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Preprint ARTICLE | doi:10.20944/preprints202010.0403.v1

Comprehensive Analysis of Subtilase Gene Family and Their Responses to Nematode in Trichoderma Harzianum

Xinming Lu, Yinghui Liang, Xun Deng, Dachuan Yin, Ruiqing Song

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Trichoderma harzianum; Subtilase genes; Bioinformatics analysis; Nematode

Online: 19 October 2020 (17:15:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202010.0145.v1

Causal Association between Periodontitis and Parkinson's Disease: A Bidirectional Mendelian Randomization Study

João Botelho, Vanessa Machado, José João Mendes, Paulo Mascarenhas

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Parkinson’s disease; Periodontitis; Periodontal disease; Mendelian Randomization; Bioinformatics; Oral Health

Online: 7 October 2020 (08:26:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202009.0050.v1

Network Protein Interaction in Parkinson's Disease and Periodontitis Interplay: A Bioinformatic Analysis

João Botelho, Paulo Mascarenhas, José João Mendes, Vanessa Machado

Subject: Medicine And Pharmacology, Dentistry And Oral Surgery Keywords: Parkinson’s disease; Periodontitis; Periodontal disease; protein-protein network interaction; Bioinformatics

Online: 3 September 2020 (04:13:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0670.v1

Histological Analysis, Bioinformatics Profile, and Expression of Methylenetetrahydrofolate Reductase (MTHFR) in Bovine Testes

Seth Yaw Afedo, Yan Cui, Sijiu Yu, Bo Liao, Zihan Zhao, Hui Li, Huizhu Zhang, Shengnan Zou, De Hong Li, Peng Zhang

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: MTHFR; bovine; bioinformatics; gene expression; testes

Online: 30 August 2020 (15:00:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0183.v2

Investigating the Influence of the Comprehensive mRNA Expression Levels of Prognostic Genes on Patient Survival in Every Type of Cancer

Minhyeong Lee

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Bioinformatics, Genomics, TCGA, Cox Model.

Online: 21 August 2020 (11:26:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0220.v1

The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology

Emma J. Griffiths, Ruth E. Timme, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Catarina Inês Mendes, Simon H. Tausch, Allison Black, Thomas R. Connor, Gregory H. Tyson, David M. Aanensen, Brian Alcock, Josefina Campos, Alan Christoffels, Anders Gonçalves da Silva, Emma Hodcroft, William W.L. Hsiao, Lee S. Katz, Samuel M. Nicholls, Paul E. Oluniyi, Idowu B. Olawoye, Amogelang R. Raphenya, Ana Tereza R. Vasconcelos, Adam A. Witney, Duncan R. MacCannell

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genomics; metadata; SARS-CoV-2; bioinformatics; data standards

Online: 9 August 2020 (15:53:58 CEST)

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Preprint REVIEW | doi:10.20944/preprints202007.0478.v2

Brief Overview. Role of Computation Biology & Bioinformatics in Drug Design

Ghafran Ali, kanza Ashfaq

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Drug Design; Small Organic Molecule; Target identification; Web-based Server

Online: 25 July 2020 (17:50:30 CEST)

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Working Paper REVIEW

The Reuse of Public Datasets in the Life Sciences: Potential Risks and Rewards

Katharina Sielemann, Alenka Hafner, Boas Pucker

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: data science; reuse; sequencing data; genomics; bioinformatics; databases; computational biology; open science

Online: 16 July 2020 (12:39:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0289.v1

Molecular, Sequencing and Bioinformatics of Insulin- like Growth Factor 1(IGF-1) Gene and Transforming Growth Factor β2 Gene Associations with Growth Traits in Three Strains of Chicken

Waleed El-Tahawy, Manal Abdel-Rahman

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: chickens; IGF-1 gene; TGFβ2 gene; DNA extraction; purification; sequencing and bioinformatics

Online: 14 July 2020 (05:17:40 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0116.v1

Computational Approaches to Functionally Annotate Long Noncoding RNA (lncRNA)

Yashpal Ramakrishnaiah, Levin Kuhlmann, Sonika Tyagi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: noncoding RNA; lncRNA; epigenomics; gene regulation; machine learning; bioinformatics

Online: 9 June 2020 (04:45:12 CEST)

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Preprint REVIEW | doi:10.20944/preprints202005.0376.v1

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, René Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria J. Martin, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric Nawrocki, Áine Niamh O'Toole, Nancy Palacios-Ontiveros, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz

Subject: Biology And Life Sciences, Virology Keywords: virus bioinformatics; SARS-CoV-2; sequencing; epidemiology; drug design; tools

