Volume 15; 2021

Original Research

Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells

Anna Mantsoki, Karla Parussel, Anagha Joshi

Bioinform Biol Insights. 2021; 15: 1177932220974623. Published online 2021 Feb 9. doi: 10.1177/1177932220974623

PMCID:: PMC7876754

Abstract Article PDF–4.3M

Functional Prediction of Long Noncoding RNAs in Cutaneous Melanoma Using a Systems Biology Approach

Mozhdeh Shahmoradi, Zahra Rezvani

Bioinform Biol Insights. 2021; 15: 1177932220988508. Published online 2021 Feb 3. doi: 10.1177/1177932220988508

PMCID:: PMC7868446

Abstract Article PDF–1.3M

[Not Accepting New Submissions] Microbiome Bioinformatics Applications

Review

Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients

Sofia Sehli, Imane Allali, Rajaa Chahboune, Youssef Bakri, Najib Al Idrissi, Salsabil Hamdi, Chakib Nejjari, Saaïd Amzazi, Hassan Ghazal

Bioinform Biol Insights. 2021; 15: 1177932221999428. Published online 2021 Mar 12. doi: 10.1177/1177932221999428

PMCID:: PMC7961713

Abstract Article PDF–591K

Review

The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment

Onyeka S Chukwudozie, Vincent C Duru, Charlotte C Ndiribe, Abdullahi T Aborode, Victor O Oyebanji, Benjamin O Emikpe

Bioinform Biol Insights. 2021; 15: 11779322211002168. Published online 2021 Mar 15. doi: 10.1177/11779322211002168

PMCID:: PMC7968009

Abstract Article PDF–560K

Original Research

Modeling and Molecular Dynamic Simulation of F(ab′)₂ Fragment of Nimotuzumab for Lung Cancer Diagnostics

Yurika Sastyarina, Ade Rizqi Ridwan Firdaus, Zuhrotun Nafisah, Ari Hardianto, Muhammad Yusuf, Martalena Ramli, Abdul Mutalib, Ukun MS Soedjanaatmadja

Bioinform Biol Insights. 2021; 15: 11779322211002174. Published online 2021 Mar 25. doi: 10.1177/11779322211002174

PMCID:: PMC8842462

Abstract Article PDF–1.7M

In Silico Analysis of Partial Fatty Acid Desaturase 2 cDNA From Reutealis trisperma (Blanco) Airy Shaw

Nurul Jadid, Indah Prasetyowati, Nur Laili Alfina Rosidah, Dini Ermavitalini, Sri Nurhatika, Tutik Nurhidayati, Hery Purnobasuki

Bioinform Biol Insights. 2021; 15: 11779322211005747. Published online 2021 Mar 27. doi: 10.1177/11779322211005747

PMCID:: PMC8842343

Abstract Article PDF–1.0M

Prediction of Anti-COVID 19 Therapeutic Power of Medicinal Moroccan Plants Using Molecular Docking

Badreddine Nouadi, Abdelkarim Ezaouine, Mariame El Messal, Mohamed Blaghen, Faiza Bennis, Fatima Chegdani

Bioinform Biol Insights. 2021; 15: 11779322211009199. Published online 2021 Apr 8. doi: 10.1177/11779322211009199

PMCID:: PMC8040561

Abstract Article PDF–1.5M

Anticancer Potential of Moringa oleifera on BRCA-1 Gene: Systems Biology

Toheeb A Balogun, Kaosarat D Buliaminu, Onyeka S Chukwudozie, Zainab A Tiamiyu, Taiwo J Idowu

Bioinform Biol Insights. 2021; 15: 11779322211010703. Published online 2021 Apr 27. doi: 10.1177/11779322211010703

PMCID:: PMC8842389

Abstract Article PDF–1.1M

In Silico Characterization of a Hypothetical Protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System

Md. Fazley Rabbi, Saiwda Asma Akter, Md. Jaimol Hasan, Al Amin

Bioinform Biol Insights. 2021; 15: 11779322211011140. Published online 2021 Apr 22. doi: 10.1177/11779322211011140

PMCID:: PMC8076777

Abstract Article PDF–2.2M

Microbiome Bioinformatics Applications

Review

Significance of African Diets in Biotherapeutic Modulation of the Gut Microbiome

PO Isibor, PA Akinduti, OS Aworunse, JO Oyewale, O Oshamika, HU Ugboko, OS Taiwo, EF Ahuekwe, YD Obafemi, EA Onibokun, O Oziegbe, MI Oniha, BK Olopade, OM Atolagbe, BT Adekeye, IB Ajiboye, OA Bello, JO Popoola, OI Ayanda, OO Akinnola, GI Olasehinde, AO Eni, OC Nwinyi, CA Omonhinmin, SU Oranusi, OO Obembe

