(PDF) RFLP analysis in 5 Sicilian families with the fragile X syndrome

(PDF) RFLP analysis in 5 Sicilian families with the fragile X syndrome | William Brown – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience.By using our site, you agree to our collection of information through the use of cookies.To learn more, view our Privacy Policy….

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Entheon Biomedical Subsidiary, HaluGen Life Sciences, Announces Agreement with Psychedelics Today

Expanding brand awareness and access to HaluGen’s Psychedelics Genetic Test Kit Vancouver, British Columbia–(Newsfile Corp. – January 18, 2022) – Entheon Biomedical Corp. (CSE: ENBI) (OTCQB: ENTBF) (FSE: 1XU1) (“Entheon” or the “Company“), a biomedical company focused on the research and development of psychedelic drugs and leading-edge biomarkers to provide…

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Simplify your life with SLURM and sync

For my first blog post of the year, we’re talking about SLURM, everyone’s favorite job manager. If like me, you have the joy of running a literal boat-load of jobs with all kinds of parameters and command-line arguments you’ll know there are a few tips and tricks that make the…

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Gst-nvivafilter – Jetson AGX Xavier

Platforms: Jetson AGX Xavier Jetpack 4.5 Cuda 10.2 IMX274 camera Hi fellow developers, I am having difficulties at making custom CUDA implementation. I have succesfully run the below pipeline. gst-launch-1.0 nvarguscamerasrc ! ‘video/x-raw(memory:NVMM), width=(int)3840, height=(int)2160, format=(string)NV12, framerate=(fraction)60/1’ ! nvivafilter cuda-process=true customer-lib-name=”libnvsample_cudaprocess.so” ! ‘video/x-raw(memory:NVMM), format=(string)NV12’ ! nvvidconv ! nvegltransform ! nveglglessink…

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Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease

This article was originally published here Brief Bioinform. 2022 Jan 17:bbab554. doi: 10.1093/bib/bbab554. Online ahead of print. ABSTRACT Health outcomes are frequently shaped by difficult to dissect inter-relationships between biological, behavioral, social and environmental factors. DNA methylation patterns reflect such multivariate intersections, providing a rich source of novel biomarkers and…

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Coul MSM – Segmentation Fault – LAMMPS Development

Without root access you cannot install gdb or valgrind from a package repository, but you can still install them by compiling from source. It is not too difficult, especially gdb. It just takes a little time. But the gdb information can make up for the time invested quickly. Please note…

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What is the file format of file provided with option -sf in gmx gangle/select/distance etc commands – User discussions

For posterity, gmx help selections syntax returns this as the first item described: A set of selections consists of one or more selections, separated by semicolons. Each selection defines a set of positions for the analysis. Each selection can also be preceded by a string that gives a name for…

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linux – How to fix Perl from anaconda not installing bioperl? Bailing out the installation for BioPerl

vep -i examples/homo_sapiens_GRCh38.vcf –database Can’t locate Bio/PrimarySeqI.pm in @INC (you may need to install the Bio::PrimarySeqI module) (@INC contains: /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/modules /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0 /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2 /home/youssef/anaconda3/envs/ngs1/lib/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/5.26.2 .) at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. Compilation failed in require at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm…

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Installing Bioconductor packages error –> Error in readRDS(dest) : error reading from connection

I have been trying to install Bioconductor in R (version 4.0.5). Each time I try to insert the following code, I get some error like: >if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(version = “3.12”) ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.csiro.au/ Bioconductor version 3.12…

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[P] I trained every single SOTA from 2021 and accidentally got a silver medal on Kaggle

Web: [P] I trained every single SOTA from 2021 and accidentally got a silver medal on Kaggle from MachineLearning Jan. 18, 2022, 8:29 a.m. | /u/yamqwe Machine Learning reddit.com ![](i.ibb.co/gwpJXBm/lb.png) I trained every single SOTA model from 2021 and accidentally got a silver medal on an image classification competition on…

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rna seq – How does DESeq2 “collapseReplicates” work on read counts data?

