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Preprint ARTICLE | doi:10.20944/preprints202102.0264.v1

SARS-CoV-2 and the Secret of the Furin Site

Antonio R. Romeu, Enric Ollé

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: SARS-CoV-2, RaTG13, Furin Site, Molecular Evolution, Bioinformatics.

Online: 10 February 2021 (15:46:12 CET)

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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 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 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 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/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

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 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 BRIEF REPORT | doi:10.20944/preprints202110.0080.v2

SARS-CoV-2 and MERS-CoV Share the Furin Site CGG-CGG Genetic Footprint

Antonio R. Romeu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SARS-CoV-2; MERS-CoV; arginine dimer; polybasic furin cleavage site; aginine codon; Markov model; bioinformatics

Online: 14 October 2021 (13:08:25 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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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 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/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 REVIEW | doi:10.20944/preprints202105.0346.v1

Role of Artificial Intelligence and Machine Learning in Bioinformatics: Drug Discovery and Drug Repurposing

Sameer Quazi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: drug discovery; drug repurposing; bioinformatics; machine learning; artificial intelligence; biomedical discoveries etc.

Online: 14 May 2021 (15:17:50 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202106.0121.v1

SARS-CoV-2 Origin: An Affair of Codons?

Antonio Ramón Romeu, Enric Ollé

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SARS-CoV-2 origin; Furin Cleavage Site; Arginine Codon Usage; Bioinformatics

Online: 4 June 2021 (08:00:03 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/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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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 REVIEW | doi:10.20944/preprints202106.0145.v1

Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs

Chao Zeng, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, Michiaki Hamada

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Repetitive element; Transposable element; Non-coding RNA; ncRNA; Functional element; Bioinformatics

Online: 4 June 2021 (15:33:17 CEST)

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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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Working Paper REVIEW

Incorporating Machine Learning Into Bioinformatics Frameworks

Noam Auslander, Ayal Gussow, Eugene Koonin

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: machine learning; deep learning; bioinformatics; phylogenetics; cancer evolution

Online: 17 February 2021 (09:40:45 CET)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202311.1130.v1

VarChat: The Generative AI Assistant for the Interpretation of Human Genomic Variations

Federica De Paoli, Silvia Berardelli, Ettore Rizzo, Ivan Limongelli, Susanna Zucca

Subject: Computer Science And Mathematics, Software Keywords: Genomics; Variant Interpretation; Generative AI; Genome analysis; Rare Diseases; Bioinformatics

Online: 17 November 2023 (05:24:56 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0903.v1

Effects of Acute and Chronic Gabapentin Treatment on Cardiovascular Function of Rats

Ved Pendyala, Sarah Pribil, Vicki Schaal, Kanika Sharma, Sankarasubramanian Jagadesan, Li Yu, Vikas Kumar, Chittibabu Guda, Lie Gao

Subject: Medicine And Pharmacology, Anesthesiology And Pain Medicine Keywords: Gabapentin; Arterial Blood Pressure; Heart Rate; Left Ventricular Function; Proteomics; Bioinformatics; Calmodulin;

Online: 13 October 2023 (12:41:55 CEST)

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Gabapentin (GBP), a GABA analogue, is primarily used as an anticonvulsant to treat partial seizures and neuropathic pain. While a majority of the side effects are associated with the nervous system, emerging evidence suggests a high risk for heart diseases in the patients taking GBP. In the present study, we used a preclinical model of rats to investigate (1) the acute cardiovascular responses to GBP (bolus i.v. injection, 50 mg/kg) and (2) the effects of chronic GBP treatment (i.p. 100 mg/kg/day x 7 days) on cardiovascular function and the myocardial proteome. Under isoflurane-anesthesia, rat blood pressure (BP), heart rate (HR), and left ventricular (LV) hemodynamics were measured using Millar pressure transducers. The LV myocardium and brain cortex were analyzed by proteomics, bioinformatics, and western blot to explore the molecular mechanisms underlying GBP-induced cardiac dysfunction. In experiment (1), we found that i.v. GBP significantly decreased BP, HR, maximal LV pressure, and maximal and minimal dP/dt, whereas it increased IRP-AdP/dt, Tau, systolic, diastolic, and cycle durations (*p < 0.05 and **p < 0.01 vs baseline; n = 4/group). In experiment (2), we found that chronic GBP treatment resulted in hypotension, bradycardia, and LV systolic dysfunction, with no change in plasma norepinephrine. In the myocardium, we identified 109 differentially expressed proteins involved in calcium pathways, cholesterol metabolism, and galactose metabolism. Particularly, we found that calmodulin, a key protein of intracellular calcium signaling, was significantly upregulated by GBP in the heart but not in the brain. In summary, we found that acute and chronic GBP treatments suppressed cardiovascular function in rats, which is attributed to abnormal calcium signaling in cardiomyocytes. These data reveal a novel side effect of GBP independent of the nervous system, providing important translational evidence to suggest that GBP can evoke adverse cardiovascular events by depression of myocardial function.

