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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/preprints202406.1766.v1

A Bioinformatic Assay of Quercetin in Gastric Cancer

Sergio Raúl Zúñiga-Hernández, Trinidad García-Iglesias, Monserrat Macías-Carballo, Alejandro Pérez-Larios, Yanet Karina Gutiérrez-Mercado, Gabriela Camargo-Hernández, Christian Martín Rodríguez-Razón

Subject: Medicine And Pharmacology, Complementary And Alternative Medicine Keywords: Gastric Cancer; Quercetin; Bioinformatics

Online: 26 June 2024 (00:03:30 CEST)

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Preprint REVIEW | doi:10.20944/preprints202304.1095.v1

Chemoinformatics Advances from Egypt: A Review Article

Mohamed A. Raslan, Sara A. Raslan, Eslam M. Shehata, Amr S. Mahmoud, Nagwa A. Sabri

Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Chemoinformatics; Bioinformatics; Tetracycline; Formulation

Online: 28 April 2023 (03:32:47 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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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/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 TECHNICAL NOTE | doi:10.20944/preprints202407.0160.v1

SeqMate: A Novel Large Language Model Pipeline for Automating RNA Sequencing

Devam Mondal, Atharva Inamdar

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: bioinformatics; natural language processing; automation

Online: 2 July 2024 (13:30:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1713.v1

The Influence of Nicotine on Trophoblast-Derived Exosomes in a Mouse Model of Pathogenic Preeclampsia

Ayane Kubo, Keiichi Matsubara, Yuko Matsubara, Hirotomo Nakaoka, Takashi Sugiyama

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: preeclampsia; exosomes; nicotine; proteomics; bioinformatics

Online: 24 May 2023 (13:29:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0747.v1

Clinical Data and In Silico Analysis Provided New Insights About COVID-19 Behavior in Smokers

Luzia Soares Dias, Nylane Maria Nunes Alencar, Felipe Pantoja Mesquita, Daiane Maria da Silva Brito, Márcio Viana Ramos, Pedro Filho Noronha Souza

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: antibodies; bioinformatics; immunoinflammation; Nicotiana tabacum

Online: 10 May 2023 (11:17:21 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 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/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/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 ARTICLE | doi:10.20944/preprints202401.0493.v1

Observations from the proteomics bench

Simone König, Karin Schork, Martin Eisenacher

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: mass spectrometry; bioinformatics; proteomics; false-positives

Online: 5 January 2024 (12:07:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0088.v1

The Anticancer Effects of Moringa oleifera Peptides on the Erythropoietin-Producing Hepatocellular Receptor (EphB4) Were Predicted In Silico

Mónica Andrea Valdez-Solana, Claudia Avitia-Domínguez, Alfredo Téllez Valencia, Erick Sierra-Campos

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Moringa oleifera; anticancer peptides; EphB4; Bioinformatics.

Online: 1 December 2023 (13:32:59 CET)

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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/preprints202308.0237.v1

TCGA and Experimental Validation-Based Analysis of the SPRR2A Gene's Expression and Clinical Relevance in Endometrial Cancer

Yunhui Li, Jie Zhang, Zhixian Liang, Ranran Zhang, Wenming Wu

Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: SPRR2A; Endometrial cancer; TCGA; Bioinformatics analysis

Online: 2 August 2023 (14:37:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0067.v1

Identification of molecular diagnostic markers in sepsis-induced acute lung injury

Yingying Huang, Jiameng Chen, Wenjie Li, Shaowei Jiang, Yuxin Leng, Chengjin Gao

Subject: Medicine And Pharmacology, Emergency Medicine Keywords: acute lung injury; biomarkers; sepsis; bioinformatics

Online: 1 August 2023 (09:15:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.1797.v1

Nightingale: Web components for protein feature visualization

Gustavo A Salazar, Aurelien Luciani, Xavier Watkins, Swaathi Kandasaamy, Daniel L Rice, Matthias Blum, Alex Bateman, Maria Martin

Subject: Biology And Life Sciences, Other Keywords: Visualization, Bioinformatics, Proteins, Software, Web services

Online: 25 May 2023 (10:19:44 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/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/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/preprints202408.1095.v1

Automated Management of AWS Instances for Training

Jorge Buenabad-Chavez, Evelyn Greeves, James P.J. Chong, Emma Rand

Subject: Computer Science And Mathematics, Software Keywords: Software and Workflows; Software Engineering; Bioinformatics; Metagenomics