Comparing read counts from an RNA-seq experiment for a couple select genes before and after using DESeq2’s collapseReplicates function yields interesting results: Before: Geneid foo1.1 foo1.2 foo2.1 foo2.2 foo3.1 foo3.2 bar1.1 bar1.2 bar2.1 bar2.2 bar3.1 bar3.2 baz1.1 baz1.2 baz2.1 baz2.2 baz3.1 baz3.2 WASH7P 6 5 0 2 7 3 1…

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Online faculty development programme begins

It is essential for faculty members to update their knowledge with cutting edge tools and techniques to motivate younger minds towards science and technology, said N. Kalaiselvi, Director, CSIR – CECRI, here on Monday. She was presiding over a five-day online Faculty Development Programme (FDP) organised by the Departments of…

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Convert list of Accession Numbers to Full Taxonomy

Using NCBI Entrez direct. $ esearch -db assembly -query “GCA_000005845” | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F “>|<” ‘BEGIN{ORS=”, “;}{print $3;}’ Escherichia coli str. K-12 substr. MG1655, cellular organisms, Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K-12, If…

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FASTA Sequences for mutant alleles : bioinformatics

Background: I’m trying to run AlphaFold on an ACT1 allele in yeast e.g. www.yeastgenome.org/allele/act1-105. It has been sequenced, and it has two known amino-acid mutations (E311A, R312A).  My question is: Is there a database that has the .fasta sequence for such alleles, which include the mutations? I can get the fasta sequence…

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Theme text size vs. annotation text size. – ggplot2

A journal to which I am submitting a paper requires that all plot text, including annotation text, should be the same size. I recognize that the units for text size in the theme definitions (points as in font size) are different from the units for text size in annotations (mms)….

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r – ggplot add horizontal line to grouped categorical data and share legend

I think for readability, it’s better to separate them out. However, for formatting purpose, you sure can bring them as close as you want by dropping the legend.title (not just assigning it an empty string) and adjusting the legend.margin and legned.spacing. For instance, library(tidyverse) data(mtcars) y = mean(mtcars$mpg) x =…

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Expression of the DNA repair gene XRCC1 in baboon tissues

doi.org/10.1016/0165-7992(95)00053-4Get rights and content Abstract XRCC1 is a DNA repair gene involved in rejoining DNA strand-breaks. We used baboon as an animal model to determine the levels of XRCC1 gene expression in different tisues. Baboons were selected because they are evolutionarily closely related to humans. A single 2.2 kb transcript…

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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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Got `AttributeError` from `from_pymc3` of ArviZ

You are passing return_inferancedata=True to pm.sample(), which according to the PyMC3 documentation will return an InferenceData object rather than a MultiTrace object. return_inferencedatabool, default=False Whether to return the trace as an arviz.InferenceData (True) object or a MultiTrace (False) Defaults to False, but we’ll switch to True in an upcoming release….

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Phihlikevirus

Phihlikevirus (synonym: PhiH-like viruses) is a genus of viruses in the order Caudovirales, in the family Myoviridae. Bacteria and archaea serve as natural hosts. There is currently only one species in this genus: the type species Halobacterium phage phiH.[1][2] Taxonomy Group: dsDNA [2] Structure Phihlikeviruses are nonenveloped, with a head…

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Functioning induced liver cells from skin tissue

Figure 1. Urea metabolism is impaired in patient-derived human-induced pluripotent stem cells (hiPSCs) differentiated into hepatocytes (hiPSC-Heps). (A) Scheme showing the urea cycle detoxifying ammonia (NH4+) into nontoxic urea in five consecutive urea cycle enzyme (UCE)–mediated reactions in mitochondria in hepatocytes. (B) Urea secretion in four control hiPSC-Hep lines (Ctrl_1-4)…

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Accepted drop-seq 2.5.1+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 16 Jan 2022 16:45:58 +0100 Source: drop-seq Architecture: source Version: 2.5.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: drop-seq (2.5.1+dfsg-1) unstable; urgency=medium . * New upstream version * Add missing build dependency…

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A guide to analysing binding sites in protein structures

This webinar gives an introduction to the information required to effectively interpret ligand binding sites in protein structures. It will highlight tools available at the Protein Data Bank in Europe (PDBe) and PDBe Knowledge Base (PDBe-KB) to analyse ligand binding pockets and interactions. It will also highlight how this information…

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Software Engineer – Python and Pytorch

Computer Vision Researcher / Research Scientist – 12 month contract This is a unique opportunity to snap up very quickly. Our client is a leading technology firm looking to hire a recent graduate / post doc graduate. An ideal role for a newly qualified individual looking to gain experience within…

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What are the likely causes of Breast Implant Associated Anaplastic Large Cell Lymphoma (BIA-ALCL)?

