Tag: EdU

[gmx-users] Why gyration radius keep dropping?

Post by ZHANG ChengDear Gromacs,I am running MD at 500 K for my protein.I used this to analyse the gyration radiusecho 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvgI thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a…

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(PDF) AntiHunter: searching BLAST output for EST antisense transcripts | Alessandro Guffanti

(PDF) AntiHunter: searching BLAST output for EST antisense transcripts | Alessandro Guffanti – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn more, view our Privacy Policy. ×…

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

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

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Postdoctoral Fellow – Plant Genomics & Bioinformatics – Fort Collins

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

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Plink Alternative Phenotype File Columns not being Read

Plink Alternative Phenotype File Columns not being Read 0 Hi, I have a plink alternative phenotype file with the following format: FID IID Phenotype 1 2 1 1 3 0 etc. As outlined in the plink documentation. zzz.bwh.harvard.edu/plink/data.shtml#pheno However, when I run the following command : plink –bfile ../Plink_Files/plink –logistic…

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Annotation of alternative cattle genome assembly

University of Maryland have assembled the cattle genome and in severalways we find this to be better than the Baylor assembly. Several groups including ours are using this version ofthe assembly. ftp.cbcb.umd.edu/pub/data/assembly/Bos_taurus/Bos_taurus_UMD_3.0/ NCBI has agreed to provide annotations for this version of the assemblyalso. I request you to host this…

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Genomics and Bioinformatics in Ames, IA for Iowa State University

Details Posted: 08-Jan-22 Location: Ames, Iowa Salary: Open Categories: Academic/Faculty Position Title: Postdoctoral – Genomics and Bioinformatics Appointment Type: Post Doc/Trainee Job Description: Summary of Duties and Responsibilities: Contribute to the Functional Annotation of Animal Genomes (FAANG) project in developing and testing of pipelines for the analysis of high-throughput genomics…

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Running Jobs on Titan

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

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Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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Bioconductor – chromhmmData

DOI: 10.18129/B9.bioc.chromhmmData     Chromosome Size, Coordinates and Anchor Files Bioconductor version: Release (3.14) Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two…

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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Haplogroup M (mtDNA)

In human genetics, Haplogroup M is a human mitochondrial DNA (mtDNA) haplogroup. An enormous haplogroup spanning many continents, the macro-haplogroup M is a branch of the haplogroup L3. M is believed to have originated in Asia [Gonzalez et al., [www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1945034 Mitochondrial lineage M1 traces an early human backflow to Africa]…

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Figure 4 | p57 Suppresses the Pluripotency and Proliferation of Mouse Embryonic Stem Cells by Positively Regulating p53 Activation

p57 suppressed the proliferation of mESCs. (a) The growth curve of control () and p57 knockdown (shp57, ) mESCs. (b, c) EdU staining results of control () and p57 knockdown (shp57, ) mESCs cultured for 48 h. (d) Real-time PCR analyses of pcna, Cyclin A, and Cyclin E expression levels of…

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Single cell RNAseq data analysis

Github repository  02-04 February 2022  SciLifeLab Solna, Tomtebodavägen 23b, Stockholm, Sweden This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours)…

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Cellular and Molecular Atlas of the Macaque Dorsal Horn

Arokiaraj, Cynthia Mary (2022) Cellular and Molecular Atlas of the Macaque Dorsal Horn. Doctoral Dissertation, University of Pittsburgh. (Unpublished) Abstract The spinal cord dorsal horn occupies a key position in the central nervous system, as it is the first site of integration of somatosensory input from the periphery. Local interneurons…

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Bioconductor – TBSignatureProfiler (development version)

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler. Profile RNA-Seq Data Using TB Pathway Signatures Bioconductor version: Development (3.15) Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates…

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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Associate Scientist, Bioinformatics – jobRxiv

Are you interested in being a key member of a bioinformatics team in a shared resource at a major cancer center?  This Associate Scientist position will support a wide array of bioinformatics research services in the Sylvester Comprehensive Cancer Center (SCCC) Biostatistics and Bioinformatics Shared Resource (BBSR) at the University…