Bioinform Biol Insights. 2021; 15: 11779322211012697. Published online 2021 Apr 27. doi: 10.1177/11779322211012697

PMCID:: PMC8107938

Abstract Article PDF–708K

Original Research

Prediction of Human-Plasmodium vivax Protein Associations From Heterogeneous Network Structures Based on Machine-Learning Approach

Apichat Suratanee, Teerapong Buaboocha, Kitiporn Plaimas

Bioinform Biol Insights. 2021; 15: 11779322211013350. Published online 2021 Jun 16. doi: 10.1177/11779322211013350

PMCID:: PMC8212370

Abstract Article PDF–5.4M

Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2

Emre Aktas

Bioinform Biol Insights. 2021; 15: 11779322211018200. Published online 2021 Jun 2. doi: 10.1177/11779322211018200

PMCID:: PMC8175844

Abstract Article PDF–1.2M

Performance of Regression Models as a Function of Experiment Noise

Gang Li, Jan Zrimec, Boyang Ji, Jun Geng, Johan Larsbrink, Aleksej Zelezniak, Jens Nielsen, Martin KM Engqvist

Bioinform Biol Insights. 2021; 15: 11779322211020315. Published online 2021 Jun 27. doi: 10.1177/11779322211020315

PMCID:: PMC8243133

Abstract Article PDF–1.5M

DGraph Clusters Flaviviruses and β-Coronaviruses According to Their Hosts, Disease Type, and Human Cell Receptors

Benjamin A Braun, Catherine H Schein, Werner Braun

Bioinform Biol Insights. 2021; 15: 11779322211020316. Published online 2021 Jun 7. doi: 10.1177/11779322211020316

PMCID:: PMC8188974

Abstract Article PDF–1.2M

Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal

Sergio Diaz-del-Pino, Esteban Perez-Wohlfeil, Oswaldo Trelles

Bioinform Biol Insights. 2021; 15: 11779322211021422. Published online 2021 Jun 8. doi: 10.1177/11779322211021422

PMCID:: PMC8191064

Abstract Article PDF–1.0M

Inhibitory Potential of Phytochemicals on Interleukin-6-Mediated T-Cell Reduction in COVID-19 Patients: A Computational Approach

Arif Malik, Anam Naz, Sajjad Ahmad, Mansoor Hafeez, Faryal Mehwish Awan, Tassadaq Hussain Jafar, Ayesha Zahid, Aqsa Ikram, Bisma Rauff, Mubashir Hassan

Bioinform Biol Insights. 2021; 15: 11779322211021430. Published online 2021 Jun 8. doi: 10.1177/11779322211021430

PMCID:: PMC8191067

Abstract Article PDF–1.1M

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Samrat Ghosh, Aditya Narayan Sarangi, Mayuri Mukherjee, Deeksha Singh, Madduluri Madhavi, Sucheta Tripathy

Bioinform Biol Insights. 2021; 15: 11779322211025332. Published online 2021 Jun 22. doi: 10.1177/11779322211025332

PMCID:: PMC8221699

Abstract Article PDF–4.3M

Review

Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins

Ritesh Gorkhali, Prashanna Koirala, Sadikshya Rijal, Ashmita Mainali, Adesh Baral, Hitesh Kumar Bhattarai

Bioinform Biol Insights. 2021; 15: 11779322211025876. Published online 2021 Jun 22. doi: 10.1177/11779322211025876

PMCID:: PMC8221690

Abstract Article PDF–4.1M

Original Research

A Computational-Based Drug Repurposing Method Targeting SARS-CoV-2 and its Neurological Manifestations Genes and Signaling Pathways

Ali Sepehrinezhad, Fariborz Rezaeitalab, Ali Shahbazi, Sajad Sahab-Negah

Bioinform Biol Insights. 2021; 15: 11779322211026728. Published online 2021 Jun 18. doi: 10.1177/11779322211026728

PMCID:: PMC8216348

Abstract Article PDF–3.5M

In Silico Integrative Approach Revealed Key MicroRNAs and Associated Target Genes in Cardiorenal Syndrome

Romana Ishrat, Mohd Murshad Ahmed, Safia Tazyeen, Aftab Alam, Anam Farooqui, Rafat Ali, Nikhat Imam, Naaila Tamkeen, Shahnawaz Ali, Md Zubbair Malik, Armiya Sultan

Bioinform Biol Insights. 2021; 15: 11779322211027396. Published online 2021 Jun 30. doi: 10.1177/11779322211027396

PMCID:: PMC8256246

Abstract Article PDF–3.4M

In Silico Exploration of Phytoconstituents From Phyllanthus emblica and Aegle marmelos as Potential Therapeutics Against SARS-CoV-2 RdRp

Khushboo Pandey, Kiran Bharat Lokhande, K Venkateswara Swamy, Shuchi Nagar, Manjusha Dake