Available online 16 January 2022 doi.org/10.1016/j.jpra.2021.11.006Get rights and content Abstract Breast implant–associated anaplastic large cell lymphoma (BIA-ALCL) is a CD30-positive, anaplastic lymphoma kinase–negative T-cell lymphoma. Where implant history is known, all confirmed cases to date have occurred in patients with exposure to textured implants. The etiopathogenesis of BIA-ALCL is likely…

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SUPPRESSION OF DIALYSIS PATIENTS’ LYMPHOCYTE IL-2R EXPRESSION BY GLUCOCORTICOIDS AND CYCLOSPORINE

Previous studies have shown interindividual heterogeneity in the suppressive effects of glucocorticoids and cyclosporine (CsA) on the proliferation responses of dialysis patients’ peripheral blood mononuclear cells (PBMC). In addition, methylprednisolone (MP) was shown to be significantly more suppressive than prednisolone (P), and PBMC from patients on peritoneal dialysis (PD) were…

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Intraspecies variability of the 16S rRNA gene of the soil bacteria Acinetobacter lwoffii and Paenibacillus taichungensis

Anastasiya Nechayeva, Konstantin Boyarshin*, Olga Bespalova, Viktoriia Iatsenko, Evgeniy Seliverstov, Violetta Klyueva and Olesya Makanina The functioning of well-studied key groups of soil microorganisms depends on the microbial ecosystem in which they function in interaction with species belonging to other ecological groups. An analysis of the composition of the soil…

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python – DeprecationWarning when importing Scikit-learn

I’m using JupyterLab. When importing some packages, or executing some functions from scikit-learn, very long list of deprecation warnings fill the screen. I googled about this problem and upgraded the packages (scikit-learn, numpy), but I still get the warnings. pip install scikit-learn –upgrade Requirement already satisfied: scikit-learn in c:users…appdatalocalprogramspythonpython39libsite-packages (1.0.2)…

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A Clinical and Immunohistochemical Study

Diffuse large B cell lymphoma is the most common type of lymphoma in Egypt with an unfavorable prognosis. The tumor microenvironment is rich in immune response either T cells or macrophages. The current study is aimed at testing CD4, CD8, CD68, and MMP9 immunohistochemistry of DLBCL activities with the prognosis…

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[slurm-users] Questions about scontrol reconfigure / reconfig

Hello, I have some questions about adding nodes in configless mode. My version of SLURM is 21.08.5. I gave logs below to ease the read of the message. First, is “scontrol reconfigure” equal to “scontrol reconfig” ? Then, I have a strange behaviour at node addition. I have an healthy…

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A Study on Polymorphism of Mitochondrial DNA (mtDNA) in Populations of D.virilis Distributing in Chinese Continent

JIA Zhen-yu, ZHU Ding-liang, GENG Zhen-cheng, T.Aotsuka. A Study on Polymorphism of Mitochondrial DNA (mtDNA) in Populations of D.virilis Distributing in Chinese Continent. Zoological Research, 1995, 16(1): 65-73. Citation: JIA Zhen-yu, ZHU Ding-liang, GENG Zhen-cheng, T.Aotsuka. A Study on Polymorphism of Mitochondrial DNA (mtDNA) in…

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repo/gentoo.git – Official Gentoo ebuild repository

dev-java/cpptasks: Fix Javadoc generation on JDK 11+HEADmaster The ‘javadoc’ program shipped in JDK 11+ requires all classes used by the input source files to be present in the classpath passed to it. This has caused numerous other bugs alike, including 780531, 788109, and 820863. Closes: bugs.gentoo.org/831294 Signed-off-by: Yuan Liao <liaoyuan@gmail.com>…

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Kokkos and SNAP work in support of EXAALT and LAMMPS. (Conference)

Moore, Stan Gerald. Kokkos and SNAP work in support of EXAALT and LAMMPS.. United States: N. p., 2020. Web. Moore, Stan Gerald. Kokkos and SNAP work in support of EXAALT and LAMMPS.. United States. …

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Building Modified DNA topology – User discussions

GROMACS version: 2021.4GROMACS modification: Yes/NoHere post your question I am having trouble generating topology for a type of modified DNA, but I’m not sure how to do it.In fact, there is a 35-nucleotide sequence of ssDNA. Using the Discovery Studio program, I converted the Thymidine Oxygen 4 atom to Sulfur…

