. http://dx.doi.org/10.1517/14622416.6.3.271.

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22

Mbareche, Hamza, Nathan Dumont-Leblond, Guillaume J. Bilodeau, and Caroline Duchaine. "An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists." Life 10, no. 9 (2020): 185. http://dx.doi.org/10.3390/life10090185.

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High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariate
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23

Lazarus, R., A. Kaspi, and M. Ziemann. "Creating reusable tools from scripts: the Galaxy Tool Factory." Bioinformatics 28, no. 23 (2012): 3139–40. http://dx.doi.org/10.1093/bioinformatics/bts573.

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24

García-García, Natalia, Javier Tamames, and Fernando Puente-Sánchez. "M&Ms: a versatile software for building microbial mock communities." Bioinformatics 38, no. 7 (2022): 2057–59. http://dx.doi.org/10.1093/bioinformatics/btab882.

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Abstract Summary Advances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze 16S rDNA sequencing data. As these tools need to be tested, it is important to simulate datasets that resemble samples from different environments. Here, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce different 16S rDNA datasets from reference sequences, based on pragmatic ecological parameters. It creates sequence libraries for ‘in silico’ microbial communities with user-controlled richness, evenness, microdiversity and source envir
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25

Thornton, Janet, Graham Cameron, and Cath Brooksbank. "The European Bioinformatics Institute: Leading the bioinformatics revolution." Biochemist 26, no. 4 (2004): 33–38. http://dx.doi.org/10.1042/bio02604033.

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Life without databases is almost inconceivable to today's researchers in the biomolecular sciences -- the world of biomolecules is freely available on the Internet, along with a powerful set of tools for analysing the data. Many of the world's most widely used data resources are hosted and developed at the European Molecular Biology Laboratory (EMBL)'s European Bioinformatics Institute (EBI), often in collaboration with partners throughout the world. The EBI is also a thriving research centre.
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26

Yan, Qing. "Bioinformatics Databases and Tools in Virology Research: An Overview." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 8, no. 2 (2008): 71–85. https://doi.org/10.3233/isb-00345.

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Viruses are major factors of human infectious diseases. Understanding of the structure-function correlation in viruses is important for the identification of potential anti-viral inhibitors and vaccine targets. In virology research, virus-related databases and bioinformatic analysis tools are essential for discerning relationships within complex datasets about viruses and host-virus interactions. Bioinformatic analyses on viruses include the identification of open reading frames, gene prediction, homology searching, sequence alignment, and motif and epitope recognition. The predictions of feat
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27

Pereira, Rute, Jorge Oliveira, and Mário Sousa. "Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics." Journal of Clinical Medicine 9, no. 1 (2020): 132. http://dx.doi.org/10.3390/jcm9010132.

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Clinical genetics has an important role in the healthcare system to provide a definitive diagnosis for many rare syndromes. It also can have an influence over genetics prevention, disease prognosis and assisting the selection of the best options of care/treatment for patients. Next-generation sequencing (NGS) has transformed clinical genetics making possible to analyze hundreds of genes at an unprecedented speed and at a lower price when comparing to conventional Sanger sequencing. Despite the growing literature concerning NGS in a clinical setting, this review aims to fill the gap that exists
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28

Najeb Mohammed, Bafreen. "A Review: Genetics Algorithms in Bioinformatics Tools." ICONTECH INTERNATIONAL JOURNAL 5, no. 1 (2021): 16–25. http://dx.doi.org/10.46291/icontechvol5iss1pp16-25.

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Bioinformaticians study biological questions by analyzing molecular data with various programs and tools. Today, bioinformatics is used in large number of fields such as microbial genome applications, biotechnology, waste cleanup, Gene therapy, fingerprint and eye detection. The field of bioinformatics, is one of the most prominent areas that our need is increasing, and the demand for it is increasing day by day. Where dealing with this vital and biological information using advanced computer technologies to generate useful information and new discoveries. For this reason, vital bioinformatics
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29

Tabassum Khan, Nida. "The Emerging Role of Bioinformatics in Biotechnology." Journal of Biotechnology and Biomedical Science 1, no. 3 (2018): 13–24. http://dx.doi.org/10.14302/issn.2576-6694.jbbs-18-2173.

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Bioinformatic tools is widely used to manage the enormous genomic and proteomic data involving DNA/protein sequences management, drug designing, homology modelling, motif/domain prediction ,docking, annotation and dynamic simulation etc. Bioinformatics offers a wide range of applications in numerous disciplines such as genomics. Proteomics, comparative genomics, nutrigenomics, microbial genome, biodefense, forensics etc. Thus it offers promising future to accelerate scientific research in biotechnology
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30

Khan, Johra, and Rajeev K. Singla. "Bioinformatics Tools for Pharmaceutical Drug Product Development." Indo Global Journal of Pharmaceutical Sciences 12, no. 12 (2022): 281–94. http://dx.doi.org/10.35652/igjps.2022.12037.