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p57 Suppresses the Pluripotency and Proliferation of Mouse Embryonic Stem Cells by Positively Regulating p53 Activation

Embryonic stem cells (ESCs) are pluripotent stem cells that have indefinite self-renewal capacities under appropriate culture conditions in vitro. The pluripotency maintenance and proliferation of these cells are delicately governed by the concert effect of a complex transcriptional regulatory network. Herein, we discovered that p57Kip2 (p57), a cyclin-dependent kinase inhibitor…

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(PDF) Knocking Down the DRD2 by shRNA Expressing Plasmids in the Nucleus Accumbens Prevented the Disrupting Effect of Apomorphine on Prepulse Inhibition in Rat | siamak alizadeh

(PDF) Knocking Down the DRD2 by shRNA Expressing Plasmids in the Nucleus Accumbens Prevented the Disrupting Effect of Apomorphine on Prepulse Inhibition in Rat | siamak alizadeh – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our…

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(PDF) Mechanism-based CYP2D6 inactivation by acridone alkaloids of Indonesian medicinal plant Lunasia amara | Yasuhiro Tezuka

(PDF) Mechanism-based CYP2D6 inactivation by acridone alkaloids of Indonesian medicinal plant Lunasia amara | Yasuhiro Tezuka – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn more,…

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Bioinformatics Analyst in Evanston, IL for Northwestern University

Details Posted: 23-Dec-21 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Center for Genetic MedSalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to…

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Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis

1. Eyun, S. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol. Biol. 17, 23 (2017). PubMed  PubMed Central  Google Scholar  2. Eyun, S. et al. Evolutionary history of chemosensory-related gene families across the Arthropoda. Mol. Biol. Evol. 34, 1838–1862 (2017). CAS  PubMed …

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From where to get a comprehensive list of genes with gene start, gene end and chromosome for build 37?

From where to get a comprehensive list of genes with gene start, gene end and chromosome for build 37? 0 Hi all, I am trying to annotate list of genes with gene start, gene end (build37) and chromosome. I mapped most of the genes from a list downloaded from Biomart/UCSC,…

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How to convert bedgraph file with bins into GRanges object?

You could convert your bedGraph bins from hg18 to hg19 using liftover, so you can overlap them with your peaks. You would read them into a GRanges object, then hand this to the liftover function to translate from hg18 to hg19, then unlist the results to get back a regular…

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Harvard University hiring Bioinformatics Engineer in Boston, Massachusetts, United States

Job-Specific ResponsibilitiesWe are looking for a motivated bioinformatics engineer to join the Department of Biomedical Informatics at Harvard Medical School, to build platforms for genome analysis. Genome sequencing is becoming a routine approach for diagnosing genetic diseases. As the number of patients referred to genetic screening is increasing, there is…

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bioinformatics vacancy

On the one hand, I really liked the diversity of the bioinformatics program, and, with a degree in bioinformatics, there are many possible career paths. Updated on 2 December 2021. Exact wages will depend on experience and the industry an individual works in. Working experience with structural antigen analyses and…

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Representable, non-homologous, non-redundant protein database

Representable, non-homologous, non-redundant protein database 1 Hello, i’m examining properties of proteins secondary structures and for examining and presenting the results: What non-redundant (or non-homologous) protein database would you recommend? I’ve obtained a list of PDB ids from PISCES (dunbrack.fccc.edu/pisces/) and obtained the protein details from UniProt, however i’m not…

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Bioinformatics Librarian job with University of Pennsylvania

Bioinformatics Librarian 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. Penn has 12 highly-regarded schools that…

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Bioconductor – HEEBOdata

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see HEEBOdata. HEEBO set and HEEBO controls. Bioconductor version: 2.9 R objects describing the HEEBO oligo set. Author: Agnes Paquet Maintainer: Agnes Paquet <apaquet at medsfgh.ucsf.edu> Citation (from within R, enter citation(“HEEBOdata”)): Installation To…

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Bioconductor – MLInterfaces

    This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see MLInterfaces. Uniform interfaces to R machine learning procedures for data in Bioconductor containers Bioconductor version: 3.3 This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers. Author:…

