Tag: bioRxiv

A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses

Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS  PubMed  Article  Google Scholar  Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….

Continue Reading A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses

Potential SARS-CoV-2 antivirals based on host miRNAs

A recent research paper posted to the bioRxiv* preprint server demonstrated micro ribonucleic acids (miRNAs) as potential antiviral options against various coronaviruses (CoVs), including severe acute respiratory syndrome CoV 2 (SARS-CoV-2). Study: Deciphering inhibitory mechanism of coronavirus replication through host miRNAs-RNA-dependent RNA polymerase (RdRp) interactome. Image Credit: ART-ur / Shutterstock Background Despite what…

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SARS-CoV-2 ORF8 protein binds to dendritic cells and induces a hyper-inflammatory cytokine storm

In a recent study posted to the bioRxiv* pre-print server, researchers examined how the interaction of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) open reading frame 8 (ORF8) protein with host dendritic cells (DCs) induced cytokine storm. ​​​​​​​Study: The unique ORF8 protein from SARS-CoV-2 binds to human dendritic cells…

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Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer

Torre, L. A., Siegel, R. L., Ward, E. M. & Jemal, A. Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol. Prev. Biomark. 25, 16–27 (2016). Article  Google Scholar  Gerasimova, E. et al. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Front….

Continue Reading Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer

Seven Bridges, Brazilian Researchers Applying Graph Analysis to Build Diverse Reference Genome

CHICAGO – The latest of Seven Bridges Genomics’ efforts to diversify reference genomes is its largest and perhaps most complex to date, an attempt to address the Brazilian population. The Charlestown, Massachusetts-based bioinformatics company recently joined with the University of São Paulo (USP), the Associação Genomas Brasil (Brazil Genome Association),…

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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In vivo hypermutation and continuous evolution

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

Wei, K. et al. Notch signalling drives synovial fibroblast identity and arthritis pathology. Nature 582, 259–264 (2020). ADS CAS PubMed PubMed Central Article Google Scholar  Cembrowski, M. S. & Menon, V. Continuous variation within cell types of the nervous system. Trends Neurosci. 41, 337–348 (2018). CAS PubMed Article Google Scholar  Maurano, M. T. et al. Systematic localization of…

Continue Reading Single-cell eQTL models reveal dynamic T cell state dependence of disease loci – Nature – Alert Breaking News

CRISPR/Cas9 deletions induce adverse on-target genomic effects

Clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) have transformed genome engineering techniques. Numerous toolsets have been created to enable easy and efficient loss-of-function perturbations of functional genomic sites. Study: CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells. Image Credit: elenabsl/Shutterstock The CRISPR/Cas9 system’s elements…

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Study explores SARS-CoV-2 Omicron variant and infected colon epithelial cells

In a recent study posted to the bioRxiv* preprint server, researchers assessed the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant on infected human cells and organs. Study: SARS-CoV-2 Omicron BA.1 variant infection of human colon epithelial cells. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock Various studies have…

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RNA interference triggers that target SARS-CoV-2 genome

Coronavirus disease 2019 (COVID-19) vaccines have played a critical role in reducing transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. However, with emerging reports of waning vaccine efficacy, there remains an urgent need to develop prophylactic measures against COVID-19. In a recent study published on the bioRxiv*…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

Continue Reading Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

High-throughput “dry and wet” experiments to explore the principles of optimal design of mRNA sequences

Today I share a preprint article Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutic uploaded by Rhiju Das on BioRxiv , to explore the universal rules for achieving mRNA stability and efficient expression. Barriers to mRNA therapeutics With rapid R&D capabilities and extensive R&D pipelines, especially in…

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Time for Proteomics To Shine

This article includes research findings that are yet to be peer-reviewed. Results are therefore regarded as preliminary and should be interpreted as such. Find out about the role of the peer review process in research here. For further information, please contact the cited source. Over the last 20 years, advances…

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Prediction of histone post-translational modification patterns based on nascent transcription data

Allfrey, V. G., Faulkner, R. & Mirsky, A. E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51, 786–794 (1964). CAS  PubMed  PubMed Central  Google Scholar  Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization….