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/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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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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Working Paper ARTICLE

Testing the Hypothesis that the Nylonase NylB Protein Arose de novo via a Frameshift Mutation

Salvador Cordova, John Sanford

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Proteomics; Protein Evolution

Online: 17 September 2021 (11:49:04 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/preprints202101.0116.v1

Computational Methods for Chromosome-Scale Haplotype Reconstruction

Shilpa Garg

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Graphs; Medical genetics; sequencing methods

Online: 6 January 2021 (12:06:39 CET)

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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 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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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 COMMUNICATION | doi:10.20944/preprints202309.0079.v1

Data Literacy in Genome Research

Katharina Wolff, Ronja Friedhoff, Friderieke Schwarzer, Boas Pucker

Subject: Biology And Life Sciences, Life Sciences Keywords: computational biology; genomics; sequencing; data literacy; bioinformatics; education

Online: 4 September 2023 (04:32:42 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 CONCEPT PAPER | doi:10.20944/preprints202104.0686.v1

Aquamoleculomics: A Thermodynamic Cornerstone of Systems Biology

Zilin Nie, Yanming Nie

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: H2O networks; Aqua biomolecule complexes; Thermodynamic mechanism; “Aquamoleculosome"; Entropic systems biology; Self-organized criticality (SOC); Self-organization triggering factor (SOTF); Bioinformatics of aquamoleculomics.

Online: 26 April 2021 (20:02:20 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/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 REVIEW | doi:10.20944/preprints202401.0789.v1

Microbiome Modeling: A Beginner’s Guide

Emanuel Lange, Lena Kranert, Jacob Krüger, Dirk Benndorf, Robert Heyer

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: systems microbiology; microbial ecology; omics data integration; metaproteomics; genome-scale modeling; constraint-based modeling; boolean modeling, bioinformatics

Online: 10 January 2024 (09:57:55 CET)

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Preprint REVIEW | doi:10.20944/preprints202206.0022.v1

Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics

Alexander Kudryavtsev, Anna V. Vakhrusheva, Valery Novoseletsky, Marine Bozdaganyan, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; Omicron; bioinformatics; immune escape; RBD mutations; vaccine development

Online: 1 June 2022 (14:12:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202103.0324.v1

Artificial Neural Network Analysis of Geo Database in Diagnosing Papillary Thyroid Carcinoma

zhoujing zhang, di xu, Ozioma Akakuru, wenjing xu, yewei zhang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Papillary thyroid carcinoma; bioinformatics analysis; artificial neural network; diagnosis

Online: 11 March 2021 (16:08:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1852.v1

Challenges to Cannabis sativa Production from Pathogens and Microbes – the Role of Molecular Diagnostics and Bioinformatics

ZAMIR PUNJA, Dieter Kahl, Ron Reade, Yu Xiang, Jack Munz, Punya Nachappa

Subject: Biology And Life Sciences, Plant Sciences Keywords: bioinformatics; cannabis; hemp; hop latent viroid; molecular diagnostics; plant pathogens

Online: 30 October 2023 (09:54:14 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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Preprint ARTICLE | doi:10.20944/preprints202301.0345.v1

Genetic Diversity and Population Structure of the Peruvian Andean Legume, tarwi (Lupinus mutabilis), With High Quality SNPs

Amelia Huaringa-Joaquin, Carla L. Saldaña, David Saravia, Sady García-Bendezú, Pedro Rodriguez-Grados, Wilian Salazar, Felix Camarena, Pedro Injante, Carlos I. Arbizu

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Fabaceae; bioinformatics; molecular markers; neglected crop; genomics

Online: 19 January 2023 (03:57:25 CET)

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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/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/preprints202203.0110.v1

