Tag: genome-wide

Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis

Wang, J., Garancher, A., Ramaswamy, V. & Wechsler-Reya, R. J. Medulloblastoma: from molecular subgroups to molecular targeted therapies. Annu. Rev. Neurosci. 41, 207–232 (2018). Article  CAS  PubMed  Google Scholar  Cavalli, F. M. G. et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell 31, 737–754.e736 (2017). Article  CAS  PubMed  PubMed Central …

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dharmacon sirna design

Please feel free to visit our Privacy Policy and Cookie Policy with regards to processing your data. Article Customer Support Sequence characteristics of functional siRNAs. Human and mouse genes are each targeted with multiple shRNA constructs that have been cloned into the pGIPZ lentiviral vector. GRCF Management Team. In the…

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An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice

Mastroberardino, L. et al. Amino-acid transport by heterodimers of 4F2hc/CD98 and members of a permease family. Nature 395, 288–291 (1998). Article  CAS  PubMed  Google Scholar  Nakamura, E. et al. 4F2 (CD98) heavy chain is associated covalently with an amino acid transporter and controls intracellular trafficking and membrane topology of 4F2…

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scRNA-seq for Microcephaly Research [I]: Single-Cell Droplet Encapsulation, mRNA Capture, and cDNA Synthesis

doi: 10.1007/978-1-0716-2752-5_8. Affiliations Expand Affiliations 1 Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA, USA. ben.babcock@emory.edu. 2 Department of Neurology, University of North Carolina Medical School, Chapel Hill, NC, USA. Item in Clipboard Benjamin Babcock et al. Methods Mol Biol. 2023….

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Liver Cancers Detected With Parallel Mutation, Methylation Liquid Biopsy Approach

NEW YORK – A Chinese research team has shown that their method for profiling mutation and DNA methylation patterns in circulating cell-free DNA (cfDNA) can detect hepatocellular carcinoma (HCC) liver cancer cases. “[W]e developed the Mutation Capsule Plus (MCP) technology, supporting parallel profiling of mutations and methylation changes (MCP profiling)…

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Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential

Weisman, D. & McKeith, I. Dementia with Lewy Bodies. Semin. Neurol. 27, 042–047 (2007). Article  Google Scholar  Foguem, C. & Manckoundia, P. Lewy Body Disease: Clinical and Pathological “Overlap Syndrome” Between Synucleinopathies (Parkinson Disease) and Tauopathies (Alzheimer Disease). Curr. Neurol. Neurosci. Rep. 2018 18:5 18, 1–9 (2018). CAS  Google Scholar …

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Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria

Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article  CAS  PubMed  PubMed Central  Google Scholar  Ayala, J. A., Garrido, T., De Pedro,…

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How to genome-wide association analysis using survival analysis in Plink?

How to genome-wide association analysis using survival analysis in Plink? 0 Hi, The most common GWAS association analyses use logistic regression. Currently, I want to do the association with survival analyses (E.g. Cox regression model) since my outcome of interest is a time-to-event variable. How can do it using Plink?…

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Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease

The heterogeneity of GABAergic neurons in human, macaque, mouse, and pig To perform a cross-species comparative study of the GABAergic neurons, we collected the snRNA-seq datasets of the cerebral cortex for human10,11, macaque12,13, mouse14,15, and pig16. After cell-type annotation and filtering out the excitatory neurons and non-neurons, the GABAergic neurons…

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Synthetic Biology Market Set for Rapid Growth 2031

Synthetic Biology Market Outlook 2031 The global synthetic biology market was valued at US$ 10.7 Bn in 2021 The global market is projected to advance at a CAGR of 21.3% from 2022 to 2031 The global synthetic biology market is anticipated to reach more than US$ 74.7 Bn by the end of 2031 Synthetic Biology Market Introduction Synthetic biology is a branch of science…

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Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

CNV analysis After the application of quality filter step I (gender mismatch), two patients were excluded. Through step II (call rate <98%), 40 patients were discarded and after step III (exceeded double of standard deviation), 12 more patients were excluded. In the remaining 396 individuals with ARM, a total of…

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ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74. Article  CAS  PubMed  PubMed Central  Google Scholar  Chang CC, Chow CC, Tellier LC, Vattikuti S,…