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(PDF) Analysis of 16S rRNA environmental sequences using MEGAN

(PDF) Analysis of 16S rRNA environmental sequences using MEGAN | Suparna Mitra – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience.By using our site, you agree to our collection of information through the use of cookies.To learn more, view our Privacy Policy. × Log in…

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Assistant Professor- Bioinformatics in El Paso, Texas

About The University of Texas at El Paso: The University of Texas at El Paso is a Carnegie R1 and Community Engaged research university at the heart of the U.S.-Mexico border region that is increasing access to excellent higher education. UTEP enrolls nearly 25,000 students – 83% of whom are…

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Bioconductor – interactiveDisplay

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see interactiveDisplay. Package for enabling powerful shiny web displays of Bioconductor objects Bioconductor version: 3.2 The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Shawn…

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(PDF) Analysis of 16S rRNA environmental sequences using MEGAN | Suparna Mitra

(PDF) Analysis of 16S rRNA environmental sequences using MEGAN | Suparna Mitra – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn more, view our Privacy Policy. ×…

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CRAN – Package ggmatplot

CRAN – Package ggmatplot ggmatplot: Plot Columns of Two Matrices Against Each Other Using ‘ggplot2’ A quick and easy way of plotting the columns of two matrices or data frames against each other using ‘ggplot2’. Although ‘ggmatplot’ doesn’t provide the same flexibility as ‘ggplot2’, it can be used as a…

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Bioconductor – flagme

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see flagme. Analysis of Metabolomics GC/MS Data Bioconductor version: 2.9 Fragment-level analysis of gas chromatography – mass spectrometry metabolomics data Author: Mark Robinson <mrobinson at wehi.edu.au> Maintainer: Mark Robinson <mrobinson at wehi.edu.au> Citation (from…

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WGCNA, what does it mean if no hub genes are identified?

WGCNA, what does it mean if no hub genes are identified? 0 I ran WGCNA for my genes following the tutorials by Horvath and Langfelder (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/). I’ve obtained my modules and the GS and MM for my list of genes – however I think my situation is a bit odd….

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Biopython Contact Us | Contact Information Finder

Listing Results Biopython Contact Us Biopython · Biopython 2 hours ago Biopython.org View All Biopython. See also our News feed and Twitter. Introduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.. It is a distributed collaborative effort to…

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Bioconductor – PAIRADISE

DOI: 10.18129/B9.bioc.PAIRADISE     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PAIRADISE. PAIRADISE: Paired analysis of differential isoform expression Bioconductor version: 3.9 This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data. Author: Levon…

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Transcriptome assembly, annotation and submission to GenBank for unannotated organisms

Monday, October 4 at 3:00pm to 4:00pm Virtual Event Transcriptome assembly and annotation is a complex process that requires the integration of multiple databases using several computational tools for best results. The advances in next-generation sequencing technologies and the decrease in the cost of sequencing a complete transcriptome are driving…

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Recruitment Of Postdoctoral Scholar in Cancer Biology/Cancer Genomics University of Chicago

EMPLOYER Northwestern University LOCATION Chicago, Illinois SALARY Commensurate with experience POSTED September 21, 2021 DISCIPLINE Life Sciences, Computational Biology, Genomics, Immunology Position Type Full Time ORGANIZATION TYPE Academia Job Type Postdoc Postdoctoral recruiting (experiential or computational) is available in murine and human innate immune interactions or precision medicine approach during the development of rheumatoid…

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Selection of DNA Aptamers Recognizing EpCAM-Positive Prostate Cancer b

Introduction Prostate cancer (PCa) is one of the most common genitourinary system malignant tumor in men worldwide. In Asian countries, many patients with PCa are often diagnosed at an advanced stage maybe mostly because of a large population base with relatively backward economic development and imperfect cancer screening system of…

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PhD Student Needed for Machine Learning (Deep Learning and Classical) in Molecular Biology

Job:PhD Student Needed for Machine Learning (Deep Learning and Classical) in Molecular Biology 0 Several openings are available immediately (or as late as Fall 2022) Looking for a highly motivated PhD student for Computational Biology research, with an algorithm development focus. The Ecological and Evolutionary Signal-processing (EESI) and Informatics lab…