Online: 15 August 2024 (12:26:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.0786.v1

The Confluence Analysis Program: A User-Friendly Tool for Automated Cell Confluence Measurement and Visualization

Abraham Lobsenz, Paul Seidler

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: confluency; bioinformatics; cell segmentation; high-throughput screening

Online: 12 August 2024 (10:24:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.1371.v1

Antimicrobial Resistance Genes in Clinical Salmonella Isolates From Cattle in the Texas Panhandle, USA

Max Chung, Ethan Dudley, Hatem Kittana, Alexis C Thompson, Matthew Scott, Keri Norman, Robert Valeris-Chacin

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Salmonella; Cattle; Texas; ARGs; Bioinformatics; Bacterial Pathogenomics

Online: 17 July 2024 (08:11:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202406.1797.v1

Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus Urealyticus from Diverse Hosts

Louisa Caroline House, Amer Hasan, Andi Asnayanti, Adnan Alrubaye, Jeff F Pummill, Douglas Duane Rhoads

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: osteomyelitis; horizontal transfer; genome evolution; Staphylococcus; bioinformatics

Online: 26 June 2024 (08:05:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1951.v1

Ascertaining Genetics of β—Thalassemia and Sickle Cell Disease Using Machine Learning Heuristics

Aswathi P, Anjana SR, Somesh Kumar, Goldy Singh, Seema Kapoor, Sangeeta Gupta, Jayaraman K Valadi, R Shyama Prasad Rao, Sunil Kumar Polipalli, Prashanth Suravajhala

Subject: Biology And Life Sciences, Life Sciences Keywords: hemoglobinopathies; β --thalassemia; machine learning; bioinformatics; genomics

Online: 30 April 2024 (03:56:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.0697.v1

Changes in the Transcriptome Profile in Young Chickens after Infection with LaSota Newcastle Disease Virus

Taina SB Lopes, Jannis Nankemann, Cassandra Breedlove, Andrea Pietruska, Raiumundo Espejo, Camila A Cuadrado, Ruediger Hauck

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Vaccine; Immunogenomics; Gene regulation; Pathway analysis; Bioinformatics.

Online: 10 April 2024 (07:58:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.1187.v1

Application of machine learning in the quantitative analysis of surface characteristics of highly abundant cytoplasmic proteins: Toward AI-based biomimetics

Jooa Moon, Guanghao Hu, Tomohiro Hayashi

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: bioinformatics; machine learning; protein surfaces; surface engineering

Online: 15 December 2023 (11:57:03 CET)

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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/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/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/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 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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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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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/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/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 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/preprints202402.0187.v2

Optimization and Performance Analysis of CAT Method for DNA Sequence Similarity Searching and Alignment

Veska Gancheva, Hristo Stoev

Subject: Computer Science And Mathematics, Computer Science Keywords: bioinformatics; biological data sequences; DNA sequences; metadada; performance analysis; similarity searching; sequence alignment

Online: 19 February 2024 (16:12:31 CET)

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Bioinformatics is a rapidly developing field enabling scientific experiments through computer models and simulations. Considering the vast databases of biological data available, it is ex-tremely important to develop efficient methods and algorithms for their processing. Sequence comparison is the best method for studying the evolutionary interaction between genes. It is based on alignment – the process of arranging two or more sequences to achieve the maximum level of identity and degree of similarity. The paper presents a new version of the algorithm for pairwise DNA sequences alignment, based on a new method called CAT, where a dependency with a previous match and the closes neighbor are taken in consideration to increase uniqueness of the CAT profile and to reduce possible collisions, i.e. two or more sequence having same CAT profiles. This makes proposed algorithm suitable for finding exact match of a concrete DNA se-quence in a big set of DNA data faster. The generation of CAT profiles is made once before data has been uploaded to the database, allowing the profiles to be used as metadata for the sequenc-es. It consists of an algorithm to calculate a CAT profile against the selected reference sequences and an algorithm to compare two sequences based on the calculated CAT profiles. Improve-ments in generation of the CAT profiles, are detailed described in the paper. Block scheme, pseudo code tables and figures were updated according to the proposed new version and ex-perimental results. Experiments have been carried out with the new version of the method and different datasets to align DNA sequences based on the CAT method. New experimental results in terms of collisions, speed, and efficiency of the proposed solutions are presented. Experiments related to the performance comparison with Needleman-Wunsch were re-executed with the new version of the algorithm to confirm that we have the same performance. An analysis of the per-formance of the proposed CAT based algorithm against Knuth–Morris–Pratt algorithm, which has a complexity of O(n) and is one of the most widely used for searching biological data, was performed. The impact of prior matching dependencies on uniqueness for generated CAT pro-files is investigated. The analysis of the experimental results obtained by sequence alignment shows a small deviation of the proposed algorithm based on the CAT method, which can be ig-nored if this deviation is acceptable at the expense of performance. The time efficiency of the CAT algorithm remains constant, regardless of the length of the sequences. Therefore, the ad-vantage of the proposed method is its fast processing in the alignment of large sequences, for which the execution of the exact algorithms takes a long time. The example code realization of the CAT Method, under the protection of the GNU General Public License v3.0, can be accessed on GitHub at: https://github.com/HristoS/CATSequenceAnalysis.

