Categories
Tag: LD
Understanding the Role of Rare Genetic Variants and Their Impact on Health
Understanding the Role of Rare Genetic Variants Recent research on the UK Biobank cohort, a large-scale genetic data set, has shed light on the significant role of rare genetic variants (RVs) in complex trait heritability. The study confirms that these RVs account for a substantial portion of the complex trait…
calculated an LD matrix for a locus using plink2
Hi Everyone, I have a genotype file in .pgen format, that I subset and would like to calculate LD Matrix for. Previously I used a .bed file format and use plink 1.9 which worked as charm. But unfortunately my file is in Pgen format which is not supported in plink…
Causality-enriched epigenetic age uncouples damage and adaptation
Gladyshev, V. N. et al. Molecular damage in aging. Nat. Aging 1, 1096–1106 (2021). Article PubMed PubMed Central Google Scholar Sziráki, A., Tyshkovskiy, A. & Gladyshev, V. N. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 17, e12738 (2018). Article PubMed …
Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing
Preferential carbohydrate import and early metabolism in PCs (but not SCs) supports renal physiology independent of ATP production Drosophila renal (Malpighian, MpT) tubules consist of two major cell types, the larger PCs and smaller SCs which perform distinct roles in ion, solute and water transport (Fig. 1a, b)16. These functional differences…
Promising Biotech Selling Way Under Cash Value
Nkarta is using CRISPR technology for cell therapies for leukemia. The FDA just approved a similar cell therapy treatment for Vertex using the same CRISPR technology. Nkarta is trading well below cash value and has a significant short position sinking underwater. We did very well with Talaris as a takeover…
Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry
To investigate potential functional SNPs in APOBEC3 genes involved in COVID-19 severity, we evaluated the COVID-19 association signals around 7 APOBEB3 genes, comprising APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H, in the two COVID-19 hospitalization GWASs with European and African ancestries (HGI-B2-EUR and HGI-B2-AFR, respectively). Around these 7 APOBEC3…
PRRG4 regulates mitochondrial function and promotes migratory behaviors of breast cancer cells through the Src-STAT3-POLG axis | Cancer Cell International
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. doi.org/10.3322/caac.21660. Article PubMed Google Scholar Hu G, Chong RA, Yang Q, Wei Y, Blanco…
Undefined reference to mbedTLS functions – Nordic Q&A – Nordic DevZone
Hi all! So I’m trying to use mbedTLS methods in my project. I got it to work on SDK v1.9.0 but when upgrading to v.2.4.0 I get a lot of “undefined references” to methods regarding mbedTLS.I see that there is some other issues regarding this but those haven’t solved my…
Archaic Introgression Shaped Human Circadian Traits | Genome Biology and Evolution
Abstract When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in…
Seeking Individual-Level Genotype Data for Linkage Disequilibrium Analysis Beyond 1000 Genomes Project
Seeking Individual-Level Genotype Data for Linkage Disequilibrium Analysis Beyond 1000 Genomes Project 0 Hi Biostars, I’m searching for databases with individual-level genotype data for linkage disequilibrium (LD) analysis. Already familiar with the 1000 Genomes Project, but I need more. Looking for something freely accessible, with detailed genotypic info. Any suggestions?…
Checking my installation via serial mode of testing – LAMMPS Installation
I have installed LAMMPS 02Aug 2023 version and now from the bench directory I am running the test cases. I loaded the environmental modules and the path where lmp_nompi is oocated, but it ended up with following: /apps/lammps-2Aug2023/02082023/bench$ mpirun -np 4 /apps/lammps-2Aug2023/02082023/bin/lmp_mpi -in in.rhodo /apps/lammps-2Aug2023/02082023/bin/lmp_mpi: error while loading shared libraries:…
Cannot install PyTorch on Orin AGX, with JP 5.0.2 – Jetson Orin NX
gbetsos December 12, 2023, 7:32pm 1 I have a custom Orin AGX board with L4T 35.1.0 and JetPack 5.0.2GA. I followed all steps from page: Installing PyTorch for Jetson Platform export TORCH_INSTALL=https://developer.download.nvidia.com/compute/redist/jp/v502/pytorch/torch-1.13.0a0+d0d6b1f2.nv22.10-cp38-cp38-linux_aarch64.whl $ python3 -m pip install –upgrade pip; $ python3 -m pip install aiohttp numpy==’1.19.4′ scipy==’1.5.3′ $ export “LD_LIBRARY_PATH=/usr/lib/llvm-8/lib:$LD_LIBRARY_PATH”;…
PyTorch for JetPack 6.0DP – Jetson Orin Nano
I see that a PyTorch wheel is available for JetPack 6.0DP:developer.download.nvidia.cn/compute/redist/jp/v60dp/pytorch/ However the installation instructions seem to be out of date: NVIDIA Docs Installing PyTorch for Jetson Platform – NVIDIA Docs This guide provides instructions for installing PyTorch for Jetson Platform. The following packages are not generally available for Ubuntu…