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Issues installing Pindel from git

Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib

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MUSC and Helix launch In Our DNA SC, first-of-its-kind population genomics program to drive preventive, precision health care for South Carolinians | MUSC

Large-scale initiative will advance innovative research, improved health outcomes CHARLESTON, S.C. and SAN MATEO, Calif., (Sept. 20, 2021) – The Medical University of South Carolina  (MUSC) and Helix have announced a strategic collaboration to develop a first-of-its-kind population genomics initiative in South Carolina called In Our DNA SC. The large-scale program is designed…

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Kaggle Training

Listing Results Kaggle training Learn Python, Data Viz, Pandas & More Tutorials Kaggle Learn Kaggle.com All Courses 8 hours agoPython Learn the most important language for data science. Intro to Machine Learning Learn the core ideas in machine learning, and build your first models. Intermediate Machine Learning Handle missing values,…

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Bioconductor – marray

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see marray. Exploratory analysis for two-color spotted microarray data Bioconductor version: 2.13 Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. Author: Yee Hwa (Jean) Yang…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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Junior Biostatistics Analyst job with University of California, San Francisco

Job Code and Payroll Title009403 BIOINFORMATICS PROGR 1 Job SummaryA smart hardworking individual with very strong communication and organizational skills is sought by the UCSF MS EPIC Study to serve as a Junior Biostatistics Analyst. Under direct supervision, individual will apply professional bioinformatics concepts and computational procedures to complete projects related…

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Biopython Contact Map | Contact Information Finder

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

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Computational Scientist-Bioinformatics in Chicago, IL for University of Chicago (UC)

  UPDATE: We are in process of fixing some issues with our job board search function. If you are experiencing any problems, we apologize for the inconvenience and thank you for your patience. Job Seekers, Welcome to HERC Jobs…

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Primo by Ex Libris

This feature requires javascript The page requested is unavailable.Please try again later. If the problem persists please contact  help staff Requested URI = /primo_library/libweb/action/display.do%253Bjsessionid=382AD2E317056B684AB60ED2CC941512%3Ftabs=viewOnlineTab&gathStatTab=true&ct=display&fn=search&doc=TN_cdi_doaj_primary_oai_doaj_org_article_7da760dddf234e9eb55d41e686093f46&indx=6&recIds=TN_cdi_doaj_primary_oai_doaj_org_article_7da760dddf234e9eb55d41e686093f46&recIdxs=5&elementId=5&renderMode=poppedOut&displayMode=full&frbrVersion=&vid=CCU&vl(12742070UI1)=all_items&mode=Basic&tab=pc_article&vl(12011063UI0)=creator&dscnt=0&scp.scps=primo_central_multiple_fe&vl(freeText0)=Tsai%252C%2520Meng-Han&vl(1UIStartWith0)=exact&dstmp=1627244584242Requested URL = primo.lib.ccu.edu.tw:80/primo_library/libweb/action/display.do%253Bjsessionid=382AD2E317056B684AB60ED2CC941512%3Ftabs=viewOnlineTab&gathStatTab=true&ct=display&fn=search&doc=TN_cdi_doaj_primary_oai_doaj_org_article_7da760dddf234e9eb55d41e686093f46&indx=6&recIds=TN_cdi_doaj_primary_oai_doaj_org_article_7da760dddf234e9eb55d41e686093f46&recIdxs=5&elementId=5&renderMode=poppedOut&displayMode=full&frbrVersion=&vid=CCU&vl(12742070UI1)=all_items&mode=Basic&tab=pc_article&vl(12011063UI0)=creator&dscnt=0&scp.scps=primo_central_multiple_fe&vl(freeText0)=Tsai%252C%2520Meng-Han&vl(1UIStartWith0)=exact&dstmp=1627244584242?vid=CCU&dscnt=0&dstmp=1631989263370User-Agent = Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.116 Safari/537.36 Read more here: Source link

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Bioconductor – VanillaICE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see VanillaICE. A Hidden Markov Model for high throughput genotyping arrays Bioconductor version: 3.4 Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. Author: Robert Scharpf <rscharpf at jhu.edu>, Kevin Scharpf,…

