Category: bioRxiv

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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Identification of electroporation sites in the complex lipid organization of the plasma membrane

Abstract The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to a strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon, termed electroporation, is already utilized…

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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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Identification of antineoplastic agents for oral squamous cell carcinoma: an integrated bioinformatics approach using differential gene expression and network biology

Abstract Oral squamous cell carcinoma (OSCC) is the most common malignant epithelial neoplasm and anatomical subtype of head and neck squamous cell carcinoma (HNSCC) with an average 5-year survival rate of less than 50%. To improve the survival rate of OSCC, the discovery of novel anti-cancer drugs is urgently needed….

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GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation

Abstract Background: Over the past three decades there have been numerous molecular biology developments that have led to an explosion in the number of gene expression studies being performed. Many of these gene expression studies publish their data to the public database GEO, making them freely available. By analysing gene…

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AlphaDesign: A de novo protein design framework based on AlphaFold

Abstract De novo protein design is a longstanding fundamental goal of synthetic biology, but has been hindered by the difficulty in reliable prediction of accurate high-resolution protein structures from sequence. Recent advances in the accuracy of protein structure prediction methods, such as AlphaFold (AF), have facilitated proteome scale structural predictions…

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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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dna seq analysis – Banya

Dna Sequencing Data Analysis Simple Software Tools . Omicscript Pipeline For Dna Seq Data Analysis Array Suite Wiki . Dna Sequencing Data Analysis Simple Software Tools . Omicscript Pipeline For Dna Seq Data Analysis Array Suite Wiki . Dna Sequence Alignment Dna Contig Assembly Software Sequence . Dna Sequence Alignment…

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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…

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

Combining CRISPR/Cas9 and brain imaging: from genes to molecules to networks

Abstract Receptors, transporters and ion channels are important targets for therapy development in neurological diseases including Alzheimer’s disease, Parkinson’s disease, epilepsy, schizophrenia and major depression. Several receptors and ion channels identified by next generation sequencing may be involved in disease initiation and progression but their mechanistic role in pathogenesis is…

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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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CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production

Abstract Cassava (Manihot esculenta Crantz) is a starchy root crop that supports over a billion people in tropical and subtropical regions of the world. This staple, however, produces toxic cyanogenic compounds and requires processing for safe consumption. Excessive consumption of insufficiently processed cassava, in combination with protein-poor diets, can have…

Continue Reading CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production

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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scatterHatch: an R/Bioconductor package for colorblind accessible visualization of single-cell data

Abstract Summary: Color is often used as a primary differentiating factor in visualization of single-cell and multi-omics analyses. However, color-based visualizations are extremely limiting and require additional considerations to account for the wide range of color perceptions in the population. The scatterHatch package provides software for accessible single-cell visualizations that…

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Keeping up with the human genome

The human genome is made up of over three billion base pairs of DNA, which in turn create the 23 chromosome pairs which make up a human being’s genetic code. The initial draft sequence of the human genome was unveiled by Celera Genomics and the International Human Genome Sequencing Consortium…

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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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Towards CRISPR/Cas9-based gene drive in the diamondback moth Plutella xylostella

Abstract Promising to provide powerful genetic control tools, gene drives have been constructed in multiple dipterans, yeast and mice, for the purposes of population elimination or modification. However, it remains unclear whether these techniques can be applied to lepidopterans. Here, we used endogenous regulatory elements to drive Cas9 and sgRNA…

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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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Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach

Abstract The acute respiratory disease induced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing…

Continue Reading Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach

Protein complex prediction with AlphaFold-Multimer

Abstract While the vast majority of well-structured single protein chains can now be predicted to high accuracy due to the recent AlphaFold [1] model, the prediction of multi-chain protein complexes remains a challenge in many cases. In this work, we demonstrate that an AlphaFold model trained specifically for multimeric inputs…

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Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)

Hi all, I am a PhD student with biology background. I recently inherit a RNA Sequencing project from another PhD student in my lab. We already have paired-ended RNA-Seq data generated from Illumina HiSeq but haven’t started analysis yet. I have basic Linux command line training but have no idea about how…

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Encounter networks from collective mitochondrial dynamics support the emergence of effective mtDNA genomes in plant cells

Abstract Mitochondria in plant cells form strikingly dynamic populations of largely individual organelles. Each mitochondrion contains on average less than a full copy of the mitochondrial DNA (mtDNA) genome. Here, we asked whether mitochondrial dynamics may allow individual mitochondria to ‘collect’ a full copy of the mtDNA genome over time,…

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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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Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

B.1.620 carries numerous VOC mutations and deletions Lineage B.1.620 attracted our attention due to large numbers of unique mutations in B.1.620 genomes from Lithuania in nextclade analyses (its genomes are 18 mutations away from nearest relatives and 26 from reference strain Wuhan-Hu-1), and those genomes initially being assigned to clade…

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Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such…

Continue Reading Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

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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A structural biology community assessment of AlphaFold 2 applications

Abstract Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods have led to protein structure predictions that have reached the accuracy of experimentally determined models. While this has been independently verified, the implementation of these…

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Genetically controlled mtDNA editing prevents ROS damage by arresting oxidative phosphorylation

Abstract Deletion of mitochondrial DNA in eukaryotes is mainly attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show…

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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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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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Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids

%PDF-1.4 % 184 0 obj > endobj 214 0 obj >stream 2021-08-22T18:54:41Z Word 2021-09-20T19:56:12-07:00 2021-09-20T19:56:12-07:00 macOS Version 11.2 (Build 20D64) Quartz PDFContext application/pdf Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids uuid:87bd5868-1dd2-11b2-0a00-480827fd5800 uuid:87bd5872-1dd2-11b2-0a00-6a0000000000 endstream endobj 5 0 obj > endobj 2 0 obj > endobj 53 0 obj >…

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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Dissemination of Mycobacterium abscessus via global transmission networks

Dataset construction, cluster identification and definition of DCCs Whole genome sequencing of two collections of isolates from Manchester, UK, and the Netherlands was carried out as previously described2. Briefly, DNA was extracted from colony sweeps of subcultured samples before to paired-end sequencing using the Illumina HiSeq platform. These samples were…

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Is a variant worse than Delta on the way? Viral evolution offers clues.