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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

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MIT Bioinformatics Seminar: Xihong Lin: Scalable Integrative Analysis of Large Biobank and Population-Based Whole Genome Sequencing Studies With Variant Functional Annotations

ABSTRACT: Whole Genome/Exome Sequencing (WGS/WES) data and Electronic Health Records (EHRs), such as large scale national and institutional biobanks, have emerged rapidly worldwide. In this talk, I will discuss the analytic tools and resources for scalable analysis of large scale biobank- and population-based Whole Genome Sequencing (WGS) association studies of…

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Syracuse University Online Employment Site | Post Doc

Job # 076742 Job Title Post Doc – Genomics and Bioinformatics Location Syracuse, NY Pay Range Commensurate with Experience FLSA Status Exempt Hours As determined by PI. Job Type Full-time Rank Post Doc Campus Syracuse, NY Unionized Position Code Not Applicable Job Description The Ahmed-Brimah Lab at Syracuse University invites…

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CRISPR Screens Identify Potential Host Targets to Reverse HIV-1 Latency

NEW YORK — Using genome-wide CRISPR screens, researchers have identified host genes that can be targeted to help induce expression of latent HIV-1, potentially enabling the otherwise unreachable virus to be targeted by drugs. HIV-1 can persist among affected individuals within their CD4+ T cells, even in face of antiretroviral…

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Noncoding RNAs responsive to nitric oxide and their protein-coding gene targets shed light on root hair formation in Arabidopsis thaliana

doi: 10.3389/fgene.2022.958641. eCollection 2022. Affiliations Expand Affiliations 1 Laboratório de Ecofisiologia e Bioquímica de Plantas, Núcleo de Conservação da Biodiversidade, Instituto de Pesquisas Ambientais, São Paulo, SP, Brasil. 2 Programa de Pós-Graduação em Biologia Celular e Estrutural, Universidade Estadual de Campinas, Campinas, SP, Brasil. Item in Clipboard Camilla Alves Santos et…

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Leptin receptor co-expression gene network moderates the effect of early life adversity on eating behavior in children

Gillespie, C. F., Phifer, J., Bradley, B. & Ressler, K. J. Risk and resilience: genetic and environmental influences on development of the stress response. Depress Anxiety 26, 984–992 (2009). CAS  PubMed  PubMed Central  Article  Google Scholar  Silveira, P. P. et al. Cumulative prenatal exposure to adversity reveals associations with a…

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Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

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Introduction to DNA Methylation Analysis: From Wet Lab Experiments to Bioinformatics Analysis

Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

GWAS identifies genetic variations associated with agronomic traits in foxtail millet A total of 827 foxtail millet cultivars collected from China were sequenced and genotyped using common single-nucleotide polymorphisms (SNPs) based on a ~423 Mb Setaria italica cv. Zhanggu reference genome (v.2.3)27. In total, 161,562 SNPs were detected after stringent steps…

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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

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The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig

Zhou, G. et al. Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat. Sci. 86(2), 440–450 (2010). CAS  PubMed  Article  Google Scholar  Alfaia, C. M. et al. Current feeding strategies to improve pork intramuscular fat content and its nutritional quality. Adv….

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A causal association of ANKRD37 with human hippocampal volume

Lisman J, Buzsáki G, Eichenbaum H, Nadel L, Ranganath C, Redish AD. Viewpoints: how the hippocampus contributes to memory, navigation and cognition. Nat Neurosci. 2017;20:1434–47. CAS  PubMed  PubMed Central  Article  Google Scholar  Kim EJ, Pellman B, Kim JJ. Stress effects on the hippocampus: a critical review. Learn Mem. 2015;22:411–6. PubMed …

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Rockefeller University Jobs – Bioinformatics Specialist in New York, New York, United States

Job: IRC28479 Description Job Title Bioinformatics Specialist Laboratory / Department Systems Cancer Biology Department Description Cancer remains a daunting problem despite decades of active research into its molecular causes. Such studies have predominantly focused on the earliest stages of cancer progression such as the formation of a cancer or genes…

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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing