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Drug discovery and production is a long and expensive process which starts with target identification followed by validation of targets to lead optimization, taking years to develop a drug which sometime false to reach marked resulting in loss of time, effort, and huge amount of money. Bioinformatics tools are becoming more and more important in drug product development. Repurposing large amount of data needs to be exploited and generated fromgenomics, epigenetics, cistromic, proteomics, transcriptomics, ribosomal profiling, and genomic based studies of drug targets. Bioinformatics analysis an
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31

Nwabueze, Ekwonwune, and E. Charles. "Impact of Bioinformatics Tools in Genomic Biomedicine." British Journal of Applied Science & Technology 19, no. 3 (2017): 1–8. http://dx.doi.org/10.9734/bjast/2017/30404.

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32

Huang, Jian, Beibei Ru, and Ping Dai. "Bioinformatics Resources and Tools for Phage Display." Molecules 16, no. 1 (2011): 694–709. http://dx.doi.org/10.3390/molecules16010694.

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33

Prabha, Ratna, D. P. Singh, and Anil Rai. "BioInfoKnowledgeBase: Comprehensive Information Resource for Bioinformatics Tools." American Journal of Bioinformatics 4, no. 2 (2015): 28–33. http://dx.doi.org/10.3844/ajbsp.2015.28.33.

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34

de Azevedo Junior, Walter Filgueira, Raquel Dias, Luis Fernando Macedo Timmers, Ivani Pauli, Rafael Caceres, and Milena Pereira Soares. "Bioinformatics Tools for Screening of Antiparasitic Drugs." Current Drug Targets 10, no. 3 (2009): 232–39. http://dx.doi.org/10.2174/138945009787581122.

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35

Lee, Michael. "bit: a multipurpose collection of bioinformatics tools." F1000Research 11 (January 31, 2022): 122. http://dx.doi.org/10.12688/f1000research.79530.1.

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bit is a collection of small scripts and programs that facilitate many common tasks in bioinformatics. It operates in a Unix-like command-line environment and is comprised of bash and python code. bit is openly available on GitHub, archived with Zenodo, and is conda installable. The package is useful for users who want to do things such as manipulate fasta files, calculate GC content, quickly summarize nucleotide assemblies, easily download assemblies from NCBI just based on accessions, pull amino-acid sequences from GenBank files, calculate Shannon uncertainty for columns in multiple sequence
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36

ORTON, R. J., Q. GU, J. HUGHES, et al. "Bioinformatics tools for analysing viral genomic data." Revue Scientifique et Technique de l'OIE 35, no. 1 (2016): 271–85. http://dx.doi.org/10.20506/rst.35.1.2432.

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37

Sirangelo, Tiziana Maria, and Grazia Calabro. "Soil Metagegomics: Approaches, Bioinformatics Tools and Applications." Scholars Journal of Agriculture and Veterinary Sciences 7, no. 6 (2020): 125–32. http://dx.doi.org/10.36347/sjavs.2020.v07i06.003.

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38

Brusic, Vladimir, and Darren R. Flower. "Bioinformatics tools for identifying T-cell epitopes." Drug Discovery Today: BIOSILICO 2, no. 1 (2004): 18–23. http://dx.doi.org/10.1016/s1741-8364(04)02374-1.

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39

Romano, P., R. Giugno, and A. Pulvirenti. "Tools and collaborative environments for bioinformatics research." Briefings in Bioinformatics 12, no. 6 (2011): 549–61. http://dx.doi.org/10.1093/bib/bbr055.

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40

Garg, Priyanka, and Pankaj Jaiswal. "Databases and bioinformatics tools for rice research." Current Plant Biology 7-8 (November 2016): 39–52. http://dx.doi.org/10.1016/j.cpb.2016.12.006.

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41

Lambrix, P., M. Habbouche, and M. Perez. "Evaluation of ontology development tools for bioinformatics." Bioinformatics 19, no. 12 (2003): 1564–71. http://dx.doi.org/10.1093/bioinformatics/btg194.

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42

Holloway, Eric. "Tutorial: Bioinformatics Basics." Communications of the Blyth Institute 2, no. 2 (2020): 35–38. http://dx.doi.org/10.33014/issn.2640-5652.2.2.holloway.1.

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 Bioinformatics can appear to be a daunting field, since it combines the complex science of biology with the complex theory of computer science. However, the basics are surprisingly simple. This tutorial gives a glimpse of the tools and techniques needed to get started in the field.
 
 
 
 
 
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43

Paul, Piby, Vimala Antonydhason, Judy Gopal, Steve W. Haga, Nazim Hasan, and Jae-Wook Oh. "Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization." International Journal of Molecular Sciences 21, no. 3 (2020): 961. http://dx.doi.org/10.3390/ijms21030961.