Somewhere in India last October, a person—likely immunocompromised, perhaps taking drugs for rheumatoid arthritis or with an advanced case of HIV/AIDS—developed COVID-19. Their case might have been mild, but because of their body’s inability to clear the coronavirus it lingered and multiplied. As the virus replicated and moved from one…

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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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87885890

%PDF-1.4 % 1 0 obj > endobj 5 0 obj >stream 2021-09-15T23:59:23-07:00 2021-09-15T09:20:35-07:00 2021-09-15T23:59:23-07:00 Appligent AppendPDF Pro 5.5 uuid:95810202-b239-11b2-0a00-782dad000000 uuid:cfca0722-1dd1-11b2-0a00-d30068a2a7ff application/pdf 87885890 caroline Trumpff macOS Version 10.15.7 (Build 19H2) Quartz PDFContext AppendPDF Pro 5.5 Linux Kernel 2.6 64bit Oct 2 2014 Library 10.1.0 endstream endobj 2 0 obj > endobj 3…

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Dynamic behavior of cell-free mitochondrial DNA in human saliva

Abstract Mitochondria release their genome as cell-free mitochondrial DNA (cf-mtDNA) in multiple biofluids including in the blood, where it predicts mortality and is a marker of mental and physical stress. Here we report cf-mtDNA in human saliva, an accessible biofluid used to study dynamic neuroendocrine changes. To map the natural…

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Structural basis for mismatch surveillance by CRISPR/Cas9

Abstract The widespread use of CRISPR/Cas9 as a programmable genome editing tool has been hindered by off-target DNA cleavage (Cong et al., 2013; Doudna, 2020; Fu et al., 2013; Jinek et al., 2013). While analysis of such off-target editing events have enabled the development of Cas9 variants with greater discrimination…

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A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

Abstract Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICE) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanism such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of…

Continue Reading A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

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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Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus

Uniparental genetic background of the Segorbe Giant We confirmed that the individual was genetically male (RY > 0.077; Supplementary Fig. S3), and both his uniparental markers point towards North African origins (Supplementary Table S2). He belongs to mtDNA haplogroup U6a1a1a (nomenclature according to Hernández et al.28). Although U6 in general, and U6a in…

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AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Abstract Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a dominant phasing method for the crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database for finding suitable templates for phasing. However,…

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Combining CRISPR/Cas9 and brain imaging: from genes to proteins to networks

Abstract Understanding how functional connections between brain regions are arranged and influenced by genes, in the healthy and diseased states, is a major goal in neuroscience. Functional connectivity alterations are linked to molecular changes in several neurodegenerative disorders and could serve as early markers of pathology. Yet, the underlying molecular…

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Methylothon: a versatile course-based high school research experience in microbiology and bioinformatics– with pink bacteria

Abstract Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here we present an overview of the module’s learning goals, describe course resources (available for public use on methylothon.com), and relate lessons learned from adapting Methylothon for…

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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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getting different value list from GATK gc content and CANOES

getting different value list from GATK gc content and CANOES 0 I was trying to run codes from this paper “A machine-learning approach for accurate detection of copy-number variants from exome sequencing” I need to get data from GATK GC content and CANOES and combined them, but I got a…

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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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CRISPR-Cas9 bends and twists DNA to read its sequence

Abstract In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide-RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that…

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A copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana.

Abstract CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana…

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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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BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

Abstract Genomics researchers do better work when they can interactively explore and visualize data. However, due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and…

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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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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor

Abstract Summary: SpatialExperiment is a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardized operations, and comprehensive documentation. Here, we demonstrate the structure and user interface with examples from the 10x Genomics Visium and seqFISH platforms,…

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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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What’s Wrong With Limiting Transformers To Just Language Models

Three years back, Google introduced Transformer, a novel neural network architecture. Modelled on the self-attention mechanism and best suited for language understanding, transformers could outperform both recurrent and convolutional neural network models.  Transformers perceive the entire input sequences simultaneously. The process depends on transforming one sequence into another, like the…

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Inferring CNVs from BAM files with SAMTools depth

Inferring CNVs from BAM files with SAMTools depth 0 Hello, I want to detect CNVs from BAM files (from a batch and one BAM file independently), I read a couple of posts about it, I read about recent tools: biorxiv review and Nature review. Read-depth is the most common approach…

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The Drug Discoverer – Reflecting on DeepMind’s AlphaFold artificial intelligence success – what’s the real significance for protein folding research and drug discovery?

Last month, DeepMind published the much anticipated, detailed methodology underlying the latest version of AlphaFold – the UK-based science company’s powerful AI system that blew away its rivals in the latest major competition to predict the 3D structure of proteins. AlphaFold’s machine learning methodology has been applied to predict structures…

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