Online: 23 May 2020 (11:01:11 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202004.0476.v1

Novel Missense Mutation in Ligand-Binding Domain of AR Gene Identified in Patient with Androgen Insensitivity Syndrome from Ukraine

Dmytro Sirokha, Olexandra Gorodna, Dmytro Lozhko, Ganna Livshits, Nataliya Zelinska, Liudmyla Livshits

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: androgen insensitivity syndrome; androgen receptor; ligand binding domain; pathogenic mutation; bioinformatics

Online: 27 April 2020 (03:59:38 CEST)

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Androgen insensitivity syndrome (AIS) is the most common disorder of sex development in people with karyotype 46,XY. Mutations in AR (androgen receptor) gene are found in most individuals with AIS. Exons 4-8, which encode LBD, were shown to be a mutation hotspot. The aim of this study was the search of mutations in the sequence of exons 6-8 which encode LBD of AR gene in patients with different clinical AIS phenotypes from Ukraine. The investigated patients were 4 women with 46,XY karyotype, SRY-positive and clinical features of AIS (2 – CAIS, 2 – PAIS). Serum levels of T, LH, and FSH were quantified by electrochemiluminescence immunoassay (ECLIA) technology. Cytogenetic studies were performed on peripheral blood lymphocytes with further use of standard protocols of chromosomal analysis (GTG-banding). The presence of SRY sequence was confirmed by FISH with LSI SRY probe. Direct Sanger sequencing of 6-8 exons was performed in patients and family members on the PCR products on the matrix of DNA samples isolated from peripheral blood lymphocytes. Detected SNPs were analysed using gnomAD, VEP, MutationTaster, Human Splicing Finder, NetPhorest 2.1, Group-based Prediction System 5.0, and PhosphoPICK bioinformatical resources. Modelling of mutant proteins based on available 3D models was conducted using the open source software UCSF Chimera 1.14rc. We have detected 3 previously described mutations (missense mutation X:67722905 Т>С (rs9332970) in PAIS patient, missense mutation X:67722943 C>T (rs886041132) in CAIS patient and, samesense mutation X:67723745 C>T (rs137852594) in PAIS patient). We determined these mutations as pathogenic using SIFT, PolyPhen, MutationTaster, Human Splicing Finder. Moreover the synonymous mutation X:67723745 C>T (rs137852594) detected in patient with PAIS was determined as mutation affecting processes of splicing. In our study we have identified novel mutation X:67722884 T>G in CAIS patient and family members. This mutation was predicted as a pathogenic using aforementioned bioinformatical tools. STRUM calculations of the protein stability change caused by single-point mutation showed a destabilization effect of the Ile836Ser substitution ΔΔG=-2.6. Possible aberrant phosphorylation analysis revealed the ability of MAPK family, Akt family, CDK1, CDK7, CDK9, PKC kinases to phosphorylate Ser836. Results concerning the pathogenicity of X:67722905 Т>С (rs9332970), X:67722943 C>T (rs886041132), X:67723745 C>T (rs137852594) mutations detected in patients with AIS from Ukraine obtained using bioinformatical resources SIFT, PolyPhen, MutationTaster, Human Splicing Finder correlate with previously published data concerning weaker binding of androgens in patients with the same mutations. This approves informativity of using such resources for mutation pathogenicity analysis. Analysis of the ortholog proteins, subdomain structure, and aberrant phosphorylation of AR-LBD suggests novel X:67722884 T>G mutation to be pathogenic. Based on analysis of mutant protein modelling followed by assessment of free energy change using STRUM it was predicted that mutant protein binds androgens 460 times worse than wild type.

Preprint ARTICLE | doi:10.20944/preprints202004.0466.v1

Angiotensin Converting Enzyme 2 in Coronavirus Disease (COVID-19): Evidence from Bioinformatics Analysis

Xiaomei Yang, Hongjin Zhao, Yan Li, Peng Zhang

Subject: Biology And Life Sciences, Endocrinology And Metabolism Keywords: COVID-19; coronavirus; ACE2; bioinformatics analysis; drug prediction

Online: 26 April 2020 (03:14:50 CEST)

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Working Paper ARTICLE

Predicting and Repurposing of Drug and Drug Like Compounds for Inhibition of the Covid-19 and Its Cytokine Storm by Computational Methods

Azhar Sallari Jazzi, Karim Mahnam, Sayed Hossein Hejazi, Mohammad Sadegh Damavandi, Parisa Sadeghi, Mehrdad Zeinalian, Faezeh Tabesh, Seyedeh Mahnaz Mirbod, Hossein Khanahmad