Preprint ARTICLE | doi:10.20944/preprints202401.1590.v1

Genome–Wide Identification, Characterization and Expression Profile of F–box Protein Family Genes Shed Light on Lateral Branch Development in cultivated peanut (Arachis hypogaea L.)

Chuheng Li, Liguo Guo, Weiqian Wang, Penghui Miao, Guojun Mu, Charles Y. Chen, Chengsheng Meng, Xinlei Yang

Subject: Biology And Life Sciences, Plant Sciences Keywords: cultivated peanut; F–box protein; bioinformatics; expression analysis

Online: 22 January 2024 (14:41:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0957.v1

Exploring the Potential Relationship Between Oxidative Stress in Fertile Individuals and Secondary Infertility: A Comparative Analysis of Proteomic Profiles in Seminal Plasma

Raneen Sawaid Kaiyal, Sromona D Mukherjee, Manesh Kumar Panner Selvam, Miller AW, Sarah C Vij, Scott D Lundy

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: sperm proteome; oxidative stress; secondary male infertility; bioinformatics

Online: 15 November 2023 (10:05:00 CET)

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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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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/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 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/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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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 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/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/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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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 REVIEW | doi:10.20944/preprints202409.1057.v1

Improving Crops Using Omics Databases of Arabidopsis (Arabidopsis Thaliana) and Other Model Plants

Andrés S. Ortiz-Morazán, Marcela María Moncada

Subject: Biology And Life Sciences, Plant Sciences Keywords: Arabidopsis (Arabidopsis thaliana); Bioinformatics; Genetic improvement; Omics databases; Crops

Online: 13 September 2024 (14:51:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202407.2461.v1

Using Association Rules to Explore Occult Patterns in Breast Cancer Mitochondrial Genomes

Claudia Karina Casillas Godínez, Felipe de Jesús Orozco Luna, Ana Elizabeth González Santiago, María Guadalupe Sánchez Parada, Arieh Roldan Mercado Sesma, Ana Rosa Jiménez Meza, Raúl C. Baptista Rosas

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Breast cancer; Bioinformatics; Data Science; Pattern Search; Association Rules

Online: 30 July 2024 (15:56:24 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202401.0499.v1

Elucidating the role of KojR in transcriptional regulation of carbon metabolism for kojic acid biosynthesis in Aspergillus oryzae

Tomoka Mizutani, Hiroya Oka, Riko Goto, Ryoga Tsurigami, Jun-ichi Maruyama, Motoyuki Shimizu, Masashi Kato, Hideo Nakano, Kojima Takaaki

Subject: Biology And Life Sciences, Life Sciences Keywords: Transcriptome, Transcription factor, Aspergillus oryzae, Kojic acid (KA), Bioinformatics

Online: 5 January 2024 (13:59:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.1438.v1

Genome-wide Identification of Universal Stress Protein Family Genes and Expression in Mechanical damage and DON stress Response of Potato Based on the Transcriptome

Tianshuai Qi, Fumeng He, Xinqi Zhang, Jiaqi Wang, Zengli Zhang, Heran Jiang, Biao Zhao, Chong Du, Yunzhu Che, Xu Feng, Yingnan Wang, Fenglan Li

Subject: Biology And Life Sciences, Plant Sciences Keywords: Potato; USP gene family; abiotic stress; bioinformatics analysis; transcriptome

Online: 19 December 2023 (11:31:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0162.v1

