Published: Myxococcus xanthus DZ2 genome assembly and Mx-alpha prophage diversity study

Utkarsha’s NAR Genomics and Bioinformatics paper is now online! What began as a simple observation 'seeing 6.4 kb difference in the genome assemblies of same strain from two different labs', transformed into this elegant work on 'microbial genome sequencing, assembly, & comparative genomics', due to UTKARSHA MAHANTA’s dedicated effort. Check out the paper using this link: https://lnkd.in/gWFc5ScE Thanks to Department of Science and Technology and their INSPIRE scheme for funding both of us (research fellowship for her and Faculty grant for me) in the last several years.

Population genetic analyses often rely on DAPC, but existing tools struggle with today’s large sequencing datasets. DAPCy addresses this challenge with a Python-based implementation that integrates classification, clustering, and visualization in an efficient, resource-conscious framework. It achieves higher accuracy and scalability than R’s adegenet, enabling robust analysis of thousands of genomes.  Explore the full paper in Bioinformatics Advances: https://lnkd.in/gUx-YFQw

🌍🔬 Exploring the Blueprint of Life with Ensembl Genome Browser The Ensembl Genome Browser is one of the flagship resources developed by the European Bioinformatics Institute (EMBL-EBI) — the UK chapter of the International Nucleotide Sequence Database Collaboration (INSDC), alongside NCBI (USA) and DDBJ (Japan). As part of EMBL-EBI’s mission, it provides one of the world’s most comprehensive, freely accessible, and up-to-date molecular databases. Beyond databases, EMBL-EBI also offers online and live training events to help scientists, students, and enthusiasts maximize these resources. 💡 Other popular EMBL-EBI resources include: ✓ Ensembl ✓ UniProt ✓ PDBe ✓ InterPro But why is Ensembl Genome Browser so important? It’s like a Google Maps for DNA — an open-access platform that allows us to explore and interpret the genetic code of humans and countless other species. ✨ With Ensembl, you can: 🔹 Visualize genes, transcripts, and regulatory regions 🔹 Explore genetic variations and their health implications 🔹 Compare genomes across species 🔹 Use tools like BLAST & Variant Effect Predictor to analyze sequences Whether you’re a researcher, a student, or simply a curious mind, Ensembl opens a window into the code that makes us who we are. 🚀 #Genomics #Bioinformatics #Ensembl #Biotechnology #Research

🌍🔬 Exploring the Blueprint of Life with Ensembl Genome Browser The Ensembl Genome Browser is one of the flagship resources developed by the European Bioinformatics Institute (EMBL-EBI) — the UK chapter of the International Nucleotide Sequence Database Collaboration (INSDC), alongside NCBI (USA) and DDBJ (Japan). As part of EMBL-EBI’s mission, it provides one of the world’s most comprehensive, freely accessible, and up-to-date molecular databases. Beyond databases, EMBL-EBI also offers online and live training events to help scientists, students, and enthusiasts maximize these resources. 💡 Other popular EMBL-EBI resources include: ✓ Ensembl ✓ UniProt ✓ PDBe ✓ InterPro But why is Ensembl Genome Browser so important? It’s like a Google Maps for DNA — an open-access platform that allows us to explore and interpret the genetic code of humans and countless other species. ✨ With Ensembl, you can: 🔹 Visualize genes, transcripts, and regulatory regions 🔹 Explore genetic variations and their health implications 🔹 Compare genomes across species 🔹 Use tools like BLAST & Variant Effect Predictor to analyze sequences Whether you’re a researcher, a student, or simply a curious mind, Ensembl opens a window into the code that makes us who we are. 🚀 #Genomics #Bioinformatics #Ensembl #Biotechnology #Research

Can human organoids help us understand and model signal transduction pathway activity? We believe the answer is yes! I was glad to share our recent progress at the BC2 conference (organized by SIB Swiss Institute of Bioinformatics), where we study cell-type–specific responses to signal transduction perturbations using human organoids. It was great to get feedback, exchange ideas, and discuss new perspectives! #bc2 #sib #organoids #singlecell