Niikawa N, Matsuura N, Fukushima Y, Ohsawa T, Kajii T. Kabuki make-up syndrome: a syndrome of mentalretardation, unusual facies, large and protruding ears, and postnatal growth deficiency. J Pediatrics. 1981;99:565–9. CAS  Article  Google Scholar  Kuroki Y, Suzuki Y, Chyo H, Hata A, Matsui I. A new malformation syndrome of long…

Continue Reading Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing

Population-level variation in enhancer expression identifies disease mechanisms in the human brain

Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central  Article  CAS  Google Scholar  Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central …

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Modelling urea cycle disorders using iPSCs

Gebhardt, R. & Matz-Soja, M. Liver zonation: Novel aspects of its regulation and its impact on homeostasis. World J. Gastroenterol. 20, 8491–8504 (2014). PubMed  PubMed Central  Article  Google Scholar  Summar, M. L. et al. The incidence of urea cycle disorders. Mol. Genet Metab. 110, 179–180 (2013). CAS  PubMed  PubMed Central …

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Genetic footprints of assortative mating in the Japanese population

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

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Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

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Ten challenges for clinical translation in psychiatric genetics

Pardinas, A. F. et al. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat. Genet. 50, 381–389 (2018). CAS  PubMed  PubMed Central  Article  Google Scholar  Stahl, E. A. et al. Genome-wide association study identifies 30 loci associated with bipolar disorder. Nat. Genet. 51,…

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Hidden paths to endless forms most wonderful: ecology latently shapes evolution of multicellular development in predatory bacteria

Carroll, S. B. Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (Quercus, 2005). Dobzhansky, T. & Spassky, B. Genetics of natural populations. XI. Manifestation of genetic variants in Drosophila pseudoobscura in different environments. Genetics 29, 270–290 (1944). CAS  PubMed  PubMed Central …

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Data Scientist – Bioinformatics at Faculty – London, England, United Kingdom

Faculty is one of Europe’s leading applied artificial intelligence companies. We build, deploy and operate AI solutions to increase our customers’ performance and help them realise their full potential. We believe that AI should be trustworthy, impactful and beneficial across society. Those principles have shaped our work with more than…

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Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….

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NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters

Abstract Resistance to endocrine therapy is a common problem in patients with estrogen receptor alpha (ERα) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the…

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Hands On Next Generation Sequencing Using Galaxy Servers | Free eBooks Download

Category: Tutorial Posted on 2022-08-20, by voska89. Description Published 08/2022MP4 | Video: h264, 1280×720 | Audio: AAC, 44.1 KHz, 2 ChGenre: eLearning | Language: English + srt | Duration: 28 lectures (2h 6m) | Size: 615.8 MBLearn about Next-generation sequencing and use of online platform and perform Data analysis of…

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Live-seq enables temporal transcriptomic recording of single cells

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

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Why isn’t GWAS used in oncology?

Forum:Why isn’t GWAS used in oncology? 1 From what I can gather, GWAS is not used in oncology because ~ cancer is characterized by rare/ random mutations that amount to an overall burden on the genes that they up/down regulate. Is this assumption correct? gwas association oncology studies somatic cancer…

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UK Biobank Copy Number-Based GWAS Discovers New Associations With Human Traits

NEW YORK – A new set of analytical tools is making it possible to systematically search for links between copy number variants and complex human traits or conditions, according to a study by a pair of investigators at the European Molecular Biology Laboratory’s European Bioinformatics Institute. “[W]e present a robust…

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

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Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

Sampson, J. N. et al. Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types. J. Natl Cancer Inst. 107, djv279 (2015). PubMed  PubMed Central  Article  CAS  Google Scholar  Bosse, Y. & Amos, C. I. A decade of GWAS results in lung cancer. Cancer Epidemiol….

Continue Reading Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

Genome-wide investigation of multiplexed CRISPR-Cas12a-mediated editing in rice

Abstract We previously reported highly specific genome editing in rice by CRISPR-Cas9 and Cas12a with single DNA double strand break (DSB) (Tang et al., 2018). Two concurrent DSBs by CRISPR-Cas9 could generate defined deletions (Zhou et al., 2014), inversions (Schmidt et al., 2020), and translocations (Beying et al., 2020). Off-target…

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SMAD4 rs10502913 | COPD

1Department of Pulmonary and Critical Care Medicine, Sinopharm Tongmei General Hospital, Datong, People’s Republic of China; 2China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China; 3Department of Emergency, Chinese PLA General Hospital -Fourth Medical Center, Beijing, People’s Republic of China; 4School…

