Tag: bioRxiv

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…

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….

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…

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 …

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…

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…

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….

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,…

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…

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…

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)…

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,…

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…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

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 …

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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)….

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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)…

(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…

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…

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…

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 …

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…

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…

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…

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…

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…

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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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…

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…

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…

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)…

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…

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…

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…