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Accelerating minimap2 for long-read sequencing applications on modern CPUs

Chaisson, M. J. et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun. 10, 1–16 (2019). Article  Google Scholar  Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 1–19 (2016). Article  Google Scholar  Beyter, D. et al. Long-read sequencing of…

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LAMP-CRISPR-Cas12a-lateral flow immunochromatographic strip | IDR

Introduction About 700,000 people die from “superbugs” globally every year. Antibiotic abuse is the culprit of extensive spread of superbugs. Currently, carbapenemase-producing organisms are among the most important pathogens of hospital infections. Especially the plasmid-mediated highly transmissible carbapenem-resistant Enterobacterales (CRE) has become an important public health issue of global concern….

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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CRISPR-Cas9 Gene Therapy for Duchenne Muscular Dystrophy

Ishino Y, Shinagawa H, Makino K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169:5429–33. CAS  PubMed  PubMed Central  Google Scholar  Jansen R, van Embden JDA, Gaastra W, et al. Identification of genes…

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Spatial components of molecular tissue biology

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes | BMC Bioinformatics

1. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, et al. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016;17:66. Article  Google Scholar  2. Minio A, Lin J, Gaut BS, Cantu D. How single…

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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New bioinformatics method to analyze viral sgRNA

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

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Finishing the Human Genome | Discover Magazine

This article appeared in the January/February 2022 issue of Discover magazine as “Finishing the Human Blueprint.” Become a subscriber for unlimited access to our archive. At long last, scientists have declared “mission accomplished” on the complete sequencing of the human genome — one of the most ambitious research undertakings of the past few decades….

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples | BMC Microbiology

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

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AlphaFold Filled

AlphaFold models enriched with ligands and co-factors Not found The entry <missing-id> was not found. Please note that the ID should be an Uniprot primary accession code. Secondary Uniprot accession codes as well as Uniprot names are not recognized. AlphaFill AlphaFill is an algorithm based on sequence and structure similarity…

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Novel bioinformatics pipeline for fast and scalable analysis of large viral phylogenies

A team of researchers recently developed a bioinformatics approach to analyze viral phylogenetic clusters and posted their findings to the bioRxiv* preprint server. Study: ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. Image Credit: M. PATTHAWEE/Shutterstock Background Coronavirus disease 2019 (COVID-19)…

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A pandemic-scale phylogenetic analysis tool

Phylogenetics is an analytical tool that quickly analyzes genomic data to provide invaluable insights into the evolution and spread of a pathogen, thereby allowing public health officials and governments to respond to it in a timely fashion. During the coronavirus disease 2019 (COVID-19) pandemic, phylogenetics, like many other pre-pandemic tools,…

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Quantum-Si Lining Up Early-Access Users for Proteomic Platform in Advance of 2022 Launch

NEW YORK – Proteomics startup Quantum-Si has lined up a number of early-access users for it semiconductor-based protein sensing system in anticipation of a 2022 launch. As of the middle of November, the Guilford, Connecticut-based company had placed instruments at 10 outside institutions, with researchers exploring its utility for purposes…

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Study finds sarbecoviruses circulating in wildlife outside Asia can infect human cells

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2) and past SARS-CoV outbreaks were a result of zoonotic spillover of sarbecoviruses from animals to humans. Although most of the animal sarbecoviruses do not infect eukaryotic cells, clade 4 sarbecoviruses recently found in China…

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Homology-directed repair (HDR) Knock-in Templates

One powerful application of CRISPR/Cas genome editing technology involves the precise insertion of DNA sequences via the homology-directed repair (HDR) pathway. While many factors may affect the efficacy of this approach, choosing the right HDR template is certainly an important one. GenScript now offers high quality, sequence verified HDR templates for…

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AlphaFold – Proteopedia, life in 3D