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man Bio::MapIO::mapmaker (3): A Mapmaker Map reader

Bio::MapIO::mapmaker(3) A Mapmaker Map reader SYNOPSIS # do not use this object directly it is accessed through the Bio::MapIO system use Bio::MapIO;my $mapio = Bio::MapIO->new(-format => “mapmaker”,-file => “mapfile.map”);while ( my $map = $mapio->next_map ) { # get each mapforeach my $marker ( $map->each_element ) {# loop through the markers…

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WaiMasterClass Event 2 – [Kaggle for Data Scientists] Tickets, Sat, Jan 29, 2022 at 10:00 AM

Welcome from WaiMasterClass 2022 by Women in AI Myanmar! Women in AI Myanmar is hosting WaiMasterClass DataScience Series in 2022. There will be a total of 4 classes for this WaiMasterClass DataScience Series. This is our second event in Datascience series. In event 2, Aye Hninn Khine and Cho Zin…

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DESeq2 input from GDAC firehose

Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…

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cnetplot: How to control the size of the legend gene number and log2FC

Hi, Does not matter what I do, the legend saying “gene number” and “log2FC” overlaps all the time with the actual plot I tried different parameters of the cnetplot function and also tried to modify the plot after storing the plot to a variable but I do not find the…

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2096: Symmetric Trimer Design with AlphaFold Predictions

2096: Symmetric Trimer Design with AlphaFold Predictions Status: Active Name: 2096: Symmetric Trimer Design with AlphaFold Predictions Status: Active Created: 01/15/2022 Points: 100 Expires: 01/21/2022 – 23:00 Difficulty: Intermediate Description: Design a symmetric protein trimer, with 3 identical…

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Senior Manager, Bioinformatics and Genomics Data Scientist

Job Description Do you want to be part of an inclusive team that works to develop innovative therapies for patients? Every day, we are driven to develop and deliver innovative and effective new medicines to patients and physicians. If you want to be part of this exciting work, you belong…

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Download full list of SNPs and their coordinates in hg38

Download full list of SNPs and their coordinates in hg38 3 What is the best / standard place to get a full list of SNPs and their coordinates in hg38? I downloaded the SNPsnap database, but just realized that those coordinates are in hg19. I’m trying to figure out how…

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Openings in Medical Coding For Biomed, Biotech & Bioinformatics Grads | Yamunai Nagar, Chennai

Job Details LocalitiesYamunai Nagar, Wimco Nagar, West Tambaram, Karappakam, Kaladipet Sub RolesBio-Technology Job ID357911341 RoleMicrobiologist Hiring Company NameAchievers Spot Max Experience1 Min Experience0 Description Medical Coding is the process of converting Verbal Descriptions into numeric or alpha numeric by using ICD 10-CM, CPT & HCPCS. As per HIPAA rules healthcare…

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Postdoctoral Fellow – Plant Genomics & Bioinformatics – Fort Collins

Working Title Postdoctoral Fellow – Plant Genomics & Bioinformatics Position Location Fort Collins, CO Research Professional Position Yes Posting Number 202101543AP Position Type Admin Professional/ Research Professional Classification Title Postdoctoral Fellows Number of Vacancies Work Hours/Week 40 Proposed Annual Salary Range $50,000-$59,000. Salary is commensurate with experience and qualifications. Employee…

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Intern- Bioinformatics – Foster City

Gilead Sciences is continuing to hire for all open roles. Our interview process may be conducted virtually and some roles will be asked to temporarily work from home. Over the coming weeks and months, we will be implementing a phased approach to bringing employees back to site to ensure the…

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biopython – Help to create a dataframe in Python from a FASTA file

I want to create a dataframe in Python starting from a FASTA format file. Given the toy FASTA file that I am attaching, I built this program in Python that returns four colums corresponding to id, sequence length, sequence, animal name and rows corresponding to all the data available. However,…

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Tutorial on Box Plot in ggplot2 with Examples – MLK

Introduction Boxplots are a useful visualization technique to understand the distribution and outliers in a dataset. In this article, we will go through the tutorial for box plot in ggplot2 function of R which is a popular visualization package. We will first understand the syntax of ggplot2 function geom_boxplot() for…

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Error on final object when generating ggplot objects in for loop with dplyr select()