Targets and Effects of Common Biocompounds of Hibiscus sabdariffa (Delphinidn-3-Sambubiosidin, Quercetin, and Hibiscus Acid) in Different Pathways of Human Cells According to a Bioinformatic Assay

Sergio Raúl Zúñiga-Hernández, Trinidad García-Iglesias, Monserrat Macías-Carballo, Alejandro Pérez-Larios, Yanet Karina Gutiérrez-Mercado, Gabriela Camargo-Hernández, Christian Martin Rodríguez-Razón

Subject: Medicine And Pharmacology, Dietetics And Nutrition Keywords: Delphinidin-3-sambubiosid; Quercetin; Hibiscus Acid; Bioinformatics; Hibiscus sabdariffa

Online: 5 December 2023 (06:11:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0360.v1

Bmtret1 Gene Family and Its Potential Role in Response to BmNPV Stress in Bombyx mori

Mingjun Lin, Yixuan Qian, Enxi Chen, Mengjiao Wang, Gui Ouyang, Yao Xu, Guodong Zhao, He-Ying Qian

Subject: Biology And Life Sciences, Insect Science Keywords: Bombyx mori; Bmtret1; BmNPV resistance; Bioinformatics analysis; Viral replication

Online: 6 November 2023 (14:21:46 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 ARTICLE | doi:10.20944/preprints202310.0185.v1

Delving into Molecular Pathways: Analyzing the Mechanisms of Action of Monoclonal Antibodies Integrated in IMGT/mAb-DB for Myasthenia Gravis

Rebecca Golfinopoulou, Véronique Giudicelli, Taciana Manso, Sofia Kossida

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: monoclonal antibodies; myasthenia gravis; bioinformatics; mechanism of action; IMGT

Online: 4 October 2023 (03:54:47 CEST)

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Background: Myasthenia Gravis (MG) is a rare autoimmune disease presenting with au-to-antibodies that affect the neuromuscular junction. Aside from symptomatic treatment options, novel therapeutics include monoclonal antibodies (mAbs). IMGT®, the international ImMunoGe-neTics information system® (https://www.imgt.org), extends the characterization of therapeutic antibodies with a systematic description of their mechanisms of action (MOA) and makes them available through its database for mAbs and fusion proteins, IMGT/mAb-DB. Methods: Using the available literature data combined with the amino acid sequence analyses from mAbs managed in IMGT/2Dstructure-DB, the IMGT® protein database, biocuration allowed to define in a standardized way descriptions of MOA of mAbs that target molecules towards MG treatment. Results: New therapeutic targets include FcRn and molecules such as CD38, CD40, CD19, MS4A1 and interleukin-6 receptor. A standardized graphical representation of the MOA of selected mAbs was created and integrated within IMGT/mAb-DB. The main mechanisms involved in these mAbs are either blocking or neutralizing. Therapies directed to B cell depletion and plasma cells have a blocking MOA with an immunosuppressant effect along with Fc-effector function (MS4A1, CD38) or FcγRIIb engager effect (CD19). Monoclonal antibodies targeting the complement also have blocking MOA with a complement inhibitor effect and treatments targeting T cells have a blocking MOA with an immunosuppressant effect (CD40) and Fc-effector function (IL6R). On the other hand, FcRn antagonists present a neutralizing MOA with an FcRn inhibitor effect. Conclusion: The MOA of each new mAb needs to be considered in association with the immuno-pathogenesis of each of the subtypes of MG in order to integrate the new mAbs as a viable and safe option in the therapy decision process. In IMGT/mAb-DB, mAbs for MG are characterized by their sequence, domains, chains and their MOA is described.

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/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/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/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/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/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/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/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/preprints202409.1777.v1

GPU Acceleration Techniques for Analyzing the Photochemical Properties of Nanoparticles in Bioinformatics Frameworks

Abiodun Okunola

Subject: Computer Science And Mathematics, Other Keywords: GPU acceleration; nanoparticle photochemistry; bioinformatics frameworks; computational simulations; biomedical applications

Online: 24 September 2024 (05:05:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202408.0558.v1

Long COVID: G Protein-Coupled Receptors (GPCRs) Associated Genes and Pathways as a Promising Therapeutic Potential Through Computational Analysis

Dhanyashri Guruparan, Suresh Kumar

Subject: Biology And Life Sciences, Virology Keywords: long COVID; GPCR signaling pathways; therapeutic targets; drug repurposing; bioinformatics

Online: 8 August 2024 (12:18:41 CEST)