From Proteopedia proteopedia link proteopedia link In 2020, the AlphaFold2[1][2] system of DeepMind[3][4] demonstrated a major breakthrough[5][6][7][8]. At CASP14, AlphaFold2 was far better able, among over 100 competing groups, to predict structures, including sidechain positions, so close to the subsequently revealed X-ray crystallographic structures as to differ by little more…

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New bioinformatics method for viral sgRNA analysis

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

Continue Reading New bioinformatics method for viral sgRNA analysis

Frontiers | Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling

Introduction Bipolar disorder (BD) features recurrent episodes of mania/hypomania and depression, interspersed with periods of euthymia. Symptoms usually include drastic changes in energy levels, sleep, thinking, and behaviors, which can significantly disrupt the daily life of BD patients (Craddock and Sklar, 2013). A mood cycle is defined as the period…

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Representation and participation across 20 years of plant genome sequencing

1. Initiative, T. A. G. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000). Google Scholar  2. Sayers, E. W. et al. GenBank. Nucleic Acids Res. 48, D84–D86 (2020). CAS  PubMed  Google Scholar  3. Li, C., Lin, F., An, D., Wang, W. & Huang,…

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Seurat citation info

Seurat citation info To cite Seurat in publications, please use: Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, III WMM, Stoeckius M, Smibert P, Satija R (2018). “Comprehensive integration of single cell data.” bioRxiv. doi: 10.1101/460147, www.biorxiv.org/content/10.1101/460147v1. Corresponding BibTeX entry: @Article{, author = {Tim Stuart and Andrew Butler…

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How to create a mutation landscape (waterfall) plot with GenVisR

This tutorial makes use of the GenVisR package. Please cite: Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print]PubMed | Bioinformatics Journal | BioRxiv | Bioconductor | GitHub Note: A more comprehensive…

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The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

1. The Plant List. The Plant List—A Working List of All Plant Species (Royal Botanic Gardens, Kew and Missouri Botanical Garden, 2019). www.theplantlist.org/. Retrieved 20 Aug 2019. 2. Christenhusz, M. J. M. & Byng, J. W. The number of known plants species in the world and its annual increase. Phytotaxa…

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The earliest Denisovans and their cultural adaptation

1. Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010). CAS  PubMed  PubMed Central  Google Scholar  2. Krause, J. et al. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464, 894–897 (2010). CAS  PubMed …

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The Biostar Herald for Tuesday, November 23, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…

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AlphaFold Heterodimers Modeling

Benchmarking AlphaFold for transient protein complex modeling Description: Here we explore the use of the recently developed deep learning method, AlphaFold, to predict structures of transient interactions between proteins from their sequences. With a benchmark of 152 heterodimeric protein complexes of various classes, including enzyme-inhibitor and antibody-antigen interactions, and an…

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Science: AlphaFold teamed up with RoseTTAFold to surpass another big mountain in protein structure prediction

The artificial intelligence (AI) revolution in the field of protein structure prediction continues. At the end of 2020, the new generation of AlphaFold (AlphaFold2) developed by DeepMind has solved the major challenges in the biological field for decades and achieved a major breakthrough in accurately predicting the 3D structure of…

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heterozygous SNV AB>0.15, heterozygous indel

heterozygous SNV AB>0.15, heterozygous indel<0.20 in UKB-WES 0 These gVCFs were joint genotyped using GLnexus (www.biorxiv.org/content/10.1101/572347v1) to create a single, unfiltered project-level VCF (pVCF). Genotype depth filters (SNV DP≥7, indel DP≥10) were applied prior to variant site filters requiring at least one variant genotype passing an allele balance filter (heterozygous…

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Uncontrollable Species Collapse Too High A Price For GE Predator Control

Saturday, 20 November 2021, 3:07 pmPress Release: GE Free NZ Using Genetic Engineering (GE) technologies such as gene editing for predator control to drive population collapse or extinction, pose unknown dangers and much suffering. [1] Scientists have openly expressed concerns about the ability to control gene trait transfer to other…

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Artificial intelligence cracks the code of protein complexes (reproduced)