I want to make many plots using multiple pairs of variables in a dataframe, all with the same x. I store the plots in a named list. For simplicity, below is an example with only 1 variable in each plot. Key to this function is a select() call that is…

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Bayesian Open Source Software for Biomedicine: Stan, ArviZ and PyMC3

Back to Proposal List Projects PyMC, ArviZ, Stan Lead Christopher Fonnesbeck (NumFOCUS) Funding Cycle 4 Proposal Summary To develop key infrastructure updates and collaboration resources for state-of-the-art Bayesian modeling software libraries. Project PyMC PyMC3 is the current version of the PyMC open source probabilistic programming framework for Python, having been…

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php-openapi make implementations of built-in interfaces PHP 8.1 friendly

Problem Unfortunately, PHP 8.1 throws Fatal Error if the built-in interface implementation is incompatible with the new, type enhanced interfaces. Example error: Fatal error: During inheritance of ArrayAccess: Uncaught Return type of cebeopenapispecResponses::offsetExists($offset) should either be compatible with ArrayAccess::offsetExists(mixed $offset): bool, or the #[ReturnTypeWillChange] attribute should be used to temporarily…

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r – I can’t load libraries into Rstudio

Summary of problem: I install packages successfully but my libraries will not load. This problem has only happened recently. What steps have I taken?: I uninstalled and reinstalled Rstudio. I uninstalled and reinstalled the packages I want while setting dependencies = TRUE. Whenever I try to load the library of…

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ChIPseq annotation with replicates

ChIPseq annotation with replicates 0 Hi, What’s the best way to annotate chip peaks in case of replicates? I have 3 replicates each group. I understand Chipseeker is a very convenient tool, but I can’t find a clear example of how to merge replicates and annotate the peaks for visualization?…

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Critical assessment of pan-genomics of metagenome-assembled genomes

Abstract Background: Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation,…

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Optical Coherence Tomography Based Biomechanical Fluid-Structure Interaction Analysis of Coronary Atherosclerosis Progression

There is a need to determine which atherosclerotic lesions will progress in the coronary vasculature to guide intervention before myocardial infarction occurs. This article outlines the biomechanical modeling of arteries from Optical Coherence Tomography using fluid-structure interaction techniques in a commercial finite element solver to help predict this progression. Atherosclerosis…

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Establishment of serum-free adapted Chinese hamster ovary cells with double knockout of GDP-mannose-4,6-dehydratase and GDP-fucose transporter

Aggarwal RS (2014) What’s fueling the biotech engine-2012 to 2013. Nat Biotechnol 32:32–39. doi.org/10.1038/nbt.2794 CAS  Article  PubMed  Google Scholar  Becker DJ, Lowe JB (2003) Fucose: biosynthesis and biological function in mammals. Glycobiology 13:41–53. doi.org/10.1093/glycob/cwg054 CAS  Article  Google Scholar  Chan KF, Shahreel W, Wan C et al (2016) Inactivation of GDP-fucose…

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Plink2.0 unrecognized flag: –het

Plink2.0 unrecognized flag: –het 1 Hi, I’m trying to run plink2.0 to calculate heterozygosity ratio, through the command: plink2.0 –pfile myFile –het but I receive this error: Error: Unrecognized flag (‘–het’) I honestly don’t have any clou about it and about it’s not recognized by plink2.0 as flag. Has this…

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Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma

Interrogation of cell-free DNA (cfDNA) represents an emerging approach to non-invasively estimate disease burden in multiple myeloma (MM). Here, we examined low-pass whole genome sequencing (LPWGS) of cfDNA for its predictive value in relapsed/ refractory MM (RRMM). We observed that cfDNA positivity, defined as ≥10% tumor fraction by LPWGS, was…

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links to Ensembl GRCh37 – gitmetadata

Open Targets Genetics reports GRCh38 coordinates but ‘External references” section points to GRCh37 (grch37.ensembl.org) rather than GRCh38 (www.ensembl.org): genetics.opentargets.org/variant/8_102432699_T_C Was this a deliberate decision (e.g. we don’t have the rsID in GRCh38 for some reason, other)? If so, we need to make this clear in the docs. If not, we…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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SCHNAPPs – Single Cell sHiNy APPlication(s)

Abstract : Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed…

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python – One Hot Encoding: Avoiding dummy variable trap and process unseen data with scikit learn