DVGfinder: A Metasearch Engine for Identifying Defective Viral Genomes in RNA-Seq Data

María J. Olmo-Uceda, Juan C. Muñoz-Sánchez, Wilberth Lasso-Giraldo, Vicente Arnau, Wladimiro Díaz-Villanueva, Santiago F. Elena

Subject: Biology And Life Sciences, Virology Keywords: benchmarking; bioinformatics; defective viral genomes; gradient boosting; machine learning; RNA-seq; SARS-CoV-2; virus replication

Online: 7 March 2022 (16:25:18 CET)

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Preprint ARTICLE | doi:10.20944/preprints202107.0280.v1

Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase

Colbie Reed, Geoffrey Hutinet, Valérie de Crécy-Lagard

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: comparative genomics; metabolic reconstruction; bioinformatics; conserved unknowns; function prediction; functional annotation; orthology

Online: 13 July 2021 (08:58:31 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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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/preprints202101.0441.v1

Andrew M. K. Nassief

Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Quantum Similarity; DNA; Molecular Biology; Meticodes; response variance; object set reference; Bioinformatics; Computational Physics; Computational Models; Mathematics; Probability; Statistics; Comparative Modeling; Biostatics; Biostatistics

Online: 22 January 2021 (11:35:18 CET)

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Preprint REVIEW | doi:10.20944/preprints202402.0461.v1

A Guide for the Bioinformatic Analysis of Metabolomics Data

Guillem Santamaria, Francisco R Pinto

Subject: Biology And Life Sciences, Other Keywords: metabolomics; bioinformatics; workflow; biostatistics; genome-scale metabolic modelling.

Online: 8 February 2024 (09:15:31 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 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/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 BRIEF REPORT | doi:10.20944/preprints202109.0349.v1

The Colon Transcriptome Explorer (CoTrEx) 2.0: a Reference Web-Based Resource for Exploring Population-Based Normal Colon Gene Expression

Virginia Díez-Obrero, Ferran Moratalla-Navarro, Christopher Dampier, Matthew Devall, Robert Carreras-Torres, Graham Casey, Victor Moreno

Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: RNA-Seq; bioinformatics; web application; gene expression; alternative splicing; visualization; molecular epidemiology

Online: 20 September 2021 (16:56:32 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0185.v1

Expanding Interactome Analyses beyond Model Eukaryotes

Katherine James, Anil Wipat, Simon Cockell

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: systems biology; integrative bioinformatics; interactomics; eukaryotes; non-models; network biology

Online: 12 October 2021 (14:24:56 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/preprints202102.0062.v1

Network Protein Interaction in the Link between Stroke and Periodontitis Interplay: A Pilot Bioinformatic Analysis

Yago Leira, Paulo Mascarenhas, Juan Blanco, Tomás Sobrino, José João Mendes, Vanessa Machado, João Botelho

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Stroke; Periodontitis; Periodontal disease; protein-protein network interaction; Bioinformatics

Online: 1 February 2021 (16:45:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202011.0501.v1

Genome Sequencing Guide: An Introductory Toolbox to Whole-Genome Analysis Methods

Alexis Burian, Wufan Zhao, Te-Wen Lo, Deborah Thurtle-Schmidt

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genomics; sequencing; ethics; bioinformatics

Online: 19 November 2020 (10:41:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202108.0149.v1

HPV DeepSeq: Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench

Jane Shen-Gunther, Qingqing Xia, Hong Cai, Yufeng Wang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Cervical cancer; Deep Sequencing; Human papillomavirus; HPV genotyping; Metagenome; Next generation sequencing; Taxonomic classification; Virome

Online: 6 August 2021 (08:00:00 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/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/preprints202104.0227.v1

Simple Method for Cutoff Point Identification In Descriptive High-Throughput Biological Studies

Alexander Suvorov

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: cutoff, dichotomization, threshold, -omics, bioinformatics, methods, values distributon

Online: 8 April 2021 (10:13:21 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0062.v1

Gene Profile Analysis and Molecular-Physiological Evaluation of Tomato Genotypes Under Drought Stress

Rahele Ghanbari Moheb Seraj, Masoud Tohidfar, Asadollah Ahmadikhah

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Bioinformatics analysis; Drought stress; Gene expression; Physiological parameters; Tomato; Transcriptome.