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Viral Macrodomain; COVID-19; TRPM2; losartan; Bioinformatics

Online: 23 April 2020 (14:56:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0394.v1

Population Genetic Considerations for Using Biobanks as International Resources in the Pandemic Era and Beyond

Hannah Carress, Daniel Lawson, Eran Elhaik

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics; population structure; population stratification bias; genomic medicine; biobanks

Online: 22 April 2020 (07:39:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0146.v2

CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing

Ömer An, Kar-Tong Tan, Ying Li, Jia Li, Chan-Shuo Wu, Bin Zhang, Leilei Chen, Henry Yang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: NGS data analysis; bioinformatics pipelines; NGS pipelines

Online: 8 April 2020 (06:21:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0413.v1

Ontological and Bioinformatic Analysis of Anti-Coronavirus Drugs and Their Implication for Drug Repurposing against COVID-19

Yingtong Liu, Wallace K.B. Chan, Zhigang Wang, Junguk Hur, Jiangan Xie, Hong Yu, Yongqun He

Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: coronavirus; drug; COVID-19; SARS; MERS; ontology; ChEBI; NDF-RT; DrON; bioinformatics

Online: 29 March 2020 (01:58:40 CET)

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Coronavirus-infected diseases have posed great threats to human health. In past years, highly infectious coronavirus-induced diseases, including COVID-19, SARS, and MERS, have resulted in world-wide severe infections. Our literature annotations identified 110 chemical drugs and 26 antibodies effective against at least one human coronavirus infection in vitro or in vivo. Many of these drugs inhibit viral entry to cells and viral replication inside cells or modulate host immune responses. Many antimicrobial drugs, including antimalarial (e.g., chloroquine and mefloquine) and antifungal (e.g., terconazole and rapamycin) drugs as well as antibiotics (e.g., teicoplanin and azithromycin) were associated with anti-coronavirus activity. A few drugs, including remdesivir, chloroquine, favipiravir, and tocilizumab, have already been reported to be effective against SARS-CoV-2 infection in vitro or in vivo. After mapping our identified drugs to three ontologies ChEBI, NDF-RT, and DrON, many features such as roles and mechanisms of action (MoAs) of these drugs were identified and categorized. For example, out of 57 drugs with MoA annotations in NDF-RT, 47 have MoAs of different types of inhibitors and antagonists. A total of 29 anticoronaviral drugs are anticancer drugs with the antineoplastic role. Two clustering analyses, one based on ChEBI-based semantic similarity, the other based on drug chemical similarity, were performed to cluster 110 drugs to new categories. Moreover, differences in physicochemical properties among the drugs were found between those inhibiting viral entry and viral replication. A total of 163 host genes were identified as the known targets of 68 anti-coronavirus drugs, resulting in a network of 428 interactions among these drugs and targets. Chlorpromazine, dasatinib, and anisomycin are the hubs of the drug-target network with the highest number of connected target proteins. Many enriched pathways such as calcium signaling and neuroactive ligand-receptor interaction pathways were identified. These findings may be used to facilitate drug repurposing against COVID-19.

Preprint ARTICLE | doi:10.20944/preprints202003.0286.v1

Network Bioinformatics Analysis Provides Insight into Drug Repurposing for COVID-2019

Xu Li, Jinchao Yu, Zhiming Zhang, Jing Ren, Alex E. Peluffo, Wen Zhang, Yujie Zhao, Kaijing Yan, Daniel Cohen, Wenjia Wang

Subject: Medicine And Pharmacology, Pharmacy Keywords: COVID-2019; SARS-CoV-2; repurposing; network bioinformatics

Online: 18 March 2020 (08:50:10 CET)

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Working Paper ARTICLE

The PDZ-binding Motif of SARS-CoV Envelope Protein Induces Cancerization and Poor Prognosis of Lung Adenocarcinoma

Long Chen, Li Zhong

Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: SARS-CoV; PBM; envelope protein; LUAD; bioinformatics

Online: 12 March 2020 (09:28:43 CET)

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Working Paper ARTICLE

Overexpression of GmRIQ2-like (Glyma.04G174400) Enhances the Tolerance of Strong Light Stress and Reduces Photoinhibition in (Glycine max L. Merr.)