Genetic architecture of cardiac dynamic flow volumes
Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article PubMed Google Scholar Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article CAS …
Pytorch installation error – General Topics and Other SDKs
Hi ,i have upgrade my cuda from 11,4 to 12.2 using the following steps:wget developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/arm64/cuda-keyring_1.1-1_all.debsudo dpkg -i cuda-keyring_1.1-1_all.debsudo apt-get updatesudo apt-get -y install cudasudo gedit ~/.bashrcexport PATH=/usr/local/cuda-12.2/bin${PATH:+:${PATH}}export LD_LIBRARY_PATH=/usr/local/cuda-12.2/${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}source ~/.bashrc after that i am ablr=e to clone the pytorch using the following steps: git clone –recursive –branch v2.1.1 github.com/pytorch/pytorch export USE_NCCL=0…
ncs v2.5.0 linker error when setting CONFIG_BOOTLOADER_MCUBOOT – Nordic Q&A – Nordic DevZone
Hello, I currently have an app using nRF Connect SDK v2.5.0. To enable FOTA I set CONFIG_NCS_SAMPLE_MCUMGR_BT_OTA_DFU and CONFIG_BOOTLOADER_MCUBOOT in my prj.conf (following the documentation instructions). After this building the app fails during linking for 3 different undefined references: [275/280] Linking C executable zephyr/zephyr_pre0.elf FAILED: zephyr/zephyr_pre0.elf zephyr/zephyr_pre0.map : && ccache /home/q/app/zephyr_workspace/toolchains/7795df4459/opt/zephyr-sdk/arm-zephyr-eabi/bin/arm-zephyr-eabi-gcc…
Installation error Gromacs 2023.3 – User discussions
GROMACS version:2023.3GROMACS modification: NoHere post your questionI am trying to install the Cuda version of Gromacs. However, I am getting the following error after executing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda. Error : [ 98%] Linking CXX executable …/…/…/bin/argon-forces-integration/bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to srot_’ /bin/ld: /home/saikat/softwares/gromacs-2023.3/build/lib/libgromacs.so.8: undefined reference to strsm_’collect2:…
Converting txt.gz to PLINK bim
Converting txt.gz to PLINK bim 0 Hello, I’m trying to do a stratified LDSC (or S-LDSC/partitioned LDSC) between locus of interest and diseases (diabetes, arthritis, etc.). For locus of interest, I have a bed file from previous research. For diseases, I have downloaded GWAS sumstats from the GWAS atlas. I…
Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study
Lo YMD, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CWG, et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997;350:485–7. Article CAS PubMed Google Scholar Warsof SL, Larion S, Abuhamad AZ. Overview of the impact of noninvasive prenatal testing on diagnostic procedures. Prenat Diagn. 2015;35:972–9….
Bioinformatics analysis of immune characteristics in tumors with alternative carcinogenesis pathways induced by human papillomaviruses | Virology Journal
de Martel C, Georges D, Bray F, Ferlay J, Clifford GM. Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob Health. 2020;8:e180–90. Article PubMed Google Scholar McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head…
tensorflow – CuDNN using wrong CUDA version
I’m re-doing my CUDA/CuDNN setup on a new profile on Ubuntu 22.04.3 because Keras raised an error with libcublasLT I couldn’t fix. For project compatibility, I need to use TF 12.12 with CUDA 11.8 and CuDNN 8.6. I’m working on a machine with multiple CUDA versions already installed. $ cd…
Panic: Could not run ‘torchvision::roi_pool’ with arguments from the ‘CUDA’ backend – Jetson Nano
Hi, Team! I have such errors, when I run my code in docker container: root@de87551d73cf:/app/src# ./main WARN[0032] CUDA is valid WARN[0044] CUDA is valid INFO[0044] Forwarding… [W TensorImpl.h:1156] Warning: Named tensors and all their associated APIs are an experimental feature and subject to change. Please do not use them for…
locuszoom error
locuszoom error 1 Hi there, I downloaded locuszoom in it’s entirty from their github page. I have everything in order but when I attempt to run the following I get an error: locuszoom_test/bin/locuszoom –metal chr7.snx13.marker.locuszoom.metal –ld chr7.imputed.concat.sorted.nomono.80.recode.maf01.pheno.vcf.2.ld.locuszoom.input –refsnp rs1533245 –prefix chr7.snx13.rs1533245 /share/hennlab/progs/locuszoom_test/bin/../src/m2zfast.py:82: SyntaxWarning: invalid escape sequence ‘\d’ RE_SNP_1000G = re.compile(“chr(\d+|[a-zA-z]+):(\d+)$”);…
Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes
Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…
The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism
Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article PubMed CAS Google Scholar Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…
Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection
Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Żaczek A, Dziadek J (2016) Methodological and clinical aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clin Microbiol Rev 29:239–290. doi.org/10.1128/cmr.00055-15 Article PubMed PubMed Central CAS Google Scholar Niemann S, Merker M, Kohl T, Supply P…
Identification of constrained sequence elements across 239 primate genomes
De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…
nrfConnect 2.5.0: mbedTLS fails to compile (calloc()) – Nordic Q&A – Nordic DevZone
Hi there: we’ve just updated from nrfConnect 2.3.0 to nrfConnect 2.5.0 and mbedTLS (which seems to have been modified in nrfConnect 2.5.0) now fails to link (in platform.c) because it needs and is unable to find calloc(): /home/arm_embedded_gcc-10-2020-q4-major/bin/ld.bfd: modules/mbedtls/libmbedTLSBase.a(platform.c.obj):/home/nrfconnectsdk-v2.5.0/modules/crypto/mbedtls/library/platform.c:56: undefined reference to `calloc’ As you can see, we are just compiling…
Potential use of iPSCs for disease modeling, drug screening, and cell-based therapy for Alzheimer’s disease | Cellular & Molecular Biology Letters
Tarawneh R, Holtzman DM. The clinical problem of symptomatic Alzheimer disease and mild cognitive impairment. Cold Spring Harb Perspect Med. 2012;2(5): a006148. Article PubMed PubMed Central Google Scholar van der Flier WM, Scheltens P. Epidemiology and risk factors of dementia. J Neurol Neurosurg Psychiatry. 2005;76(suppl 5):v2-7. Article PubMed PubMed Central …
East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease
We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…
Population-specific distribution of TPMT deficiency variants
Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…
PyTorch 2.1 compatibility with CUDA 12.3
llama fails running on the GPU.Traced it to torch! Torch is using CUDA 12.1.Tried multiple different approaches where I removed 12.1 to make it use 12.3 downgraded the Nvidia driver. No joy! All help is appreciated. Running on a openSUSE tumbleweed.PyTorch Version: 2.1.1CUDA Version: 12.1CUDA Available: False | NVIDIA-SMI 545.29.06…
python – Different behavior in the same conda-pytorch env on different GPUs
Want to improve this question? Add details and clarify the problem by editing this post. I have a project that uses conda env with old pytorch version. It works smoothly if I use Nvidia V100, but it won’t run on other GPUs (I’ve tried RTX3080, TeslaA10, RTX2080TI, TeslaA2, TeslaT4) using…
Error: Atomtype N3 not found while trying to obtain ions.tpr – User discussions
sam13 November 27, 2023, 12:33am 1 GROMACS version: 🙂 GROMACS – gmx grompp, 2023.3-Homebrew (-:GROMACS modification: No Hello,I have been trying to do MD simulation for a protein whose 3D structure is predicted by AlphaFold. The ligand is Aspartate molecule. I am following a similar approach to the Protein-Ligand GROMACS…
Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value
Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…
Decline of DNA damage response along with myogenic differentiation
Introduction Proper functioning of all living organisms depends on the faithful maintenance and transmission of genomic information stored in the molecule of DNA. However, DNA integrity is continuously challenged by a variety of endogenous and exogenous agents causing DNA lesions which have a critical impact on cellular activities and homeostasis….
Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article Google Scholar Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…
merge .pdata and .xdata sections from host object files
diff –git a/src/cmd/cgo/internal/test/callback_windows.go b/src/cmd/cgo/internal/test/callback_windows.gonew file mode 100644index 0000000..95e97c9— /dev/null+++ b/src/cmd/cgo/internal/test/callback_windows.go@@ -0,0 +1,133 @@+// Copyright 2023 The Go Authors. All rights reserved.+// Use of this source code is governed by a BSD-style+// license that can be found in the LICENSE file.++package cgotest++/*+#include <windows.h>+USHORT backtrace(ULONG FramesToCapture, PVOID *BackTrace) {+#ifdef _AMD64_+ CONTEXT context;+…
GenAlEx Haploid Data Detecting Recombination
GenAlEx Haploid Data Detecting Recombination 0 Hello, I am currently using GenAlEx to try and detect if recombination is present in both of my populations. My data consists of 4 Loci with one allele per locus. GenAlEx seems to have options for Paired biallelic LD, but I am struggling with…
ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry
Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article Google Scholar American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…
Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications
Inclusion and ethics statement We included researchers from the iPSYCH biobank and the PGC, who played a role in study design. This research was not restricted or prohibited in the setting of any of the included researchers. All studies were approved by local instituational research boards and ethics review committees….