Bioinform Biol Insights. 2021; 15: 11779322211027403. Published online 2021 Jun 24. doi: 10.1177/11779322211027403

PMCID:: PMC8236766

Abstract Article PDF–2.0M

Comparison of Hyaluronic Acid Biosynthetic Genes From Different Strains of Pasteurella multocida

Pailin Pasomboon, Pramote Chumnanpuen, Teerasak E-kobon

Bioinform Biol Insights. 2021; 15: 11779322211027406. Published online 2021 Jun 21. doi: 10.1177/11779322211027406

PMCID:: PMC8221702

Abstract Article PDF–10M

In Silico Identification and Functional Characterization of Conserved miRNAs in the Genome of Cryptosporidium parvum

Md. Irtija Ahsan, Md. Shahidur Rahman Chowdhury, Moumita Das, Sharmin Akter, Sawrab Roy, Binayok Sharma, Rubaiat Nazneen Akhand, Mahmudul Hasan, Md Bashir Uddin, Syed Sayeem Uddin Ahmed

Bioinform Biol Insights. 2021; 15: 11779322211027665. Published online 2021 Jun 27. doi: 10.1177/11779322211027665

PMCID:: PMC8243136

Abstract Article PDF–1.1M

DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity

Asad Ahmed, Bhavika Mam, Ramanathan Sowdhamini

Bioinform Biol Insights. 2021; 15: 11779322211030364. Published online 2021 Jul 7. doi: 10.1177/11779322211030364

PMCID:: PMC8274096

Abstract Article PDF–1.7M

Review

Cloud Computing Enabled Big Multi-Omics Data Analytics

Saraswati Koppad, Annappa B, Georgios V Gkoutos, Animesh Acharjee

Bioinform Biol Insights. 2021; 15: 11779322211035921. Published online 2021 Jul 28. doi: 10.1177/11779322211035921

PMCID:: PMC8323418

Abstract Article PDF–1.1M

Original Research

Genome Plasticity by Insertion Sequences Learned From a Case of Radiation-Resistant Bacterium Deinococcus geothermalis

Chanjae Lee, Min K Bae, Nakjun Choi, Su Jeong Lee, Sung-Jae Lee

Bioinform Biol Insights. 2021; 15: 11779322211037437. Published online 2021 Aug 4. doi: 10.1177/11779322211037437

PMCID:: PMC8369957

Abstract Article PDF–1006K

Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors

K Harini, S Jayashree, Vikas Tiwari, Sneha Vishwanath, Ramanathan Sowdhamini

Bioinform Biol Insights. 2021; 15: 11779322211037769. Published online 2021 Oct 28. doi: 10.1177/11779322211037769

PMCID:: PMC8558589

Abstract Article PDF–1.4M

Deep Learning Approach for Quantification of Fluorescently Labeled Blood Cells in Danio rerio (Zebrafish)

Samrat Thapa, David L Stachura

Bioinform Biol Insights. 2021; 15: 11779322211037770. Published online 2021 Aug 7. doi: 10.1177/11779322211037770

PMCID:: PMC8369963

Abstract Article PDF–1.1M

Expression, Interaction, and Role of Pseudogene Adh6-ps1 in Cancer Phenotypes

Martin C Nwadiugwu

Bioinform Biol Insights. 2021; 15: 11779322211040591. Published online 2021 Aug 14. doi: 10.1177/11779322211040591

PMCID:: PMC8369952

Abstract Article PDF–1024K

A Computational Approach to Modeling an Antagonistic Angiogenic VEGFR1-IL2 Fusion Protein for Cancer Therapy

Qurrat ul Ain Shafique, Hafiz Muzzammel Rehman, Tahreem Zaheer, Rana Adnan Tahir, Munir Ahmad Bhinder, Roquyya Gul, Mahjabeen Saleem

Bioinform Biol Insights. 2021; 15: 11779322211043297. Published online 2021 Sep 20. doi: 10.1177/11779322211043297

PMCID:: PMC8458685

Abstract Article PDF–1.8M

ProTG4: A Web Server to Approximate the Sequence of a Generic Protein From an in Silico Library of Translatable G-Quadruplex (TG4)-Mapped Peptides

Siddhartha Kundu

Bioinform Biol Insights. 2021; 15: 11779322211045878. Published online 2021 Sep 28. doi: 10.1177/11779322211045878

PMCID:: PMC8482721

Abstract Article PDF–968K

Molecular Modeling and Bioinformatics Analysis of Drug-Receptor Interactions in the System Formed by Glargine, Its Metabolite M1, the Insulin Receptor, and the IGF1 Receptor

Margarita González-Beltrán, Claudio Gómez-Alegría

Bioinform Biol Insights. 2021; 15: 11779322211046403. Published online 2021 Sep 23. doi: 10.1177/11779322211046403