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Long COVID, also referred to as post-COVID-19 condition, describes the lingering after-effects of COVID-19 infection. This complex syndrome encompasses a range of symptoms affecting physical well-being, cognitive function, and mental health. The widespread impact of long COVID extends beyond individual sufferers, placing significant strain on healthcare systems and causing far-reaching socioeconomic consequences. The scale of this multifaceted health crisis is unparalleled in recent history, affecting millions globally and challenging our understanding of post-viral conditions. This study aimed to explore the possibility of targeting G protein-coupled receptors (GPCRs) signaling pathway-related genes as therapeutics for long COVID using computational analysis. Targeting GPCRs and their signaling pathways holds significant promise for long COVID therapeutics, as these receptors are involved in crucial physiological processes including immune regulation, inflammation control, and neurotransmission. All of these are implicated in the diverse and persistent symptoms of long COVID, potentially offering a versatile approach to addressing multiple aspects of the condition simultaneously. This study identified 21 genes associated with GPCRs for further exploration as potential targets. Notably, GPCR genes such as HRAS, KRAS, GNAQ, and GNA11 were determined to be possible therapeutic targets for the pathophysiological mechanisms of long COVID. FDA-approved drugs targeting these genes were identified, including Binimetinib, Cabozantinib, Selumetinib, Panitumumab, Cetuximab, Adagrasib, Tipifarnib, and Sotorasib. Additionally, Naltrexone and Tipifarnib have emerged as potential new treatment options for long COVID. SARS-CoV-2 may hijack GPCR signaling pathways to dysregulate lung ion and fluid transport, contributing to the pathophysiology of pulmonary edema in patients with COVID-19. Further research is required to translate the findings into the development of therapeutics and to investigate the relationship between viral infection and GPCR signalling.

Preprint ARTICLE | doi:10.20944/preprints202407.2292.v1

High LETM1 Expression Associates with Impaired Mitophagy and Bad Prognosis in Diffuse Large B-cell Lymphomas and Acute Myeloid Leukemias

Amreen Salwa, Alessandra Ferraresi, Letizia Vallino, Chinmay Maheshwari, Riccardo Moia, Gianluca Gaidano, Ciro Isidoro

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: personalized medicine; lymphoma; leukemia; autophagy; mitochondria; overall survival; TCGA; bioinformatics

Online: 29 July 2024 (10:54:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202405.2133.v1

Protein C Pretreatment Protects Endothelial Cells from SARS-CoV-2-Induced Activation

Bruna Rafaela Santos Silva, Davi Sidarta-Oliveira, Bruna Bombassaro, Pierina Lorencini Parise, Carlos Poblete Jara, Jose Luiz Proenca-Modena, Joseane Morari, Licio A Velloso, William H Velander, Eliana Pereira Araujo

Subject: Biology And Life Sciences, Life Sciences Keywords: bioinformatics; blood coagulation disorders; endothelial cell; SARS-CoV-2; inflammation

Online: 31 May 2024 (12:17:06 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202404.0156.v1

Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation

Anna Visibelli, Rebecca Finetti, Neri Niccolai, Ottavia Spiga, Annalisa Santucci

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rare diseases; missense mutations; protein structure; databank analysis; structural bioinformatics

Online: 2 April 2024 (08:52:56 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0268.v1

A New Cloud‐Native Tool for Pharmacogenetic Analysis

David Yu Yuan, Jun Hyuk Park, Zhenyu Li, Rohan Thomas, David M Hwang, Lei Fu

Subject: Computer Science And Mathematics, Software Keywords: Pharmacogenetics; bioinformatics pipeline; cloud‐native technologies; workflow; genomic data analysis

Online: 5 February 2024 (10:54:41 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/preprints202310.1852.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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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/preprints202308.0543.v1

Identification and validation of blood miRNAs as diagnostic markers of gastric cancer

Qingyu Wang, Zhouhan Xu, Xuesi Yang, Ruiqi Zhao, Xueling Li, Shujie Li, Xize Li, Jiping Zeng

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Gastric cancer; Blood-based miRNAs; Differentially expressed genes; Biomarkers; Bioinformatics

Online: 8 August 2023 (10:14:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.1157.v1

Aldehyde Dehydrogenase Genes as Prospective Actionable Targets in Acute Myeloid Leukemia