Nccl_external fails while trying to compile pytroch from source – torch.compile
Hello, I’m trying to compile pytorch from source and encountering the following build error. $ CC=gcc-10 CXX=g++-10 python setup.py develop … [5995/6841] Linking CXX executable bin/HashStoreTest Warning: Unused direct dependencies: /home/netfpga/research/collective/pytorch/build/lib/libc10.so /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_intel_lp64.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_gnu_thread.so.1 /home/netfpga/anaconda3/envs/pytorch_base/lib/libmkl_core.so.1 /lib/x86_64-linux-gnu/libdl.so.2 /home/netfpga/anaconda3/envs/pytorch_base/lib/libgomp.so.1 [5996/6841] Performing build step for ‘nccl_external’ FAILED: nccl_external-prefix/src/nccl_external-stamp/nccl_external-build nccl/lib/libnccl_static.a /home/netfpga/research/collective/pytorch/build/nccl_external-prefix/src/nccl_external-stamp/nccl_external-build /home/netfpga/research/collective/pytorch/build/nccl/lib/libnccl_static.a cd /home/netfpga/research/collective/pytorch/third_party/nccl/nccl &&…
Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance
De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…
python – Docker with Rstudio & conda virtual env – unable to load R packages
I have this dockerfile: # Use the rocker/rstudio image with R version 4.1.2 FROM rocker/rstudio:4.1.2 # Install deps RUN apt-get update && apt-get install -y \ wget \ bzip2 \ bash-completion \ libxml2-dev \ zlib1g-dev \ libxtst6 \ libxt6 \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ libfontconfig1-dev \ libcairo2-dev \…
Error in compiling lammps after interfacing with AENET
Dear Dr. Artrith and team, Greetings! I’m new to aenet. Thank you Dr. Artrith and team for develping aenet and opensourcing it. I downloaded USER-AENET and interfaced with lammps 4Feb2020-version. However, I’m getting the following error (complete error response attached ) when I compile the lammps using “make mpi”. Kindly…
Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis
Rg3 elicits protection against local and systemic enteric virus infection by regulating the intestinal microbiome To assess the antiviral effects of Rg3 in vivo, groups of C57BL/6J mice (referred to as WT B6 hereafter) were orally administered Rg3 for 3 consecutive days, inoculated with MNV-1 by the peroral route, and…
132arm64-default][science/votca] Failed for votca-2022.1_1 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/132arm64-default/d5268d5f7157/logs/votca-2022.1_1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=d5268d5f7157 Log: =>> Building science/votca build started at Fri Nov 10…
A software tool to adjust codeine dose based on CYP2D6 gene-pair polymorphisms and drug-drug interactions
Review doi: 10.1038/s41397-023-00318-7. Online ahead of print. Affiliations Expand Affiliations 1 Pharmaceutical Sciences Department, School of Pharmacy, Lebanese American University, Byblos, Lebanon. ysaab@lau.edu.lb. 2 Electrical and Computer Engineering Department, School of Engineering, Lebanese American University, Byblos, Lebanon. zahi.nakad@lau.edu.lb. Item in Clipboard Review Yolande Saab et al. Pharmacogenomics J. 2023. Show details…
Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Kessler, R. C. et al. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Arch. Gen. Psychiatry 62, 593–602 (2005). Article PubMed Google Scholar Kessler, R. C. et al. Prevalence, persistence, and sociodemographic correlates of DSM-IV disorders in the National Comorbidity Survey Replication Adolescent Supplement….
Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article PubMed Google Scholar Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…
RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics
Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…
Go Lang Developer to fix one rest API issue
I have a Go Lang Project where it creates tickets by using JSON LD objects. The requirements are : -1. Currently the JSONLD data is stored in “Content” field in string format, while creating the ticket , we are sending the jsonld in string format only as its expecting in…
Pytorch installation error – Jetson Xavier NX
I am installing pytorch. While installing according to the installation guide, an error such as a photo occurred. Hi @seongone.156, there appears to be a missing semicolon between scipy==’1.5.3′ and export “LD_LIBRARY_PATH=…” Also set export TORCH_INSTALL=https://developer.download.nvidia.cn/compute/redist/jp/v511/pytorch/torch-2.0.0+nv23.05-cp38-cp38-linux_aarch64.whl first, or set it to the path of the whl file that you downloaded….
Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis
Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…
significant SNPs from per-phenotype GWAS summary statistics
significant SNPs from per-phenotype GWAS summary statistics 0 I performed an analysis for a specific gene/region of interest using GWAS summary statistics for a binary phenotype (+/- disease). Using the corrected p values in the summary statistics and mapping in FUMA, I found a significant missense/coding SNP, with p=0.025. Other…
Figure S12 – compa WG
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Non-coding RNA-mediated endothelial-to-mesenchymal transition in human diabetic cardiomyopathy, potential regulation by DNA methylation | Cardiovascular Diabetology
Raghavan S, Vassy JL, Ho Y, Song RJ, Gagnon DR, Cho K, et al. Diabetes mellitus-related all-cause and cardiovascular mortality in a national cohort of adults. J Am Heart Assoc. 2019;8(4): e011295. Article PubMed PubMed Central Google Scholar Jia G, Whaley-Connell A, Sowers JR. Diabetic cardiomyopathy: a hyperglycaemia—and insulin-resistance-induced heart…
HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases
HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…
Plink2 –extract not working
Hi Chris, This problem seems so silly but I just got stuck here for a long time. I tried to extract a set of SNPs (I’m pretty sure they all appear in the .bim file) and rename their IDs with –set-all-var-ids, and…
LD D-prime (D’) calculation
LD D-prime (D’) calculation 0 Hi all, I am trying to compute LD statistics with gaston package in R and plotting them, but I do not know how to obtain D’ values. I do obtain r2 and D values but I would very interested in D’ statistic. Is it possible…
Production of leishmanin skin test antigen from Leishmania donovani for future reintroduction in the field
Study design and ethical statement All research complies with all relevant ethical regulations. Animal experiments in this study were reviewed and approved by the Animal Care and Use Committee of the Center for Biologics Evaluation and Research, U.S. Food and Drug Administration (ASP-1999#23 and ASP-1995#26) and the National Institute of…
140releng-armv7-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere3/data/140releng-armv7-default/08943441f26e/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=08943441f26e Log: =>> Building misc/py-pytorch build started at Thu Nov 2…
Get errors in loading packages/ calling functions in sc-seq data analysis
Get errors in loading packages/ calling functions in sc-seq data analysis 1 Hi, I am learning to process sc-seq data in Rstudio. There are 2 problems I have: I tried to install scater package using BiocManager::install(“scater”) but it failed. This is the error message: ld: warning: directory not found for…
Generating ion.tpr file – User discussions
AF1 November 1, 2023, 11:49am 1 Hi I am getting the following error from Lysozyme in water tutorial. I successfully completed this tutorial a few months ago but this week it seems the file gets broken at the ions.tpr output step. Please see message and file generated. Command line:gmx grompp…
papain family cysteine protease containing protein, maker-scaffold1702_size30647-snap-gene-0.14 (gene) Tigriopus kingsejongensis
Associated RNAi Experiments Homology BLAST of papain family cysteine protease containing protein vs. L. salmonis genes Match: EMLSAG00000006045 (supercontig:LSalAtl2s:LSalAtl2s327:400616:404607:-1 gene:EMLSAG00000006045 transcript:EMLSAT00000006045 description:”augustus_masked-LSalAtl2s327-processed-gene-4.0″) HSP 1 Score: 590.497 bits (1521), Expect = 0.000e+0Identity = 283/525 (53.90%), Postives = 368/525 (70.10%), Query Frame = 0 Query: 49 GHVARPLGKSPPNFVRDPPPRTTPPAQWLWNNVNETNFLTVSRNQHLPTYCGSCWAHAATSSLSDRIKIARQGAWPDINLAPQVLISCGPGDGCHGGEAGDANAYMHAQGITDETCSIYRARGQDNGLPCSKLEICSTCE—SKCYQPQHFFTYRVDEFHDVEGESNGEQEANMMAEIHHRGPISCGIAVTQALV-NYTGGLFHDKTGAQEIDHDISVVGYGVDEGTQEKYWLIRNSWGTYWGEQGFFRLIRGVNNLGIESGTCSWATPADTWSDAARE—RAAILSNEITLQKP——LWKQLWTVVADFVDNTRDTDLFRRLKLMQKGCKKLSSPRVPVVNIRPRPQDYVSTADLPEALDWRSVNGTNFLSWSVNQHLPVYCGSCWAQAGLSSLADRFTIADRKRFANLALSVQYILNCQAGGSCHGGDAFPLYAFIQKQGVPDVTCQPYEALDEGPLTDCSKPSKLVCKDCTWPPPEPGQEGNCWAKEKFHRYYVDEYNGVEGADNMKKEILERGPVT 560 GH+ R G+…
Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species
Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, et al. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Arch Virol. 2021;166:2633–48. Article CAS PubMed Google Scholar Koonin EV, Dolja VV,…
Do different microarray chips yield different accuracy of polygenic scores?