Online: 4 October 2021 (15:01:07 CEST)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202109.0183.v1

CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin

Annelien Morlion, Eva Hulstaert, Jasper Anckaert, Celine Everaert, Jo Vandesompele, Pieter Mestdagh

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics; circRNA

Online: 10 September 2021 (11:17:04 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 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/preprints202009.0019.v2

Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria

Jenny Schwarz, Stephan Lütz

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mass spectrometry; OSMAC approach; natural products; silent BGC activation; bioinformatics; screening

Online: 23 December 2020 (11:19:38 CET)

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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/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/preprints202208.0241.v1

Integrating Genetic and Chromosome Maps of Allium Cepa: From Markers Visualization to Genome Assembly Verification

Aleksey Ermolaev, Natalia Kudryavtseva, Anton Pivovarov, Ilya Kirov, Gennady Karlov, Ludmila Khrustaleva

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Tyr-FISH; integration genetic; cytogenetic and pseudochromosome maps; transcript based markers; genome assembly; bioinformatics; Allium cepa

Online: 12 August 2022 (12:54:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202104.0475.v1

Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform

Matthew L. Hudson, Ram Samudrala

Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: drug repurposing; virtual screening; multiscale; multitargeting; polypharmacology; computational biology; drug repositioning; structural bioinformatics; molecular docking; proteomic signature

Online: 19 April 2021 (12:22:05 CEST)

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Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multidisease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines via large scale modelling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is then compared to all other signatures that are then sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions in the platform used to create the drug-proteome signatures may be determined by any screening or docking method but the primary approach used thus far has been an in house similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and cheminformatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the corresponding two docking-based pipelines it was synthesized from, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking based signature generation methods can capture unique and useful signal for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.

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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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/preprints202202.0297.v1

Integrated Analysis of the miRNA-mRNA Regulatory Network Involved in the HIV-Associated Neurocognitive Disorder

Chang Liu, Qian Ding, Xiaohong Kong

Subject: Biology And Life Sciences, Virology Keywords: miRNA; mRNA; HIV; network; bioinformatics; HAND; viral infection; CNS damage

Online: 23 February 2022 (14:13:59 CET)

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Preprint ARTICLE | doi:10.20944/preprints202010.0543.v1

Hepatitis C Virus E2—Host Cell Receptor, HSPA5, Binding Site Prediction

Alaa Elgohary, Abdo Elfiky

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: HSPA5; GRP78; BiP; HCV E2; protein-protein docking; structural bioinformatics

Online: 27 October 2020 (09:11:13 CET)

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Preprint REVIEW | doi:10.20944/preprints202209.0327.v1

Bioinformatic Methods for Identifying Differentially Abundant Subpopulations in scRNA-seq Data

Giona Kleinberg, Ashwini Shinde, Sai Batchu, Michael Diaz, Kevin Root, Brandon Lucke-Wold

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: scRNA-seq; bioinformatics; subpopulations; analysis methods; single-cell RNA sequencing

Online: 21 September 2022 (11:22:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0014.v1

Bioinformatics Analyzes of Selectins Polymorphisms Reveal New Potential Cancer Biomarkers

Larissa Teodoro Rabi, Davi Zanoni Valente, Elisangela de Souza Teixeira, Karina Colombera Peres, Natassia Elena Bufalo, Laura Sterian Ward

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics analysis; selectins; cancer

Online: 1 March 2023 (08:48:00 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202211.0440.v1

Exome Sequencing reveals characteristic KMT2C mutations in the Indian Phenotype of Cervical Cancer

Santosh Kumari Duppala, Bhumandeep Kour, Nidhi Shukla, Maruti A Dhakane, Ashwani Kumar Mishra, Raghunadharao Digumarti, Smita C Pawar, Prashanth N Suravajhala, Sugunakar Vuree

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cervical cancer; Functional genomics; Bioinformatics; Next Generation Sequencing; Exome

Online: 23 November 2022 (07:42:19 CET)

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Preprint ARTICLE | doi:10.20944/preprints202207.0038.v1

Progeria and Aging - Omics Based Comparative Analysis

Aylin Caliskan, Samantha Agnetz Wilhelmine Crouch, Sara Giddins, Thomas Dandekar, Seema Dangwal

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: progeria; aging; omics; RNA Sequencing; bioinformatics; sun exposure; HGPS; IGFBP2; ACKR4; WNT

Online: 4 July 2022 (08:10:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0306.v1

Investigation and Computational Analysis of Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights Into Sulfur Adjustment for Proper Development and Stimuli Responses