I’m building a model, pretty much similiar to the well known House Price Prediction. I got to the point that I need to encode my nominal categorical variables by using scikit-learns OneHotEncoder. The so called “Dummy Variable Trap” is clear to me so I need to drop one of my…

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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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Applications of iPSCs in Gaucher Disease and other rare sphingolipidoses

Chapter contents Book contents Volume 16 in Advances in Stem Cell Biology 2022, Pages 197-224 doi.org/10.1016/B978-0-323-85767-3.00001-3Get rights and content Abstract In this chapter, an overview of various applications of induced pluripotent cells (iPSCs) is given. This chapter focuses on the uses of iPSCs in inherited diseases and, particularly, in the…

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FGFR2 signaling enhances the SHH-BMP4 signaling axis in early ureter development

The patterned array of basal, intermediate and superficial cells in the urothelium of the mature ureter arises from uncommitted epithelial progenitors of the distal ureteric bud. Urothelial development requires signaling input from surrounding mesenchymal cells, which, in turn, depend on cues from the epithelial primordium to form a layered fibro-muscular…

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Ubuntu Manpage: samtools reheader – replaces the header in the input file

Provided by: samtools_1.13-2_amd64 NAME samtools reheader – replaces the header in the input file SYNOPSIS samtools reheader [-iP] [-c CMD | in.header.sam ] in.bam DESCRIPTION Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default…

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[slurm-users] Strange sbatch error with 21.08.2&5

Running test job with srun works: wayneh@login:~$ srun -G16 -p v100 /home/wayne.hendricks/job.sh 179851 Linux dgx1-1 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 179851 Linux dgx1-2 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Submitting the same with sbatch does…

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Why is mtDNA maternal only? : explainlikeimfive

Mitochondria are kind of like an in-between of cell-organelles and bacteria that live in your cells. They are not made by your cells, but they replicate on their own (by splitting in two). For this, they use their own DNA (the mtDNA), not the DNA of your cells. When an…

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Unable to convert from sam to bam file.

Unable to convert from sam to bam file. 0 samtools view -S -b BD143_TGACCA_L005.sam -o BD143_TGACCA_L005.bam When I am running this command the following error is appearing: [main_samview] fail to read the header from “BD143_TGACCA_L005.sam”. As a result, if anyone knows how to fix this error and thanks. converting File…

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Applying manybody potential in Hybrid pair style – #4 by pranavkumar – LAMMPS General Discussion

pranavkumar: It will be great if you can quickly comment Bogus, too. You are ignoring core properties of the EAM model: every time you use multiple EAM pair styles in a hybrid setup, the embedding term will be incorrectly computed. Each instance will compute and apply only the contributions from…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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man Bio::Root::Version (3): provide global, distribution-level versioning

Bio::Root::Version(3) provide global, distribution-level versioning SYNOPSIS package Bio::Tools::NiftyFeature;require Bio::Root::RootI;# later, in client code:package main;use Bio::Tools::NiftyFeature 3.14;## alternative usage: NiftyFeature defines own $VERSION:package Bio::Tools::NiftyFeature;my $VERSION = 9.8;# later in client code:package main;# ensure we’re using an up-to-date BioPerl distributionuse Bio::Perl 3.14;# NiftyFeature has its own versioning scheme:use Bio::Tools::NiftyFeature 9.8; DESCRIPTION This…

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Python For Machine Learning (ML) Course

Course Instructor: Fabio Mardero is a data scientist from Italy. He graduated in physics and statistical and actuarial sciences. He is currently working at a well-known Italian insurance company as a data scientist and Non-Life technical provisions evaluator.  Course Overview & Lectures Duration: 14+ hours Project Insurance Project Italian COVID dataset (official…

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Job Application for Director, Bioinformatics Applications at Recursion

Recursion is a clinical-stage biotechnology company decoding biology by integrating technological innovations across biology, chemistry, automation, data science and engineering to radically improve the lives of patients and industrialize drug discovery. Our team is working to solve some of the hardest, most meaningful problems facing human health today. Come join…

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Obs_name

Obs_name 0 Can someone please help explain what the Obs_name represents? I exported the anndata matrix (h5ad) and attempted to transform it to the Seurat object using something similar to the following: exprs <- t(adata$X) colnames(exprs) <- adata$obs_names$to_list() rownames(exprs) <- adata$var_names$to_list() # Create the Seurat object seurat <- CreateSeuratObject(exprs) #…