Garrett M. Dancik, Lokman Varisli, Veysel Tolan, Spiros A Vlahopoulos

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: cancer bioinformatics; aldehyde dehydrogenase; biomarkers; gene expression; leukemia; myeloid; acute

Online: 18 July 2023 (04:58:23 CEST)

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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/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 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/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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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 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/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 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 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 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/preprints202407.0837.v1

BacSPaD: A Robust Bacterial Strains’ Pathogenicity Resource Based on Integrated and Curated Genomic Metadata

Sara Ribeiro, Guillaume Chaumet, Karine Alves, Julien Nourikyan, Lei Shi, Jean-Pierre Lavergne, Ivan Mijakovic, Simon de Bernard, Laurent Buffat

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Bacterial pathogenicity; Genomic metadata analysis; Bioinformatics; Microbiology research; Public health surveillance

Online: 11 July 2024 (00:01:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1312.v1

TF-Target Finder: An R Web Application Bridging Multiple Predictive Models for Decoding Transcription Factor-Target Interactions

Jin Wang

Subject: Biology And Life Sciences, Other Keywords: transcription factors; gene regulatory networks; bioinformatics; TF-target prediction; Shiny app

Online: 19 April 2024 (12:03:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202402.0171.v1

Screening for Metal Chelating Activity in Potato Protein Hydrolysates Using Surface Plasmon Resonance and Peptidomics

Mads Bjørlie, Julie Christina Hartmann, Line Hyrup Rasmussen, Betül Yesiltas, Ann-Dorit Moltke Sørensen, Simon Gregersen Echers, Charlotte Jacobsen

Subject: Biology And Life Sciences, Food Science And Technology Keywords: lipid oxidation; surface plasmon resonance; bioinformatics; peptidomics; emulsion; protein hydrolysate; EDTA

Online: 2 February 2024 (13:01:22 CET)

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Preprint ARTICLE | doi:10.20944/preprints202306.2207.v1

Expression of Phospholipase D Family Member 6 in Bovine Testes and Its Molecular Characteristics

Rui Yang, Bo-Yang Zhang, Wen-Qian Zhu, Chun-Ling Zhu, Lan-Xin Chen, Yan-sen Zhao, Yue-Qi Wang, Yan Zhang, Amjad Riaz, Bo Tang, Xue-Ming Zhang

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Bovine; Bioinformatics; Phospholipase D family member 6; Testes; Spermatogonial stem cells

Online: 30 June 2023 (14:45:51 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202212.0275.v1

Bioinformatics and Connectivity Map Analysis Suggest Viral Infection as a Critical Causative Factor of Hashimoto’s Thyroiditis

Dong-Woo Lim, Min-Seo Choi, Seok-Mo Kim

Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: Hashimoto’s thyroiditis; bioinformatics; viral infection; mRNA splicing; GSEA; autoimmune disease; CMap

Online: 15 December 2022 (07:44:33 CET)

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Hashimoto’s thyroiditis (HT) is a common autoimmune disease, with its prevalence rapidly increasing. Both genetic and environmental risk factors contribute to the development of HT. Recently, viral infection has been suggested to act as a trigger of HT by eliciting the host immune response and subsequent autoreactivity. We analyzed features of HT through bioinformatics analysis so as to identify markers of HT development. We accessed public microarray data of HT patients from the Gene Expression Omnibus (GEO) and obtained differentially expressed genes (DEGs) under HT. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed for functional clustering of our protein-protein interaction (PPI) network. Utilizing ranked gene lists, we performed Gene Set Enrichment Analysis (GSEA) using the clusterprofiler R package. By comparing the expression signatures of the huge perturbation database with the queried rank-ordered gene list, connectivity map (CMap) analysis was performed to screen potential therapeutic targets and agents. The gene expression profile of the HT group was in line with general characteristics of HT. Biological processes related to the immune response and viral infection pathways were obtained for the upregulated DEGs. GSEA results revealed activation of autoimmune disease-related pathways and several viral infection pathways. Autoimmune disease and viral infection pathways were highly interconnected by common genes, while the HLA genes which are shared by both were significantly upregulated. CMap analysis suggested that perturbagens, including SRRM1, NLK, and CCDC92, have the potential to reverse the HT expression profile. Several lines of evidence suggested that viral infection and the host immune response are activated during HT. Viral infection is suspected to act as a key trigger of HT by causing autoimmunity. SRRM1, an alternative splicing factor, which responds to viral activity, might serve as potential marker of HT.

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 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 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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