Sahar Faraji, Parviz Heidari, Hoorieh Amouei, Ertugrul Filiz, Abdullah ., Peter Poczai

Subject: Biology And Life Sciences, Plant Sciences Keywords: Sulfur; Sulfotransferase; Potato; Bioinformatics; Proteins structure; Stimuli coping

Online: 21 October 2021 (12:41:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202111.0004.v1

N1-Methyladenosine (m1A) Regulator-Mediated Methylation Modification Modes and Tumor Microenvironment Infiltration Characteristics in Head and Neck Squamous Cell Carcinomas

Yan-Dong Miao, Lin-Jie Mu, Xiao-Long Tang, Jiang-Tao Wang, Jing-Jing Wu, Yong-Gang Chen, Deng-Hai Mi

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: m1A; Tumor microenvironment; PD-1/PD-L1; CTLA-4; Tumor Mutation Burden; Bioinformatics Analysis

Online: 1 November 2021 (10:39:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints202209.0098.v1

Comparison of Two Bacterial Characterization Techniques for the Genomic Analysis of Aquatic Environments

Roberto Bonelly, Victor V. Calderón, Confesora Pinales, Irene Ortiz, Argenys Ovando, Willy Lara, Santo E. Mateo-Perez, Oscar Cardenas-Alegría, Rommel T. Jucá Ramos, Edian F. Franco, Luis O. Maroto

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: MALDI-TOF; DNA Sequencing; environment; bacteria; Microbiome; bioinformatics; Dominican Republic

Online: 7 September 2022 (04:26:40 CEST)

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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/preprints202302.0056.v1

Untangling the Complexities of Processing and Analysis for Untargeted LC-MS Data Using Open-source Tools

Εlizabeth J. Parker, Kathryn C. Billane, Nichola Austen, Anne Cotton, Rachel M. George, David Hopkins, Janice A. Lake, James K. Pitman, James N. Prout, Heather J. Walker, Alex Williams, Duncan D. Cameron

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: metabolomics; untargeted; mass-spectrometry; open-source; bioinformatics

Online: 3 February 2023 (04:16:00 CET)

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Preprint ARTICLE | doi:10.20944/preprints202304.1073.v1

Comparative Analysis of Cell Mixtures Deconvolution and Gene Signatures Generated for Blood, Immune and Cancer Cells

Natalia Alonso-Moreda, Alberto Berral-Gonzalez, Enrique De La Rosa, Oscar González-Velasco, Jose Manuel Sanchez-Santos, Javier De Las Rivas

Subject: Biology And Life Sciences, Life Sciences Keywords: cell mixture; deconvolution; immune cells; blood cells; cancer cells; gene signature; bioinformatics

Online: 27 April 2023 (10:34:59 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202211.0165.v1

Data-Independent Acquisition (DIA) is Superior for High Precisely Phospho-Peptide Quantification in Fungi

Katharina Bersching, Thomas Michna, Stefan Tenzer, Stefan Jacob

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Proteomics; LC-MS/MS; phosphopeptide enrichment; bioinformatics; cellular signaling; Mag-naporthe oryzae; phosphorylation; DDA; DIA; phospho-peptidomics

Online: 9 November 2022 (02:09:17 CET)

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Preprint REVIEW | doi:10.20944/preprints202310.1465.v1

Integrating Bioinformatics in Drug Discovery

Mujahed Mustafa, Ahmed Mohammed, Awad Alzebair, Abdelrafie Makhawi

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: drug discovery; target identification; target validation; lead identification; bioinformatics

Online: 24 October 2023 (04:09:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints202311.0673.v1

Introduction of Plant Transposon Annotation for Beginners

Dongying Gao

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Transposon annotation; plant; genome; bioinformatics pipeline; database

Online: 10 November 2023 (07:32:14 CET)

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Preprint ARTICLE | doi:10.20944/preprints202307.0466.v1

PlantMetSuite: A User-Friendly Web-Based Tool for Metabolomics Analysis and Visualisation

Yu Liu, Hao-Zhuo Liu, Ding-Kang Chen, Hong-Yun Zeng, Yi-Li Chen, Nan Yao

Subject: Biology And Life Sciences, Plant Sciences Keywords: plant metabolomics; metabolite identification; data visualisation; omics data; bioinformatics tools

Online: 10 July 2023 (13:49:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1712.v1