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Strangely too low P-value and Adjusted P-value(FDR) DESeq2 and edgeR

My data is experimental data that has been overexpressed for a specific gene. Data samples are divided into 3 groups according to the over-expression time and each group has 3 samples. (total 9 samples) I conducted DGE analysis on the control group and one case group with DESeq2. cts <-…

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File:Alpha fold model for DmBCA – Drosophila melanogaster.png

No higher resolution available. Summary DescriptionAlpha fold model for DmBCA – Drosophila melanogaster.png English: This is an alpha fold model of the beta class Carbonic Anhydrase enzyme DmBCA from the invertebrate Drosophila melanogaster. Date 17 December 2021 Source alphafold.ebi.ac.uk/entry/Q9VHJ5 Author AlphaFold Data Copyright (2021) DeepMind Technologies Limited. Jumper, J et…

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Top Quantum Computing Jobs to Apply for in January 2022

Quantum computing has emerged as an interesting career option in recent years Experts believe that quantum computing can change the world. It possesses the capabilities of revolutionizing the drug discovery process, facilitating deciphering codes for security purposes, and so much more. Currently, it is safe to say that quantum computing…

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Postdoctoral Position, PostDoc II in Evolutionary Ecology job with MASARYK UNIVERSITY

Department: Department of Botany and Zoology – Faculty of Science Deadline: 6 Feb 2022 Start date: 1.3.2022 (date is negotiable) Job type: full-time Job field: Science and research Bursar of the Faculty of Science, Masaryk University announces an open competition for the position Postdoctoral position (PostDoc II) in Evolutionary Ecology, Department of Botany and Zoology, Faculty of Science,…

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Bioinformatics Specialist Job Opening in Aliso Viejo, CA at Ambry Genetics

JOB OVERVIEW: The main role of this position is project coordination, timeline management, and requirement gathering. To this end, the Bioinformatics Specialist analyzes and refines business and user requirements, and coordinates with developers to facilitate bioinformatics solutions through the entire SDLC, from discovery, design, development, and validation. The Bioinformatics Specialist…

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Genetic strategies reverse pesticide resistance

Nature Communications i>In a new empirical study published in, a gene drive designed to bias heredity, called an allelic drive, was applied without pesticide treatment to create natural-level insects that were balanced with pesticide susceptibility. Population that has been shown to be recoverable. Credits: Bier Lab, University of California, San…

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Research Manager Jobs – Apply Online at jobs.ac.uk

From academic, teaching and research jobs to managerial and support roles, jobs.ac.uk advertises for over 7,000 organisations worldwide including: universities, research institutes, colleges, charities and commercial organisations. Refine your Research Manager jobs search This is just a selection of jobs that are currently available on jobs.ac.uk, to see all a…

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samtools sort

samtools sort 1 I am transforming sam files to bam, to facilitate their ordering I use this command, % cd /Volumes/GENOMA/BWA % samtools sort -n -O V350019555_L03_B5GHUMqcnrRAABA-551.sam | samtools fixmate -m -O bam V350019555_L03_B5GHUMqcnrRAABA-551.bam but it gives me the following error, As elsewhere in samtools, use ‘-‘ as the filename…

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ggplot2 – R knitr Markdown: Output Plots within For Loop

I am using child Rmd files in markdown, also works in sweave. in Rmd use following snippet: “`{r run-numeric-md, include=FALSE} out = NULL for (i in c(1:num_vars)) { out = c(out, knit_child(‘da-numeric.Rmd’)) } “` da-numeric.Rmd looks like: Variabele `r num_var_names[i]` ———————————— Missing : `r sum(is.na(data[[num_var_names[i]]]))` Minimum value : `r min(na.omit(data[[num_var_names[i]]]))`…

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apache spark – Pyspark kernel in jupyterhub, access to master remotely

i have two kernels for Spark, one to run locally and one to run towards a cluster. Is there a way to set an environment variable to my spark master so that users dont have to define master in SparkContext in the kernel which is to speak with the spark…

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how to make 2d rendering on directx 11 more faster – Graphics and GPU Programming

I make an editor for own game engine and I used for 2d rendering Direct2D but I wanted to render a directx texture on window in editor, I didn’t find convenient way to convert directx texture to direct2d bitmap. I decided to make own 2d render on directx 11 and…