When replicating a polygenic score, labs have multiple microarray chips to choose from. (E.g., GSA, GDA, UK Biobank Axiom Array, UK BiLEVE Axiom array, GeneChip 2.0 array, Infinium Core-24 Kit, etc.). Will using different chips impact the accuracy of the polygenic score? If so, by how much? I’ve been unable…
CYP1A2 expression rather than genotype is associated with olanzapine concentration in psychiatric patients
Owen, M. J., Sawa, A. & Mortensen, P. B. Schizophrenia. Lancet 388, 86–97 (2016). Article PubMed PubMed Central Google Scholar Bhana, N., Foster, R. H., Olney, R. & Plosker, G. L. Olanzapine: An updated review of its use in the management of schizophrenia. Drugs 61, 111–161 (2001). Article CAS PubMed …
Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly
Di Donato N, Chiari S, Mirzaa GM, Aldinger K, Parrini E, Olds C, et al. Lissencephaly: expanded imaging and clinical classification. Am J Med Genet A. 2017;173:1473–88. Article PubMed PubMed Central Google Scholar Guerrini R, Dobyns WB. Malformations of cortical development: clinical features and genetic causes. Lancet Neurol. 2014;13:710–26. Article …
main-powerpc64le-default][misc/pytorch] Failed for pytorch-1.13.1_1 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/pytorch build started at Tue Oct 24…
Genome-wide association study of traumatic brain injury in U.S. military veterans enrolled in the VA million veteran program
Helmick KM, Spells CA, Malik SZ, Davies CA, Marion DW, Hinds SR. Traumatic brain injury in the US military: Epidemiology and key clinical and research programs. Brain Imaging Behav. 2015;9:358–66. Article PubMed Google Scholar DoD Numbers for Traumatic Brain Injury Worldwide – Totals (Defense Health Agency) (2021). Karr JE, Areshenkoff…
main-powerpc64le-default][misc/py-pytorch] Failed for py39-pytorch-2.1.0 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/pbc0e38d0f08e_s0afcac3e37/logs/py39-pytorch-2.1.0.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=pbc0e38d0f08e_s0afcac3e37 Log: =>> Building misc/py-pytorch build started at Sun Oct 22…
Expanding causal genes for Parkinson’s disease via multi-omics analysis
Proteins causally associated with PD in the brain MR analysis of brain dorsolateral prefrontal cortex (dlPFC) pQTLs identified six genetically determined significant proteins on PD after multiple testing corrections (P < 8.55E-05 (0.05/585)). Specifically, the increased abundance of 3 proteins was significantly associated with an increased risk of PD, including GPNMB (OR:1.464,…
Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability
MacDonald SW, Li SC, Bäckman L. Neural underpinnings of within-person variability in cognitive functioning. Psychol Aging. 2009;24:792–808. Article PubMed Google Scholar Haynes BI, Bunce D, Kochan NA, Wen W, Brodaty H, Sachdev PS. Associations between reaction time measures and white matter hyperintensities in very old age. Neuropsychologia. 2017;96:249–55. Article PubMed …
Systematic differences in discovery of genetic effects on gene expression and complex traits
Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article CAS PubMed PubMed Central Google Scholar Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article CAS PubMed PubMed Central Google Scholar Gusev, A. et…
IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation
1. Introduction Human population genetics benefitted from the completion of the human genome sequence [1], which was further advanced by creating the reference of global genome variation [2] and, finally, the establishment of regional references assessing fine details of local variation in whole-genome sequences. Although European populations are relatively well…
Using cmdstanr crashing RStudio – Interfaces
I’ve recently updated to macOS Sonoma and started using {renv} when using cmdstanr started causing fatal errors and crashing RStudio (i.e., loading it using library(cmdstanr) or just making function calls using cmdstanr::). After lots of trial and error, it appears to be an RStudio thing since I can run the…
Analysis of gut bacteriome of in utero arsenic-exposed mice using 16S rRNA-based metagenomic approach
. 2023 Sep 29:14:1147505. doi: 10.3389/fmicb.2023.1147505. eCollection 2023. Affiliations Expand Affiliations 1 Department of Microbiology, Dr. Shakuntala Misra National Rehabilitation University, Lucknow, Uttar Pradesh, India. 2 Systems Toxicology and Health Risk Assessment Group, Council of Scientific & Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, India. 3 Department…