Facilitating “Omics” to Phenotype Classification Using a User-Friendly AI-Driven Platform: Application to Cancer Prognostics

Uraquitan Lima Filho, Tiago Alexandre Pais, Ricardo Jorge Pais

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: software tools; bioinformatics; cancer prognostics; predictive modelling

Online: 24 August 2023 (07:23:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0139.v1

Spatial Transcriptomic Analysis of Focal and Normal Areas of Myocyte Disarray in Human Hypertrophic Cardiomyopathy

Jason Laird, Gayani Perera, Rebecca Batorsky, Hongjie Wang, Knarik Arkun, Michael T. Chin

Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Hypertrophic Cardiomyopathy; spatial transcriptomics; single nucleus RNA-sequencing; gene expression; bioinformatics; cardiovascular disorder; genetic disorder

Online: 4 July 2023 (05:18:51 CEST)

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Hypertrophic Cardiomyopathy (HCM) is a common inherited disorder that can lead to heart failure and sudden cardiac death, characterized at the histological level by focal areas of myocyte disarray, hypertrophy and fibrosis, and few disease-targeted therapies exist. To identify, focal, spatially restricted alterations in transcriptional pathways and reveal novel therapeutic targets, we performed a spatial transcriptomic analysis of areas of focal myocyte disarray compared to areas of normal tissue, using a commercially available platform (GeoMx, nanoString). We analyzed surgical myectomy tissue from four patients with HCM and control interventricular septum tissue from two unused organ donor hearts that were free of cardiovascular disease. Histological sections were reviewed by an expert pathologist and 72 focal areas with varying degrees of myocyte disarray (normal, mild, moderate, severe) were chosen for analysis. Areas of interest were interrogated with the Human Cancer Transcriptome Atlas designed to profile 1800 transcripts. Differential expression analysis revealed significant changes in gene expression between HCM and Control tissue, and functional enrichment analysis indicated these genes were primarily involved in interferon production and mitochondrial energetics. Within HCM tissue, differentially expressed genes between areas of mild and moderate disarray were enriched for genes related to mitochondrial energetics (moderate disarray) and response to oxygen/cytokine levels (mild disarray). The comparison between areas of moderate and severe disarray were enriched for genes related to the c-Jun N-terminal kinase (JNK) cascade in severe disarray. Analysis of ligand-receptor pair gene expression revealed that HCM tissue exhibited downregulation of platelet-derived growth factor (PDGF), NOTCH, junctional adhesion molecule, and CD46 signaling, while showing upregulation of fibronectin, CD99, cadherin, and amyloid precursor protein signaling. A deconvolution analysis utilizing the matched single nuclei RNA-sequencing (snRNA-seq) data to determine cell type composition in areas of interest revealed significant differences in fibroblast and vascular cell composition in areas of severe disarray when compared to normal areas in HCM samples. Cell composition in normal areas from control tissue was also divergent from normal areas in HCM samples, which was consistent with the differential expression results. Overall, our data identify novel and potential disease-modifying targets for therapy in HCM.

Preprint ARTICLE | doi:10.20944/preprints202210.0317.v1

Genome-Wide Characterization of Sulfate Transporter Gene Family in Oilseed Crops: Camelina sativa and Brassica napus

Parviz Heidari, Soosan Hasanzadeh, Sahar Faraji, Sezai Ercisli, Freddy Mora-Poblete

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Bioinformatics; Biotic stresses; Regulatory mechanisms; Protein structure; Gene expression; Evolution analysis

Online: 21 October 2022 (03:37:45 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1891.v1

A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping to Advance Translational Mitogenomics

Jane Shen-Gunther, Rutger S. Gunther, Hong Cai, Yufeng Wang

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics 1; hypervariable region 2; mitochondrial DNA 3; mitochondrial genomics 4; mitochondrial haplogroup 5; molecular anthropology 6; next generation sequencing 7; oncogenetics 8; phylogeography 9

Online: 27 July 2023 (09:29:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0612.v1

Novel RNA-Seq Signatures Post-Methamphetamine and Oxycodone Use in a Model of HIV-Associated Neurocognitive Disorders

Pranavi Athota, Nghi M Nguyen, Victoria L Schaal, Sankarasubramanian Jagadesan, Chittibabu Guda, Sowmya V Yelamanchili, Gurudutt Pendyala