In terms of protein structure prediction, the artificial intelligence revolution continues. A year ago, a software program successfully simulated the 3D shape of a single protein for the first time, and its accuracy was as accurate as measured by experimental techniques decades ago. This summer, researchers used artificial intelligence programs…

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Perfect and imperfect views of ultraconserved sequences

1. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001). CAS  PubMed  Google Scholar  2. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004). Google Scholar  3. Mouse Genome Sequencing Consortium. et al. Initial…

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Open source code for AlphaFold

This package provides an implementation of the inference pipeline of AlphaFoldv2.0. This is a completely new model that was entered in CASP14 and published inNature. For simplicity, we refer to this model as AlphaFold throughout the restof this document. We also provide an implementation of AlphaFold-Multimer. This represents a workin…

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github.com-deepmind-alphafold_-_2021-11-02_17-14-38 : deepmind : Free Download, Borrow, and Streaming : Internet Archive

Open source code for AlphaFold. This package provides an implementation of the inference pipeline of AlphaFoldv2.0. This is a completely new model that was entered in CASP14 and published inNature. For simplicity, we refer to this model as AlphaFold throughout the restof this document. We also provide an implementation of…

Continue Reading github.com-deepmind-alphafold_-_2021-11-02_17-14-38 : deepmind : Free Download, Borrow, and Streaming : Internet Archive

Molecular Characterisation of Class 1, 2 and 3 Integrons

Introduction Gram-negative rods of the genus Serratia are environmental bacteria which play an increasing role as etiological agents of healthcare-associated infections (HAI). These bacteria were previously classified in the family Enterobacteriaceae, but due to 2016 taxonomy change, the genus Serratia at present belongs to the newly formed family Yersiniaceae in…

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Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator

1. Pérez, J., Moraleda-Muñoz, A., Marcos-Torres, F. J. & Muñoz-Dorado, J. Bacterial predation: 75 years and counting!. Environ. Microbiol. 18, 766–779 (2016). PubMed  Article  PubMed Central  Google Scholar  2. Linares-Otoya, L. et al. Diversity and antimicrobial potential of predatory bacteria from the Peruvian coastline. Mar. Drugs. 15, E308. doi.org/10.3390/md15100308 (2017)….

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The Biostar Herald for Monday, November 01, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, GenoMax, and was…

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Genome Spotlight: Mandarinfish (Synchiropus splendidus)

If any fish deserves the name spendidus, it is the mandarinfish. Its magnificent colors have made this fish popular in the aquarium industry despite the fact that it’s covered in poison, has notoriously picky eating habits, and smells terrible. The secrets of how it produces its vibrant hues and foul…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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The Biostar Herald for Tuesday, October 26, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from GenoMax, Istvan Albert, lethalfang, and was edited…

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AI revolutions in biology: The joys and perils of AlphaFold

doi: 10.15252/embr.202154046. Online ahead of print. Affiliations Expand Affiliation 1 Oncode Institute and Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands. Item in Clipboard Anastassis Perrakis et al. EMBO Rep. 2021. Show details Display options Display options Format AbstractPubMedPMID doi: 10.15252/embr.202154046. Online ahead of print. Affiliation 1 Oncode Institute…

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Telomere-To-Telomere Consortium Shares Insights From Gapless Human Genome at ASHG

NEW YORK – Researchers from the Telomere-To-Telomere Consortium shared the first insights from analyzing the gapless human complete hydatidiform mole genome assembly this week at the American Society of Human Genetics annual meeting, held virtually. The assembly, which was first released as a preprint earlier this year, includes more information…

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Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

Akbari MT, Izadi P, Izadyar M, Kyriacou K, Kleanthous M (2008) Molecular basis of thalassemia intermedia in Iran. Hemoglobin 32:462–470 CAS  Article  Google Scholar  Al-Allawi NA, Jubrael JM, Hughson M (2006) Molecular characterization of β-thalassemia in the Dohuk region of Iraq. Hemoglobin 30:479–486 CAS  Article  Google Scholar  Alibakhshi R, Kianishirazi…