main-armv7-default][biology/viennarna] Failed for viennarna-2.6.3 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-armv7-default/p08943441f26e_s6e92fc9309/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p08943441f26e_s6e92fc9309 Log: =>> Building biology/viennarna build started at Mon Oct 16…
Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton
Gene expression atlas in fiber development To uncover the genetic regulation of gene expression in fiber development, we collected 376 diverse G. hirsutum accessions for genome and transcriptome analysis. A total of 13.5 Tb of genome resequencing data were generated, with an average depth of 15.6× (Supplementary Table 1). Accessions were…
eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants
Bajaj D, Upadhyaya HD, Khan Y, Das S, Badoni S, Shree T, Kumar V, Tripathi S, Gowda CL, Singh S, Sharma S, Tyagi AK, Chattopdhyay D, Parida SK (2015) A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Sci…
Genotyping, sequencing and analysis of 140,000 adults from Mexico City
Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…
The activation of cGAS-STING in acute kidney injury
Introduction AKI, which is characterised by necroinflammation due to damage and necrosis of the kidney’s intrinsic cells,1 is a common clinical syndrome, occurring in 10–15% of hospitalized patients, whereas in the ICU this percentage is as high as 50%.2 The development of AKI is involved in the production of reactive…
Fatal Error: Too many warnings (1) Use -maxwarn option in gromacs 2023.2 – User discussions
Respected Sir/Ma’am,I am getting an error as shown below.🙂 GROMACS – gmx grompp, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmxData prefix: /usr/local/gromacsWorking dir: /home/drr-18/Complex_02_EMinimizedCommand line:gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr Ignoring obsolete mdp entry ‘title’Ignoring obsolete mdp entry ‘ns_type’ WARNING 1 [file npt.mdp]:The…
main-powerpc64le-default][misc/py-pytorch] Failed for py39-pytorch-2.0.1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/main-powerpc64le-default/p2a7484393abf_s0afcac3e37/logs/py39-pytorch-2.0.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=p2a7484393abf_s0afcac3e37 Log: =>> Building misc/py-pytorch build started at Sun Oct 8…
Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin
Mapping eQTLs in patients with psoriasis We obtained longitudinal lesional and non-lesional skin biopsies from participants at baseline, during treatment, and at the time of psoriasis relapse after study medication withdrawal over a course of 22 months. We used genome-wide genotyping and RNA-seq to assay samples. After stringent quality control,…
Identification of eQTL from porcine muscle and liver mRNA sequencing
Master’s Dissertation DOI doi.org/10.11606/D.11.2023.tde-02102023-151405 Document Author Freitas, Felipe André Oliveira (Catálogo USP) Full name Felipe André Oliveira Freitas E-mail Institute/School/College Escola Superior de Agricultura Luiz de Queiroz Knowledge Area Animal Science and Pastures Date of Defense Published Piracicaba, 2023 Supervisor Cesar, Aline Silva Mello (Catálogo USP) Committee Cesar, Aline Silva…
The effect of oleic acid supplementation on lipid droplet production, betaoxidation and rotavirus replication
Abstract Rotavirus (RV) is the most common cause of severe acute gastroenteritis in infants and young children globally. Rotavirus infections induce cytoplasmic inclusion bodies called viroplasms serving as a site of RV genome replication and assembly. Viroplasms recruit lipid droplets (LDs), which play major roles in energy homeostasis and is…
“Installing PyTorch for Jetson Platform”: Error in pytorch install instructions? (Missing semicolon?) – Jetson Nano
Tried to install PyTorch for Jetson Platform using the command shown on Installing PyTorch for Jetson Platform – NVIDIA Docs and got errors about LD_LIBRARY_PATH . I’m not a PIP expert, but it looks to me like that export was intended to be a separate command and a semicolon was…
The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons
The genome assembly was performed with the pipeline v1.5 of the Vertebrate Genomes Project (VGP) and can be found under NCBI BioProject PRJNA558064, accession number GCA_009819655.1, for further details on the sample collection and assembly see Ishigohoka et al.9. In brief, a female blackcap from mainland Spain was caught to…
Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification
Timmis, A. et al. European Society of Cardiology: Cardiovascular Disease Statistics 2017. Eur. Heart J. 39, 508–579 (2018). Article PubMed Google Scholar Tsao, C. W. et al. Heart Disease and Stroke Statistics—2022 Update: a report from the American Heart Association. Circulation 145, e153–e639 (2022). Article PubMed Google Scholar Libby, P.,…
Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease
Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…
RPM Search opensuse slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm
Content of RPM slurm-plugins-18.08.9-lp152.2.1.x86_64.rpm : /etc/ld.so.conf.d/slurm.conf /usr/lib64/slurm /usr/lib64/slurm/accounting_storage_filetxt.so /usr/lib64/slurm/accounting_storage_none.so /usr/lib64/slurm/accounting_storage_slurmdbd.so /usr/lib64/slurm/acct_gather_energy_ibmaem.so /usr/lib64/slurm/acct_gather_energy_ipmi.so /usr/lib64/slurm/acct_gather_energy_none.so /usr/lib64/slurm/acct_gather_energy_rapl.so /usr/lib64/slurm/acct_gather_energy_xcc.so /usr/lib64/slurm/acct_gather_filesystem_lustre.so /usr/lib64/slurm/acct_gather_filesystem_none.so /usr/lib64/slurm/acct_gather_interconnect_none.so /usr/lib64/slurm/acct_gather_interconnect_ofed.so /usr/lib64/slurm/acct_gather_profile_influxdb.so /usr/lib64/slurm/acct_gather_profile_none.so /usr/lib64/slurm/burst_buffer_generic.so /usr/lib64/slurm/checkpoint_none.so /usr/lib64/slurm/checkpoint_ompi.so /usr/lib64/slurm/core_spec_none.so /usr/lib64/slurm/crypto_openssl.so /usr/lib64/slurm/ext_sensors_none.so /usr/lib64/slurm/ext_sensors_rrd.so /usr/lib64/slurm/gres_gpu.so /usr/lib64/slurm/gres_mic.so /usr/lib64/slurm/gres_nic.so /usr/lib64/slurm/job_container_cncu.so /usr/lib64/slurm/job_container_none.so /usr/lib64/slurm/job_submit_all_partitions.so /usr/lib64/slurm/job_submit_defaults.so /usr/lib64/slurm/job_submit_logging.so /usr/lib64/slurm/job_submit_partition.so /usr/lib64/slurm/job_submit_require_timelimit.so /usr/lib64/slurm/job_submit_throttle.so /usr/lib64/slurm/jobacct_gather_cgroup.so /usr/lib64/slurm/jobacct_gather_linux.so /usr/lib64/slurm/jobacct_gather_none.so /usr/lib64/slurm/jobcomp_elasticsearch.so /usr/lib64/slurm/jobcomp_filetxt.so /usr/lib64/slurm/jobcomp_none.so /usr/lib64/slurm/jobcomp_script.so /usr/lib64/slurm/launch_slurm.so /usr/lib64/slurm/layouts_power_cpufreq.so /usr/lib64/slurm/layouts_power_default.so /usr/lib64/slurm/layouts_unit_default.so…
Saving the output of LD pruning from SNPRelate package as a new GDS file
Saving the output of LD pruning from SNPRelate package as a new GDS file 1 I successfully ran LD pruning from SNPRelate package and obtained the selected SNPs IDs. I would like to create a new GDS file with only the pruned SNPs so I can use it in another…
132releng-armv7-quarterly][misc/pytorch] Failed for pytorch-1.13.1_1 in configure
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere1/data/132releng-armv7-quarterly/2be22e0743b5/logs/pytorch-1.13.1_1.log Build URL: pkg-status.freebsd.org/ampere1/build.html?mastername=132releng-armv7-quarterly&build=2be22e0743b5 Log: =>> Building misc/pytorch build started at Mon Sep 25…
r – How to align weeks in different years in ggplot2?
How can I align the weeks from different years on the x-axis so that weeks occurring in the same month, like June, are aligned? Please note that data was not collected during same weeks in different years, so some weeks can’t be aligned, and that’s okay. I just wish to…
main-arm64-default][biology/viennarna] Failed for viennarna-2.6.3 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/ampere2/data/main-arm64-default/p85ccf094713a_sc584bb9cac1/logs/viennarna-2.6.3.log Build URL: pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p85ccf094713a_sc584bb9cac1 Log: =>> Building biology/viennarna build started at Sat Sep 23…
CP2K version 2023.2 compile error
Thank you for helping me, Mishra. However, I still got problems. I modified the script according to my architecture, as below:“spack -d install cp2k@2023.1+elpa %g…@8.3.1 target=icelake ^elpa+openmp ^ope…@4.1.4 fabrics=auto”Then I got very, very long error message below and I dont’ know what is the reason. ———————————————————————————————————————————————————————————– ==> [2023-09-22-11:22:05.969419] Error: ProcessError:…
Functional characterization of Alzheimer’s disease genetic variants in microglia
Nott, A. et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science 366, 1134–1139 (2019). Article CAS PubMed PubMed Central Google Scholar Neuner, S. M., Tcw, J. & Goate, A. M. Genetic architecture of Alzheimer’s disease. Neurobiol. Dis. 143, 104976 (2020). Article CAS PubMed PubMed Central Google Scholar …
KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies | BMC Bioinformatics
User interface The user interface of KidneyGPS is organized into five tabs: Three tabs enable the specific search for genes, variants and regions (underlying data structure shown in Additional file 1: Fig. S4): (1) “gene search” tab: search for genes using their gene names (synonyms automatically mapped to their official HGNC…