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Polysubstance use; methamphetamine; oxycodone; HIV; transgenic rat; RNA-sequencing, bioinformatics

Online: 10 July 2023 (11:34:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202210.0470.v1

Temporal Dissection of Altered Pathways during the Evolution of Cancer

Johanne Ahrenfeldt, Ditte S. Christensen, Mateo Sokač, Judit Kisistók, Nicholas McGranahan, Nicolai J. Birkbak

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: metastasis; cancer evolution; bioinformatics; cancer biology; cancer genomics

Online: 31 October 2022 (07:06:45 CET)

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Preprint REVIEW | doi:10.20944/preprints202306.1487.v1

Circular and Circulating DNA in IBD: from Pathogenesis to Potential Molecular Therapies

Federica Di Vincenzo, Ylenia Yadid, Valentina Petito, Valeria Emoli, Letizia Masi, Daniela Gerovska, Marcos Jesus Araúzo-Bravo, Antonio Gasbarrini, Birgitte Regenberg, Franco Scaldaferri

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: cell-free nucleic acids; cell-free DNA; circular DNA; microvescicles; inflammatory bowel disease; cGAS-STING; TLR9; oligonucleotides; bioinformatics; molecular therapies.

Online: 21 June 2023 (08:55:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1684.v1

Identification of Rice RRM1 Gene Family and Its Resistance to Rice Blast

Xinlei Jiang, Shangwei Yu, Yuhan Huang, Junying Huang, Shaochun Liu, Deiwei Yang, Junru Fu, Haohua He, Haihui Fu

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: rice; gene family; rice blast; bioinformatics.

Online: 24 August 2023 (09:51:49 CEST)

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In order to enhance understanding of RNA-binding proteins in rice, a comprehensive investigation was conducted on the RRM1 gene family of rice, encompassing genome-wide identification and exploration of its role in rice blast resistance. Physical and chemical properties of the OsRRM1 gene family in rice was analyzed, including conserved domain, motif, location information, gene structure, phylogenetic tree, collinearity analysis, cis-acting elements, GO, and KEGG. Furthermore, the expression patterns of the OsRRM1 gene were examined at different time intervals following rice blast treatment. Furthermore, the alterations in expression patterns of selected OsRRM1 genes were assessed using quantitative real-time PCR(qRT-PCR). A total of 212 members of the OsRRM1 gene family were identified, which were dispersed across 12 chromosomes. Many of these genes exhibit multiple exons and introns, all of which encompass the conserved RRM1 domain and share analogous motifs. This observation suggests a high degree of conservation within the encoded sequence domain of these genes. Phylogenetic analysis revealed the existence of five subfamilies within the OsRRM1 gene family. Furthermore, the investigation of the promoter region identified homeopathic elements that are involved in nucleic acid binding and interaction with multiple transcription factors. By employing GO and KEGG analysis, four RRM1 genes were tentatively identified as crucial contributors to plant immunity, while the RRM1 gene family was also found to have a significant involvement in the complex of alternative splicing. Additionally, gene expression analysis indicated that the majority of OsRRM1 genes exhibited constitutive expression. The results of the qRT-PCR analysis revealed distinct temporal changes in the expression pattern of the OsRRM1 gene following rice blast treatment. These findings contribute to the existing knowledge of the OsRRM1 gene family, establish a foundation for further investigation into the role of the OsRRM1 gene in response to rice blast infection, and hold theoretical significance for future studies on the functionality of the OsRRM1 gene.

Preprint ARTICLE | doi:10.20944/preprints202309.1576.v1

Stepwise In Silico Specificity Approach for NGT PCR-Based Detection Methods in the Context of the EU GMO Regulations

Caroline Bedin Zanatta, Aline Martins Hoepers, Rubens Onofre Nodari, Sarah Zanon Agapito-Tenfen

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genetically modified organisms; detection; site directed nucleases; traceability; CRISPR; bioinformatics

Online: 25 September 2023 (04:18:38 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202310.1146.v1

A Proposal for a Consolidated Structural Model of the CagY Protein of Helicobacter pylori

Mario Angel López-Luis, Eva Elda Soriano-Pérez, José Carlos Parada-Fabián, Rogelio Maldonado-Rodríguez, Javier Torres, Alfonso Méndez-Tenorio

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics; structural biology; CagY protein; T4SS; deep learning

Online: 18 October 2023 (09:56:34 CEST)

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