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Nanopore Single-Molecule Sequencing for Mitochondrial DNA Methylation Analysis: Investigating Parkin-Associated Parkinsonism as a Proof of Concept

doi: 10.3389/fnagi.2021.713084. eCollection 2021. Affiliations Expand Affiliations 1 Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany. 2 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg. 3 Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg. Item in Clipboard Theresa…

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Haplotype Diversity of Mongolian and Tuvan Goat Breeds (Capra hircus) Based on mtDNA and Y-Chromosome Polymorphism

1 Zonaed Siddiki, A., Miah, G., Islam, M.S., et al., Goat genomic resources: the search for genes associated with its economic traits, Int. J. Genomics, 2020, 5940205. doi.org/10.1155/2020/5940205 2 Amills, M., Capote, J., and Tosser-Klopp, G., Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing…

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Postdoc Position in post-translational Modifications on neurodegeneration-linked RNA-binding Proteins at the Institute of Molecular Biology in Mainz, Germany

The laboratory of Dorothee Dormann focuses on the molecular mechanisms of neurodegenerative diseases, most notably FTD (frontotemporal dementia) and ALS (amyotrophic lateral sclerosis). FTD and ALS are currently incurable, with patients usually dying within a few years of disease onset. Existing therapies are designed to treat only the symptoms of…

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October 2021 Galactic News – Galaxy Community Hub

Hello all, October brings Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of trainings, talksm and a Galaxy Papercuts CoFest day too. It also brings news of new job openings on two continents, two new platforms, blog posts (where My Little Pony makes an appearance, really), GTN updates…

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Mitochondrial DNA is released by cigarette smoke

In a recent study, researchers have discovered that mitochondrial DNA is released extracellularly upon exposure to cigarette smoke and in COPD patients. COPD and its risk factors Chronic obstructive pulmonary disease (COPD) is a group of lung conditions that cause difficulties in breathing. It results in remodelling of airway wall…

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Study supports efficacy and safety of lung-selective nanotherapy against SARS-CoV-2 infection

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to evade neutralization by antibodies elicited by vaccination and natural infection with the ancestral strains by the emergence of new variants. New therapeutic measures are essential to achieve better control of viral spread and disease severity. Study: Lung-selective Cas13d-based nanotherapy…

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CryoSky – Github Help

Cryosky’s Projects AlloType Methods to predict allosteric regulation type. alphafold Open source code for AlphaFold. alphafold-1 Install alphafold on the local machine, get out of docker. AlphaFold_oligomer The repository for modeling of oligomeric protein structure using AlphaFold. alphafold_pytorch An implementation of the DeepMind’s AlphaFold based on PyTorch for research awsemmd…

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DeepMind Introduce AlphaFold-Multimer to Predict Multi-Chain Protein Complexes with Better Accuracy

The London-based AI research firm DeepMind has introduced AlphaFold-Multimer, a model that can predict the structure of multi-chain protein complexes with increased accuracy. The recent AlphaFold model can accurately predict many single protein chains. However, in many cases, the prediction of multi-chain protein complexes remains a challenge. Compared to the…

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Single cell RNA sequencing (scRNA-seq) in cardiac tissue

Introduction Cardiovascular diseases (CVDs) are the leading cause of death globally, taking an estimated 17.9 million (32.1%) lives in 2015, up from 12.3 million (25.8%) in 1990.1,2 CVDs are highly heterogeneous diseases involving a group of disorders of the heart and blood vessels, which include cardiomyopathy, hypertensive heart disease, heart…

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Subject Collection(s) | bioRxiv

Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search Animal Behavior and Cognition (3008) Biochemistry (6116) Bioengineering (4348) Bioinformatics (17664) Biophysics (8412) Cancer Biology (6469) Cell Biology (9414) Clinical Trials (138) Developmental Biology (5462) Ecology (8588) Epidemiology (2062) Evolutionary Biology (11759) Genetics (8462)…