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Postdoctoral Position in Statistical Genetics / Bioinformatics / Epigenetics job with National Institute on Aging (NIA) / National Institute of Health (NIH)

Postdoctoral Position in Statistical Genetics/Bioinformatics/Epigenetics   Health Disparities Research Section of the Laboratory of Epidemiology and Population Science National Institute on Aging (NIA) National Institute of Health (NIH)   A fully funded postdoctoral position is available immediately in the Health Disparities Research Section of the Laboratory of Epidemiology and Population…

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

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The evolutionary origin of host association in the Rickettsiales

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

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Escherichia coli K-12 substr. MG1655 sdsN

BioCyc ID:TU0-42620 Local Context (not to scale — see Genome Browser for correct scale) Transcription Unit Notes: Click on a binding site (if any) to navigate to the page for its transcription factor. Click on a gene to navigate to its gene page. Roll the mouse over any element in…

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New study investigates the epigenetic drift of time passing

A new research paper was published in Aging (Aging-US) on the cover of Volume 14, Issue 12, entitled, “Time makes histone H3 modifications drift in mouse liver.” Aging is known to involve epigenetic histone modifications, which are associated with transcriptional changes, occurring throughout the entire lifespan of an individual. “So…

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Genome-wide siRNA screening reveals a number of host receptors for the binding of human intestine commensal Bifidobacterium bifidum

On this research we developed a high-throughput siRNA silencing assay to display proteins which may function host floor receptors for bacterial binding and uncovered 4 receptors for the commensal B. bifidum. Bifidobacteria are members of regular intestine microbiota and they’re considered health-promoting micro organism and for that they’re broadly used…

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Stabilizing and Anti-Repressor Elements Effectively Increases Transgene Expression in Transfected CHO Cells

doi: 10.3389/fbioe.2022.840600. eCollection 2022. Affiliations Expand Affiliations 1 School of Basic Medicine, Xinxiang Medical University, Xinxiang, China. 2 International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China. Free PMC article Item in Clipboard Qin Li et al. Front Bioeng Biotechnol. 2022. Free PMC…

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Tramadol Therapy and CYP2D6 Genotype – Medical Genetics Summaries

Introduction Tramadol (brand names ConZip, Ultram, UltramER, Odolo) is an analgesic used to treat moderate to severe pain. It is used for a variety of pain conditions, including post-operative pain, cancer pain, and musculoskeletal pain. Tramadol is a centrally acting opioid analgesic with mu-opioid binding activity as well as weak…

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Genome-wide association study of musical beat synchronization demonstrates high polygenicity

Savage, P. E., Brown, S., Sakai, E. & Currie, T. E. Statistical universals reveal the structures and functions of human music. Proc. Natl Acad. Sci. USA 112, 8987–8992 (2015). CAS  PubMed  PubMed Central  Article  Google Scholar  Ravignani, A., Delgado, T. & Kirby, S. Musical evolution in the lab exhibits rhythmic…

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TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies

doi: 10.1093/genetics/iyac088. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA. 2 Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA. 3 Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA. 4 Gilead…

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A desirable transgenic strategy using GGTA1 endogenous promoter-mediated knock-in for xenotransplantation model

Lai, L. et al. Production of alpha-1,3-galactosyltransferase knockout pigs by nuclear transfer cloning. Science 295, 1089–1092. doi.org/10.1126/science.1068228 (2002). ADS  CAS  Article  PubMed  Google Scholar  Kuwaki, K. et al. Heart transplantation in baboons using alpha1,3-galactosyltransferase gene-knockout pigs as donors: initial experience. Nat. Med. 11, 29–31. doi.org/10.1038/nm1171 (2005). CAS  Article  PubMed  Google…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

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

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

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

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

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

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

Penetrance of Mendelian Disease Variants Ranges in Heterozygous Carriers

NEW YORK – Using genetic data from the UK Biobank, a team from Brigham and Women’s Hospital, the Broad Institute, Harvard Medical School, and the Massachusetts Institute of Technology has documented various levels of recessiveness for variants previously implicated in Mendelian conditions. “With increasing exome sequencing of population biobank cohorts,…