Want to dive deeper into Bioinformatics and Computational Biology? Here is the ocean of resources: 1. https://lnkd.in/gm9gBKDS 2. http://sandbox.bio 3. https://lnkd.in/gedAw6Ej 4. https://lnkd.in/gAguBvjY 5. https://lnkd.in/g4fr9Wsd 6. https://lnkd.in/g_F4ESPk 7. https://lnkd.in/gV62mJ-R 8. https://lnkd.in/gD2VTGD3 9. https://lnkd.in/gDfYC67M 10. https://lnkd.in/gNxrB-mX 11. https://lnkd.in/gKnTZUrH Thanks Abu Reza for sharing this amazing resource with us. #bioinformatics #computationalbiology #genomics #transcriptomics #proteomics #structuralbioinformatics #precisionmedicine #molecularbiology #biotechnology #lifesciences #bigdata #omics #systemsbiology #biostatistics #ngs #datadrivenscience #sequenceanalysis #variantanalysis #proteinbioinformatics #geneticengineering #genomeanalysis #bioinformaticstools #researchresources #scientificresearch #biologyresources #biomedicalresearch #drugdiscovery #personalizedmedicine #moleculardiagnostics #researchskills #sciencetraining #futureofscience #academicresources #globallearning #scientificinsights #biologytools #functionalgenomics #clinicalgenomics #environmentalgenomics #agriculturalgenomics #publichealthgenomics #databasedesign #biologicaldatabases #cancerresearch #pharmacogenomics #knowledgebuilding #researchcommunity #sciencestudents #lifesciencestudents #careeradvancement #researchopportunities

This review offers an overview of the #HiddenMarkovModel, outlining its fundamental concepts & corresponding algorithms, and examines their applications in modern #Bioinformatics, thereby fostering a deeper understanding of HMM among bioinformatics researchers. Harbin Medical University #OpenAccess: https://lnkd.in/ejn39AZ3

Estimating genotype tissue expression profiles traditionally requires extensive RNA-seq experiments. This paper presents a vicinity set cover algorithm that exploits the similarity of neighboring genes to predict genome-wide profiles from a reduced set of reference genes. The approach ensures tractable runtime, high accuracy, and broad applicability, including single-cell datasets and other optimization problems involving consecutive ordered sets.  Explore the full study in Bioinformatics Advances: https://lnkd.in/gY6Y4t3P

I had the privilege of attending the session on “Bioinformatics and Your Field” organized by Genomac Institute. The session offered valuable insights into how bioinformatics serves as a powerful bridge between biology, technology, and data science. It highlighted practical applications of bioinformatics in research and emphasized its growing role in solving complex scientific challenges. This experience has enhanced my perspective on applying bioinformatics tools and approaches within my field, paving the way for more impactful research. #Bioinformatics #GenomacInstitute #Research #AcademicGrowth #Learning

🔬 Most-Cited Research Articles in Science (All Time) – #10 CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice 📖 Thompson, Higgins & Gibson, 1994 📊 ~40,300 citations This landmark work introduced CLUSTAL W, a breakthrough software for multiple sequence alignment (MSA). It brought: ✅ Sequence weighting – reducing bias in alignments ✅ Position-specific gap penalties – more accurate alignments ✅ Flexible weight matrix choice – improved sensitivity across diverse datasets CLUSTAL W has been indispensable in bioinformatics, shaping fields like: 🧬 Comparative genomics 🦠 Evolutionary biology 💊 Drug discovery 🌍 Phylogenetics Even decades later, its influence continues across computational biology, setting the foundation for advanced algorithms in genome research. 📌 This is a reminder that algorithms can be as transformative as experiments in shaping scientific discovery. #Bioinformatics #Genomics #SequenceAlignment #MostCit