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java – OpenApi Generator to generate parameter with @RequestBody as String

I have the following OpenApi specs: paths: /student: post: requestBody: required: true content: application/json: schema: $ref: “#/components/schemas/Student” responses: 204: components: schemas: Student: type: object properties: name: type: string school: type: string With org.openapitools.generator, it generates a controller with function like below void addStudent(@RequestBody Student student) { } Is there any…

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How to perform deconvolution with RPKM values

Hi Xuran, I tried to apply MuSiC to RNAseq bulk data with RPKM as the input. According to your paper(Discussion), “MuSiC can utilize RPKM if estimates of cell type-specific total RNA abundance can be provided.” I am wondering how I can incorporate cell-type-specific total RNA abundance into your function? Or…

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Process Development for the Production and Purification of Adeno-Associated Virus (AAV)2 Vector using Baculovirus-Insect Cell Culture System

In this protocol, AAV2 vector is produced by co-culturing Spodoptera frugiperda (Sf9) insect cells with baculovirus (BV)-AAV2-green fluorescent protein (GFP) or therapeutic gene and BV-AAV2-rep-cap infected Sf9 cells in suspension culture. AAV particles are released from the cells using detergent, clarified, purified by affinity column chromatography, and concentrated by tangential…

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RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

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Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression

Significance Tools that afford spatiotemporal control of gene expression are crucial for studying genes and processes in multicellular organisms. Stop cassettes consist of exogenous sequences that interrupt gene expression and flanking site-specific recombinase sites to allow for tissue-specific excision and restoration of function by expression of the cognate recombinase. We…

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A one-pot CRISPR/Cas13a-based contamination-free biosensor for low-cost and rapid nucleic acid diagnostics

Available online 13 January 2022, 113994 doi.org/10.1016/j.bios.2022.113994Get rights and content Highlights • A one-pot CRISPR/Cas13a-based visual biosensor for the rapid and low-cost nucleic acid detection is proposed. • With a newly developed tube-in-tube vessel used in the biosensor, aerosol cross contamination could be completely avoided. • The sensor can not…

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Identification of a regulatory pathway inhibiting adipogenesis via RSPO2

Integration of APC scRNA-seq data reveals heterogeneity of adipocyte progenitor cells In a previous study9, we defined Lin−Sca1+CD142+ APCs as adipogenesis regulatory (Areg) cells and demonstrated that these cells are both refractory toward adipogenesis and control adipocyte formation of APCs through paracrine signaling. In contrast, Merrick et. al.4 observed that Lin−CD142+ cells…

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ChromHMM | SCAI

ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence…

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R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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Long non-coding RNA MSTRG.81401 short hairpin RNA relieves diabetic neuropathic pain and behaviors of depression by inhibiting P2X4 receptor expression in type 2 diabetic rats

1. Nicodemus JM, Enriquez C, Marquez A, Anaya CJ, Jolivalt CG (2017) Murine model and mechanisms of treatment-induced painful diabetic neuropathy. Neuroscience 354:136–145. doi.org/10.1016/j.neuroscience.2017.04.036 CAS  Article  PubMed  Google Scholar  2. Morimoto SS, Kanellopoulos D, Manning KJ, Alexopoulos GS (2015) Diagnosis and treatment of depression and cognitive impairment in late life….

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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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Fail to install Ensembl VEP

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

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Bound State of a Protein through kmeans (or GMVAE) Clustering : comp_chem

I am an undergraduate researching in a computational chem lab at UMD. I am done running many HMMM and then AA simulations via CHARMM and NAMD. So far HMMM simulations were converted to AA when the secondary structure seemed stable and the distance to the bilayer was minimal through visual…

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PyTorch’s Cult Following

PyTorch’s popularity spread only three years after its launch: the open-source ML library posted a 194% user growth in the first half of 2019. Since then PyTorch has not looked back. According to the survey by Stackoverflow, while TensorFlow is the most in-demand library, PyTorch is more preferred. Data from…

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mVIRs – SIB Swiss Institute of Bioinformatics

Genes & Genomes Software tool mVIRs is a command line tool that uses high-throughput sequencing data from cultured or natural communities of bacteria to locate inducible prophages, including novel ones. It identifies candidate prophages by detecting outward-oriented paired-end reads with unusually large insert sizes, and their exact genomic location by…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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