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Bioconductor – FunciSNP

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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BIOINFORMATICIAN II

Apply at: uab.taleo.net/careersection/ext/jobdetail.ftl?job=T190159&tz=GMT-05%3A00&tzname=America%2FChicago A Bioinformatician II is needed to participate in research activities involved in the analysis of Next Generation Sequencing such as data derived from genomics and transcriptomics (bulk and single-cell sequencing) to the UAB Biological Data Science institutional core (www.uab.edu/cores/ircp/bds & Twitter page: twitter.com/UAB_BDS) . This position will…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Liftover nonmodel VCF

Liftover nonmodel VCF 1 Hi all, I have a FASTA genome assembly and a VCF for my (nonmodel) study species. Now I want to liftover the VCF to the Zebra Finch genome (www.ncbi.nlm.nih.gov/assembly/GCF_003957565.1). I’ve found Picard LiftOver GATK and CrossMap, but both require a UCSC chain file, which apparently can…

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UCSC MySQL access

UCSC MySQL access 1 Anyone know if the public can still access UCSC db remotely? Can’t seem to get access :/ genome.ucsc.edu/goldenPath/help/mysql.html XXX@XXX-MacBook-Pro:~$ mysql –user=genome –host=genome-mysql.soe.ucsc.edu -A -P 3306 ERROR 2002 (HY000): Can’t connect to MySQL server on ‘genome-mysql.soe.ucsc.edu‘ (36) XXX@XXX-MacBook-Pro:~$ mariadb –version mariadb Ver 15.1 Distrib 10.5.8-MariaDB, for osx10.15…

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SNP exon region UCSC

SNP exon region UCSC 2 how i can get SNP in only exons regions genome with UCSC? UCSC get the all SNP of gene region, and there is no filter option to get only exon region. tx ucsc SNP exon • 245 views • link updated 2 hours ago by…

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Bioconductor – pdInfoBuilder

Platform Design Information Package Builder Bioconductor version: 2.5 Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg….

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New research provides an additional overview of optimistic reasons related to heart regeneration

CRISPR / Cas9 Wls knockdown in cardiomyocytes promotes cardiac fibroblast proliferation during neonatal cardiac regeneration. Green indicates vimentin-positive cardiac fibroblasts. Red indicates cells that are proliferating with the EdU label. Blue indicates nuclei with DAPI staining. Credit: Texas Heart Institute Texas Heart Institute has new research from its abundant cardiomyocyte…

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Bioconductor – TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler. Profile RA-Seq Data Using TB Pathway Signatures Bioconductor version: 3.12 Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to…

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Bioinformatician job with Clemson University – Center for Human Genetics

The Clemson University Center for Human Genetics and the Greenwood Genetic Center have been awarded a five year Phase I Center of Biomedical Research Excellence (COBRE) in Human Genetics grant to understand the genetic, genomic, and epigenetic mechanisms by which molecular genetic variation affects transcriptional and other molecular networks in…

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Faculty Receives National Institutes of Health Grant to Further Single-cell RNA Sequencing Analysis

Newswise — Rutgers School of Public Health assistant professor, Wei Vivian Li, has received a five-year $1,953,068 National Institute of General Medical Sciences Maximizing Investigators’ Research Award (R35GM142702) to develop novel statistical methods and bioinformatics software to further analyze RNA sequencing data at the single-cell level. The work will be…

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R Bioconductor Courses

Listing Results R bioconductor courses Bioconductor Introduction To R / Bioconductor Harvard Bioconductor.org All Courses 016-05-16 Just NowIntroduction to R / Bioconductor. Buffalo, NY. 2016-05-16 ~ 2016-05-17. Instructors. Martin Morgan; Lori Shepherd; Description. This is a two-day course introducing R and Bioconductor for the analysis and comprehension of high-throughput genomic…

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Bioconductor – systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata. systemPipeRdata: NGS workflow templates and sample data Bioconductor version: 3.9 systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used…