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No weak links: A W&M-based collaborative advances understanding of neural control of respiration

(Most of) the team:  Team members that successfully completed a Patch-Seq analysis of respiratory-control neurons are (from left) Greg Smith, Margaret Saha, Prajkta Kallurkar and Christopher Del Negro. Not pictured are team members Tina Picardo and Yae Sugimura.  Courtesy photo by Joseph McClain |  September 24, 2021 Patch-Seq is shorthand…

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GitHub – AI-sandbox/gnomix

This repository includes a python implemenation of Gnomix, a fast and accurate local ancestry method. Gnomix can be used in two ways: training a model from scratch using reference training data or loading a pre-trained Gnomix model (see Pre-Trained Models below) In both cases the models are used to infer…

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The Biostar Herald for Tuesday, September 21, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020

1. Dudas, G. et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544, 309–315 (2017). ADS  CAS  Article  Google Scholar  2. Kafetzopoulou, L. E. et al. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 363, 74–77 (2019). ADS  CAS  Article …

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Bioinformatician I/II/III – Job posted on PostdocJobs.com

Job Description Farmington, Connecticut Apply Summary The Robinson lab is seeking a Bioinformaticician to join our team that focuses on the development of software and ontologies for biomedical research. Our team of expert biological curators, bioinformaticians, and computer scientists maintain and enhance a knowledge extraction and refinement process that delivers…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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rosetta fold vs alphafold 2

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

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Next Generation Sequencing in tissues: Fully in situ methods

Here, Synthetic Biology Platform Lead at the Wyss Institute for Biologically Inspired Engineering, Richie Kohman, continues exploring the breakthroughs of Next Generation Sequencing (NGS) Exploring the locations and identities of RNA within biological tissues can uncover important information about cell types and states as well as give insight into cellular…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias

Abstract Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or…

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| bioRxiv

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Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae)

Arista M, Berjano R, Viruel J, Ortiz MÁ, Talavera M, Ortiz P (2017) Uncertain pollination environment promotes the evolution of a stable mixed reproductive system in the self-incompatible Hypochaeris salzmanniana (Asteraceae). Ann Bot 120(3):447–456 CAS  PubMed  PubMed Central  Article  Google Scholar  Barrett SC (2019) ‘A most complex marriage arrangement’: recent…

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The Biostar Herald for Friday, September 03, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from zx8754, Istvan Albert, and was edited by…

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the Genomic Rearrangement IDentification Software Suite

Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…

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A framework to prioritize miRNA-driven post-transcriptional signals using exonic and intronic regions of RNAseq data

Tool:A framework to prioritize miRNA-driven post-transcriptional signals using exonic and intronic regions of RNAseq data 0 Dear all, Please let me introduce an R package we have developed which can be accessed through the following link: github.com/emarmolsanchez/EISACompR EISAcompR is a comprehensive and user-friendly pipeline for performing Exon/Intron Split Analysis (EISA)…

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Tissue-specific heteroplasmy dynamics is accompanied by a sharp drop in mtDNA copy number during development

Mitochondrial mutation phenotypes are highly unpredictable as they depend on 3 variables; mutant-to-wildtype ratio (heteroplasmy level), total number of mitochondrial genomes (mtDNA), and the bioRxiv Tissue-specific heteroplasmy dynamics is accompanied by a sharp drop in mtDNA copy number during development t.co/LNwe5ci20D #bioRxiv…

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Build protein-protein interaction prediction deep learning model

Build protein-protein interaction prediction deep learning model 0 0 I’m an undergraduate biology student and my thesis is on designing a deep learning architecture to predict whether two proteins interact or not given their primary sequences. I have read some papers with different approaches to the problem including the paper…

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UMAP vs “rigorous” t-SNE

UMAP vs “rigorous” t-SNE 1 I’ve heard a lot of people discussing UMAP recently as though it has essentially superseded t-SNE for visualizing scRNA-seq data. UMAP is certainly impressive, but it seems to me that there are a lot of things one can do to pretty dramatically improve the output…

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