Jing Deng, Huayi Yin, Li Ma, Jiukun Zhang, Dongmei Li, Bibin Zhang

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: soybean (Glycine max L.); NPQ; photoinhibition; bioinformatics; subcellular localization; qRT-PCR

Online: 10 February 2020 (09:47:05 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0097.v1

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

Kathy Le, Jared Adolf-Bryfogle, Jason Klima, Sergey Lyskov, Jason Labonte, Steven Bertolani, Shourya Roy Burman, Andrew Leaver-Fay, Brian Weitzner, Jack Maguire, Ramya Rangan, Matt Adrianowycz, Rebecca Alford, Aleexan Adal, Morgan Nance, Rhiju Das, Roland Dunbrack, William Schief, Brian Kuhlman, Justin Siegel, Jeffrey Gray

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Protein structure and dynamics; Molecular structure and modeling; Protein and macromolecules; Computational methods and bioinformatics; Computer-based teaching tools; Learning materials and teaching tools; Multimedia teaching tools

Online: 7 February 2020 (11:42:09 CET)

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Preprint ARTICLE | doi:10.20944/preprints202001.0274.v1

Conventional Data Science Techniques to Bioinformatics and Utilizing a Grid Computing Approach to Computational Medicine

Andrew M. K. Nassief

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: bioinformatics; computational genomics; computational medicine; data science; data visualization; parallel processing; grid computing; fog computing

Online: 24 January 2020 (10:26:26 CET)

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Preprint ESSAY | doi:10.20944/preprints202001.0107.v1

Ten Recommendations for Supporting Open Pathogen Genomic Analysis in Public Health Settings

Allison Black, Duncan R. MacCannell, Thomas R. Sibley, Trevor Bedford

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: pathogen genomics; public health; bioinformatics

Online: 11 January 2020 (11:30:10 CET)

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Preprint REVIEW | doi:10.20944/preprints201911.0252.v1

From Sequence to Information

Ovidiu Popa, Ellen Oldenburg, Oliver Ebenhöh

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: data; sequence; information; entropy; genome; gene; proteins; time-series; modeling; meta-genomics; transcriptomics; proteomics; bioinformatics; DNA

Online: 22 November 2019 (02:28:15 CET)

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Preprint REVIEW | doi:10.20944/preprints201911.0085.v1

Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing

Charles F Rowlands, Diana Baralle, Jamie M Ellingford

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mendelian disease; diagnostics; variant interpretation; variant prioritization; rna splicing; bioinformatics; machine learning; genomic medicine; effect prediction

Online: 8 November 2019 (04:07:16 CET)

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Working Paper ARTICLE

PigLeg: Prediction of Swine Phenotype Using Machine Learning

Siroj Bakoev, Lyubov Getmantseva, Maria Kolosova, Olga Kostyunina, Duane Chartier, Tatiana V. Tatarinova

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: artificial intelligence; bioinformatics; computational biology; data mining & machine learning; evolutionary studies; mathematical biology; animal behavior

Online: 6 November 2019 (05:07:24 CET)

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Preprint ARTICLE | doi:10.20944/preprints201909.0171.v1

Amplicon Analysis I

Eduardo Pareja-Tobes, Raquel Tobes

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: Bioinformatics; NGS; DNA sequencing; DNA sequence analysis; amplicons; ultrametric spaces; indexing

Online: 16 September 2019 (16:45:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201909.0170.v1

ARSA-16S: A New and Conceptually Different Approach for 16S-based Taxonomic Profiling

Eduardo Pareja-Tobes, Raquel Tobes

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: 16S analysis, metagenomics, amplicons, bioinformatics, DNA sequencing

Online: 16 September 2019 (16:41:43 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0074.v1

2DE-pattern: A Database for Inventory of Human Proteoforms

Stanislav Naryzhny, Nikolay Klopov, Natalia Ronzhina, Elena Zorina, Victor Zgoda, Olga Kleyst, Natalia Belyakova, Olga Legina

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: proteoforms; database; bioinformatics; pattern; 2DE

Online: 4 July 2019 (10:29:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0051.v1

Identification of Biomarker Signatures and Candidate Drugs in Non-Small Cell Lung Cancer

Amina Rownaq, Md. Parvez Mosharaf, S. M. Shahinul Islam, Md. Nurul Haque Mollah

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: lung cancer; molecular signature; molecular pathway; differentially expressed genes; protein-protein interaction; reporter biomolecules and bioinformatics

Online: 3 July 2019 (08:54:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0018.v1

Identification of Hub Genes and Key Pathways Associated with Atopic Dermatitis via Integrated Bioinformatics

Yue Sun, Angela Weihong Yang, George Binh Lenon

Subject: Medicine And Pharmacology, Dermatology Keywords: atopic dermatitis; AD; dermatology; target identification; pathway identification; bioinformatics; protein-protein networks

Online: 1 July 2019 (12:47:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201903.0124.v1

Strandedness During cDNA Synthesis, the Stranded Parameter in htseq-count, and Analysis of RNA-Seq Data