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MicrobioSeq Releases Nanopore-Based Microbial Epigenomics Solutions to Accelerate Your Research

MicrobioSeq is the microbial genomics division of CD Genomics, committed to delivering comprehensive microbial solutions to human health, agriculture, the environment, and industry by characterizing microbiomes and leveraging microorganisms. The company recently announced the launch of Nanopore-Based Microbial Epigenomics Solutions to detect more types of DNA modifications.   Epigenetic modifications…

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Tempo and drivers of plant diversification in the European mountain system

Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article  Google Scholar  Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS  CAS  PubMed  Article  Google…

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

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

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MND1 Expression as a Predictor of Breast Cancer Survival

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

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WGS Facilitates Gene Editing System Upgrade

Researchers at the Korean Institute of Life Sciences and Technology engineered an efficient, miniaturized CRISPR-Cas gene-editing system that may be more easily packed into vectors for clinical applications. Their system employs the Cas variant Cas12f1 with a guide RNA (gRNA) remodeled to mitigate off-target effects, a design that could potentially…

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

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Identifying Mechanisms of Methylation in Stem Cells

Normal cells (red) survive much longer than Set1A-mutant cells (green) when ING5 is deleted. Northwestern Medicine scientists have identified critical regulatory processes that govern differentiation in embryonic stem cells, according to a study published in the Proceedings of the National Academy of the Sciences (PNAS). Bercin Cenik, MD, PhD, postdoctoral…

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Recent developments in miRNA based recombinant protein expression in CHO

Aguiar TQ, Santos SB, Martins IM, Domingues L, Oliveira C (2019) Production and bioengineering of recombinant pharmaceuticals. Proteins: sustainable source, processing and applications. Elsevier, Amsterdam, pp 259–293 Chapter  Google Scholar  Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH (2020) Inhibition of endogenous miR-23a/miR-377 in CHO cells…

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Landscape of helper and regulatory antitumour CD4+ T cells in melanoma

Sallusto, F. & Lanzavecchia, A. Heterogeneity of CD4+ memory T cells: functional modules for tailored immunity. Eur. J. Immunol. 39, 2076–2082 (2009). CAS  PubMed  Article  Google Scholar  Swain, S. L., McKinstry, K. K. & Strutt, T. M. Expanding roles for CD4+ T cells in immunity to viruses. Nat. Rev. Immunol….

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Biogenesis, biology and characterization of circular RNAs

Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…

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Author Correction: Genome-wide autosomal, mtDNA, and Y chromosome analysis of King Bela III of the Hungarian Arpad dynasty

Author Correction: Using energy time”“frequency of Hilbert Huang transform to analyze the performance of the variable valve timing engine Correction to: Scientific Reports doi.org/10.1038/s41598-022-06404-3, published online 11 February 2022. The original version of this Article contained errors in the Reference list, where references 1,2,4,5,12,13,14,15,18,21,22,23,34,36,37,39,40,41,42,43,44 and 45 were incorrectly given as….

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Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases

Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS  Article  PubMed  Google Scholar  El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS  Article …

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Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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Could DNA be linked to Premature Aging in Cancer Survivors?

In this interview, we speak to Dr. Zhaoming Wang about his latest research that investigated accelerated aging in childhood cancer survivors and the underlying genetics causing this. Please could you introduce yourself and tell us what inspired your latest research? I’m an associate member of the faculty at St. Jude…

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Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Cattle are among the largest populations of domesticated animals and used as food resources for humans; therefore, their phenotypes and genetic structure have been shaped by artificial selection for human needs and natural adaptation to environmental changes. The phenotypic selection causes genomic changes in breeding traits within breeds, resulting in…

Continue Reading Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Still doubts over embryo selection based on PGT for polygenic conditions

Advances in genomic technologies continue to expand the possibilities of PGT. In a preclinical research study recently published in Nature Medicine, scientists from Silicon Valley-based genetic testing companies have examined the potential of using PGT to predict complex polygenically inherited conditions in human embryos. While the authors present interesting data,…

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Bioinformatics Specialist (Pathology and Laboratory Medicine) at University of Pennsylvania in Philadelphia, Pennsylvania

Job Description: Bioinformatics Specialist (Pathology and Laboratory Medicine) University Overview The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey….