PMCID:: PMC8477355

Abstract Article PDF–1.5M

In Silico Investigation of Conserved miRNAs and Their Targets From the Expressed Sequence Tags in Neospora Caninum Genome

Moumita Das, Mahmudul Hasan, Sharmin Akter, Sawrab Roy, Binayok Sharma, Md. Shahidur Rahman Chowdhury, Md. Irtija Ahsan, Rubaiat Nazneen Akhand, Md Bashir Uddin, Syed Sayeem Uddin Ahmed

Bioinform Biol Insights. 2021; 15: 11779322211046729. Published online 2021 Dec 6. doi: 10.1177/11779322211046729

PMCID:: PMC8655437

Abstract Article PDF–1.1M

Identification of Terpenoids From Abrus precatorius Against Parkinson’s Disease Proteins Using In Silico Approach

Damilola Alex Omoboyowa, Toheeb Adewale Balogun, Oluwaseun Motunrayo Omomule, Oluwatosin A Saibu

Bioinform Biol Insights. 2021; 15: 11779322211050757. Published online 2021 Oct 20. doi: 10.1177/11779322211050757

PMCID:: PMC8544761

Abstract Article PDF–1.2M

Methods and Protocols

Regression Models, Fantastic Beasts, and Where to Find Them: A Simple Tutorial for Ecologists Using R

Luca Corlatti

Bioinform Biol Insights. 2021; 15: 11779322211051522. Published online 2021 Oct 22. doi: 10.1177/11779322211051522

PMCID:: PMC8544769

Abstract Article PDF–1.6M

Original Research

Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach

Md. Shahadat Hossain, Mahafujul Islam Quadery Tonmoy, Atqiya Fariha, Md. Sajedul Islam, Arpita Singha Roy, Md. Nur Islam, Kumkum Kar, Mohammad Rahanur Alam, Md. Mizanur Rahaman

Bioinform Biol Insights. 2021; 15: 11779322211054684. Published online 2021 Oct 26. doi: 10.1177/11779322211054684

PMCID:: PMC8554545

Abstract Article PDF–1.6M

Genetic Variants Assessing Crohn’s Disease Pattern in Pediatric Inflammatory Bowel Disease Patients by a Clinical Exome Survey

Dago Dougba Noel, Pinelli Marinella, Giacomelli Mauro, Serena Ilaria Tripodi, Alessia Pin, Arrigo Serena, Bramuzzo Matteo, Fuoti Maurizio Giuseppe, Alvisi Patrizia, Calza Stefano, Alberto Tommasini, Badolato Raffaele

Bioinform Biol Insights. 2021; 15: 11779322211055285. Published online 2021 Dec 22. doi: 10.1177/11779322211055285

PMCID:: PMC8728778

Abstract Article PDF–1.0M

Plasma Phospholipids: A Promising Simple Biochemical Parameter to Evaluate COVID-19 Infection Severity

Mohammed Abdalla Hussein, Noor Eldin Mohamed Ismail, Ahmed H Mohamed, Rita M Borik, Ali Abdelaziz Ali, Yasser O Mosaad

Bioinform Biol Insights. 2021; 15: 11779322211055891. Published online 2021 Nov 18. doi: 10.1177/11779322211055891

PMCID:: PMC8619733

Abstract Article PDF–1.6M

Prognostic Value Estimation of BRIP1 in Breast Cancer by Exploiting Transcriptomics Data Through Bioinformatics Approaches

Umama Khan, Md. Salauddin Khan

Bioinform Biol Insights. 2021; 15: 11779322211055892. Published online 2021 Nov 19. doi: 10.1177/11779322211055892

PMCID:: PMC8619737

Abstract Article PDF–2.8M

Structural and Energetic Insights Into the Interaction of Niacin With the GPR109A Receptor

Kiran Kumar Adepu, Sangita Kachhap, Andriy Anishkin, Sree V Chintapalli

Bioinform Biol Insights. 2021; 15: 11779322211056122. Published online 2021 Nov 27. doi: 10.1177/11779322211056122

PMCID:: PMC8637708

Abstract Article PDF–1.5M

Short Report

FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies

Enzo Guerrero-Araya, Marina Muñoz, César Rodríguez, Daniel Paredes-Sabja

Bioinform Biol Insights. 2021; 15: 11779322211059238. Published online 2021 Nov 27. doi: 10.1177/11779322211059238

PMCID:: PMC8637782

Abstract Article PDF–741K

Original Research

Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis

G Prashanth, Basavaraj Vastrad, Chanabasayya Vastrad, Shivakumar Kotrashetti

Bioinform Biol Insights. 2021; 15: 11779322211067365. Published online 2021 Dec 23. doi: 10.1177/11779322211067365

PMCID:: PMC8725226

Abstract Article PDF–3.9M

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