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The clinical sampling of urine is noninvasive and unrestricted, whereby huge volumes can be easily obtained. This makes urine a valuable resource for the diagnoses of diseases. Urinary and renal proteomics have resulted in considerable progress in kidney-based disease diagnosis through biomarker discovery and treatment. This review summarizes the bioinformatics tools available for this area of proteomics and the milestones reached using these tools in clinical research. The scant research publications and the even more limited bioinformatic tool options available for urinary and renal proteomi
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44

Anashkina, Anastasia A., Elena Y. Leberfarb, and Yuriy L. Orlov. "Recent Trends in Cancer Genomics and Bioinformatics Tools Development." International Journal of Molecular Sciences 22, no. 22 (2021): 12146. http://dx.doi.org/10.3390/ijms222212146.

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We overview recent research trends in cancer genomics, bioinformatics tools development and medical genetics, based on results discussed in papers collections “Medical Genetics, Genomics and Bioinformatics” (https://www [...]
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45

S. Atheena, Milagi Pandian, Murugan Rashika, Manoj Kumar N. Sri, N. Aparna, and Sakthi M. Kriya. "Utilizing bioinformatics tools for analyzing high-throughput data in biomedical research." i-manager’s Journal on Future Engineering and Technology 19, no. 3 (2024): 33. http://dx.doi.org/10.26634/jfet.19.3.20561.

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Bioinformatics has become crucial in biomedical research, enabling the processing of massive volumes of high- throughput data generated by various omics technologies. This work investigates the use of bioinformatics tools to process, analyze, and interpret omics data, including genomics, transcriptomics, proteomics, and metabolomics. It provides an overview of widely used bioinformatics methodologies and algorithms for data preparation, quality control, differential expression analysis, pathway analysis, and functional annotation. The study also highlights current trends and challenges in bioi
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46

KMS, Rana, Ahammad K, and Salam MA. "Bioinformatics: scope and challenges in aquaculture research of Bangladesh- a review." International Journal of Agricultural Research, Innovation and Technology 10, no. 2 (2020): 137–45. https://doi.org/10.3329/ijarit.v10i2.51587.

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Bioinformatics is one of the ongoing trends of biological research integrating gene based information and computational technology to produce new knowledge. It works to synthesize complex biological information from multiomics data (results of high throughput technologies) by employing a number of bioinformatics tools (software). User convenience and availability are the determining factors of these tools being widely used in bioinformatics research. BLAST<strong>,&nbsp;</strong>FASTA (FAST-All), EMBOSS, ClustalW, RasMol and Protein Explorer, Cn3D, Swiss PDB viewer, Hex, Vega, Bioeditor etc. a
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47

Stankov, Karmen. "Bioinformatic tools for cancer geneticists." Archive of Oncology 13, no. 2 (2005): 69–75. http://dx.doi.org/10.2298/aoo0502069s.

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Early detection is essential for the control and prevention of many diseases, particularly cancer, which is the reason why the need for new disease markers with improved sensitivity and specificity continues to grow. Utilization of sophisticated bioinformatic tools enables the increased specificity and a relatively large quantity of high quality assays for any gene of interest. Understanding the molecular characteristics of diseases, such as cancer and the detection of mutations or changes in gene expression patterns that occur as a result of the disease, will bring researchers one step closer
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48

Dr., Subhan Shahid Dr. Erum Naseem Ahmed Dr. Dujanah Siddique Bhatti. "TOOLS FOR TRACKING ANTIBIOTIC RESISTANCE." INDO AMERICAN JOURNAL OF PHARMACEUTICAL SCIENCES 05, no. 05 (2018): 4270–73. https://doi.org/10.5281/zenodo.1254075.

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Objective: Antibiotic resistance is amongst leading problems in pharmaceutical and medicinal science. The resistive genes are imposed a pressure by antibiotics which cause excessive genetic material exchange by resulting malfunctioning. Microbial population has also been terminated by undue antibiotic uses. Therefore, the problem needs a solution to introduce new tools to measure accurate resistance level. Bioinformatic and pharmaceutical technologies can revolutionize the industry. Patients and Methods: The molecular study was conducted to determine protein natures, structures and functioning
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49

Shevtsov, V., A. Ismailova, U. Aitimova, and O. Khapilina. "APPLICATION OF INFORMATION SYSTEMS AND TOOLS IN BIOINFORMATICS." Scientific Journal of Astana IT University, no. 9 (March 30, 2022): 14–21. http://dx.doi.org/10.37943/aitu.2022.59.49.002.

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Abstract. The pace at which scientific data is produced and disseminated has never been ashigh as it is currently. Modern sequencing technologies make it possible to obtain the genomeof a specific organism in a few days, and the genome of a bacterial organism in less than a day,and therefore researchers from the field of life science are faced with a huge amount of datathat needs to be analyzed. In this connection, various fields of science are converging with eachother, giving rise to new disciplines. So, bioinformatics is one of these fields, it is a scientificdiscipline that has been active
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50

Joppich, Markus, and Ralf Zimmer. "From command-line bioinformatics to bioGUI." PeerJ 7 (November 21, 2019): e8111. http://dx.doi.org/10.7717/peerj.8111.

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Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface only. Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary work. With our bioGUI framework we address two main problems
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