Continue Reading Bioinformatics Specialist (Pathology and Laboratory Medicine) at University of Pennsylvania in Philadelphia, Pennsylvania

CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology

Bartel, D. P. MicroRNAs: Target recognition and regulatory functions. Cell 136, 215–233 (2009). CAS  Article  Google Scholar  Bassett, A. R. et al. Understanding functional miRNA–target interactions in vivo by site-specific genome engineering. Nat. Commun. 5, 4640 (2014). ADS  CAS  Article  Google Scholar  Moore, M. J. et al. miRNA–target chimeras reveal…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Polygenic Transcriptome Risk Scores for COPD Show Improved Cross-Ancestry Portability

NEW YORK — Polygenic transcriptome risk scores may be better at gauging chronic obstructive pulmonary disease susceptibility across human ancestry groups than polygenic risk scores, a new study has found. COPD affects about 16 million people in the US and is typically diagnosed through two measures of lung function: forced…

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Bioinformatics analysis identifies widely expressed genes

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

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Kits for the preparation of Illumina libraries

ChIP-Seq or ChIP sequencing is a new generation sequencing technique (NSG) for studying the interactions between proteins and DNA, to identify genome-wide DNA binding sites for transcription factors and other proteins. ChIP-Seq sequencing is therefore a key tool in epigenomics research. It is an approach based on a sequencing technique…

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Single-Cell Technology Measures Epigenetic States and Gene Expression in One Go

Advances in single-cell technologies have not only made it possible to analyze multiple molecular families in individual cells, they have also enabled scientists to parse through limitations in data analysis arising from the intercellular diversity of measured parameters. Although single-cell sequencing is now widely available, techniques to detect epigenetic markers…

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Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…

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MAGeCK – BioGrids Consortium – Supported Software

AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther MAGeCK Description (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. Installation Use the following command to install this title with the CLI client: $ biogrids-cli install mageck Copy to clipboard Primary Citation* W….

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Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands Aysu Okbay, Hyeokmoon Kweon & Philipp D. Koellinger Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia Yeda Wu, Julia Sidorenko, Jian Yang, Loic Yengo & Peter M. Visscher National Bureau of Economic Research, Cambridge, MA, USA Nancy Wang, Hariharan Jayashankar, Michael Bennett, Grant Goldman, Tamara Gjorgjieva, Steven…

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Human distal lung maps and lineage hierarchies reveal a bipotent progenitor

Verleden, S. E. et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir. Med. 8, 573–584 (2020). CAS  PubMed  PubMed Central  Google Scholar  Hogg, J. C., Macklem, P. T. & Thurlbeck, W. M. The resistance of small airways in normal and diseased human lungs. Aspen…

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Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

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A CRISPR Kitty? Gene Editing Breathes New Life into the Hypoallergenic Cat

The ability to edit an organism’s genome using CRISPR has provided myriad applications ranging from crop development to novel therapeutics, while editing of various animal species offers hope in areas from de-extinction to xenotransplantation. But what about the domestic cat? In a new report published in The CRISPR Journal, researchers…

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Bioinformatics Scientist – GWAS – Invitae

Invitae is a rapidly growing, purposeful company. Our mission is to empower doctors and patients with genetic information to help them make informed medical decisions at all stages of life. The Integrated Risk Assessment Platform plays a meaningful role in rapidly growing our understanding of genomic health and personalized medicine….

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AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS  PubMed  PubMed Central  Google Scholar  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

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South-to-north migration preceded the advent of intensive farming in the Maya region

Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018). ADS  PubMed  Google Scholar  Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018). CAS  PubMed  PubMed Central  Google Scholar  Raghavan, M. et al. Genomic evidence for…

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Towards the Genetic Architecture of Complex Gene Expression Traits: Challenges and Prospects for eQTL Mapping in Humans

Review doi: 10.3390/genes13020235. Affiliations Expand Affiliation 1 Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, Korea. Free PMC article Item in Clipboard Review Chaeyoung Lee. Genes (Basel). 2022. Free PMC article Show details Display options Display options Format AbstractPubMedPMID doi: 10.3390/genes13020235. Affiliation 1 Department of…

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Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…

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A genome-scale screen for synthetic drivers of T cell proliferation

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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