Krishna Srinivasan, Suman Virdee, Andrew McArthur

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: RNA-Seq, htseq-count, HISAT2, bioinformatics, strandedness

Online: 11 March 2019 (09:06:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints201811.0629.v1

Explore the Potential Mechanism of Bufadienolides-Like Chemicals on Breast Cancer through Bioinformatics Analysis

Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: bufadienolides-like chemicals; molecular mechanism; anti-cancer; bioinformatics

Online: 30 November 2018 (10:14:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints201811.0463.v1

Sex-Specific Proteomics Changes Induced by Genetic Deletion of the Fibroblast Growth Factor 14 (FGF14) Regulator of Neuronal Ion Channels

Mark Sowers, Jessica Di Re, Paul Wadsworth, Alexander Shavkunov, Cheryl Lichti, Kangling Zhang, Fernanda Laezza

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Mass Spectroscopy, Bioinformatics, FGF14, Voltage Gated Channels, Schizophrenia, Alzheimer’s Disease, Sex-Specific Differences, Synaptic Plasticity, Cognitive Impairment, Excitatory/Inhibitory Tone

Online: 19 November 2018 (11:54:50 CET)

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Preprint ARTICLE | doi:10.20944/preprints201811.0183.v2

Integrating Molecular Biology and Bioinformatics Education

Boas Pucker, Hanna Marie Schilbert, Sina Franziska Schumacher

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: sequencing technologies; NGS; genome research; genome assembly; variant calling; RNA-Seq; transcriptome assembly; bioinformatics; molecular biology; education

Online: 13 November 2018 (10:22:06 CET)

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Preprint ARTICLE | doi:10.20944/preprints201808.0423.v1

mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data

Alex Schomaker-Bastos, Francisco Prosdocimi

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: mitochondrial DNA; mitochondrial genome; genome assembly; genome annotation; next generation sequencing; animal genomics; partial genomics; bioinformatics

Online: 24 August 2018 (03:24:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0618.v1

Mountains and Chasms - Surveying the Oncogenomic Publication Landscape

Paula Carrio Cordo, Michael Baudis

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Cancer genomics; CNA; CGH; bioinformatics

Online: 31 July 2018 (10:21:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0339.v1

Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology

Ishtiaque Ahammad

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: myocardial infarction; heart attack; gene set enrichment analysis; protein-protein interaction network; bioinformatics; systems biology; in silico study

Online: 26 April 2018 (10:22:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0311.v1

Gene Set Enrichment Analysis (GSEA) of Upregulated Genes in Cocaine Addiction Reveals miRNAs as Potential Therapeutic Agents

Ishtiaque Ahammad

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: GSEA; cocaine; addiction; enrichment analysis; bioinformatics; in silico research

Online: 24 April 2018 (08:46:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201711.0041.v1

Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE)

Constantinos Yeles, Efstathios-Iason Vlachavas, Olga Papadodima, Eleftherios Pilalis, Constantinos E. Vorgias, Alexandros G. Georgakilas, Aristotelis Chatziioannou

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Ionizing radiation; Microarrays; Radiation-induced bystander effects; Transcriptomics

Online: 6 November 2017 (15:02:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints201708.0080.v1

A Unique TGFB1-Driven Genomic Program Links Astrocytosis, Low-Grade Inflammation and Partial Demyelination in Periplaques of Spinal Cords from Progressive Multiple Sclerosis Patients

Serge Nataf, Marc Barritault, Laurent Pays

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: multiple sclerosis; neuroinflammation; astrocytes; myelin; bioinformatics

Online: 23 August 2017 (17:46:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201707.0078.v1

An In Silico Study of a Novel rpoB Insertion in a Cluster of Clinical Strains of Mycobacterium tuberculosis Highly-Rifampicin Resistant

Maria Lucia R. Rossetti, Pedro Almeida da Silva, Raquel Maschmann, Andrea von Groll, Leonardo S. Esteves, Fernanda S. Spies, Evelin Sabini, Rubia Raubach Trespach, Elis R. Dalla Costa, Hermes Luís Neubauer de Amorim

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Rifampicin; insertion; biological cost; M. tuberculosis; resistance; structural bioinformatics

Online: 27 July 2017 (11:07:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201610.0025.v1

A Protocol for Identifying Potentially Repurposable Drugs Using Online Tools and Databases

Aditi Chattopadhyay, Madhavi Ganapathiraju

Subject: Medicine And Pharmacology, Other Keywords: drug repurposing; translational bioinformatics; transcriptomics; transcriptome analysis; drug discovery; protocol; gene expression

Online: 9 October 2016 (08:42:23 CEST)

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143 articles found