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Bioconductor – gaschYHS

DOI: 10.18129/B9.bioc.gaschYHS     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see gaschYHS. ExpressionSet for response of yeast to heat shock and other environmental stresses Bioconductor version: 3.12 Data from PMID 11102521 Author: Audrey Gasch and colleagues Maintainer: Vince Carey <stvjc at channing.harvard.edu>…

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Bioconductor – mouse430a2frmavecs

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see mouse430a2frmavecs. Vectors used by frma for microarrays of type mouse430a2 Bioconductor version: 2.13 This package was created by frmaTools version 1.11.0. Author: Matthew N. McCall <mccallm at gmail.com>, Rafael A. Irizarry <rafa at…

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Bioconductor – Clomial

DOI: 10.18129/B9.bioc.Clomial     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Clomial. Infers clonal composition of a tumor Bioconductor version: 3.12 Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained…

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Bioconductor – methylationArrayAnalysis

DOI: 10.18129/B9.bioc.methylationArrayAnalysis     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see methylationArrayAnalysis. A cross-package Bioconductor workflow for analysing methylation array data. Bioconductor version: 3.11 Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation…

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Bioinformatics Analyst I

Dr. Fazal is seeking a Bioinformatics Analyst I to develop and apply genomic analysis tools to identify cis- and trans- factors associated with RNA localization. The Fazal lab is a young laboratory focusing on systematically interrogating the subcellular transcriptomes of mammalian cells and characterizing the scope, regulation, and function of…

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Postdoctoral Research Associate / Bioinformatics Analyst Job Opening in North Chicago, IL at Rosalind Franklin University of Medicine & Science

Position Summary Dr. Monika Waszczuk (Department of Psychology, Rosalind Franklin University of Medicine and Science) is seeking to appoint a Postdoctoral Research Fellow / Bioinformatics Analyst to work on a variety of ongoing research projects that explore the role of genetic vulnerability in PTSD, depression, and other mental health problems….

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Bioconductor – dsQTL

DOI: 10.18129/B9.bioc.dsQTL     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see dsQTL. dsQTL, data excerpt from Degner et al. 2012 Nature letter Bioconductor version: 3.11 dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity Author:…

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Bioconductor – fcScan

DOI: 10.18129/B9.bioc.fcScan     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see fcScan. fcScan for detecting clusters of coordinates with user defined options Bioconductor version: 3.12 This package is used to detect combination of genomic coordinates falling within a user defined window size…

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Bioconductor – WES.1KG.WUGSC

DOI: 10.18129/B9.bioc.WES.1KG.WUGSC     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see WES.1KG.WUGSC. Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). Bioconductor version: 3.10 The assembled…

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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

. 2021 Sep;39(9):1129-1140. doi: 10.1038/s41587-021-01049-5. Epub 2021 Sep 9. Jonathan Foox  1   2 , Scott W Tighe  3 , Charles M Nicolet  4 , Justin M Zook  5 , Marta Byrska-Bishop  6 , Wayne E Clarke  6 , Michael M Khayat  7   8 , Medhat Mahmoud  7   8 , Phoebe K Laaguiby  3 , Zachary T…

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Research Scientist- Bioinformatics & Computational Biology

Position Description: Research Scientist- Bioinformatics & Computational Biology, position in Christopher S. Bond Life Science Center, University of Missouri-Columbia. Potential Start Date: November 1, 2021 Duration: 24-month initial appointment, renewable afterwards Minimum Qualifications: Applicant must have a PhD degree in Computer Science, Bioinformatics, or related field. Strong publication record, especially…

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Bioinformatics Systems Analyst – Job posted on PostdocJobs.com

Job Description Job-Specific Responsibilities The Department of Biomedical Informatics (DBMI) at Harvard Medical School is looking for a Bioinformatics Systems Analyst to help us build cutting-edge research platforms. We seek an individual to work on our multidisciplinary team of data scientists, medical doctors, post-doctoral fellows, project managers, and software developers….

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University of Maryland, Baltimore (UMB) hiring Senior Bioinformatics Analyst in Baltimore, Maryland, United States

Job DescriptionThe University of Maryland, Baltimore (UMB), Institute of Human Virology (IHV) is currently recruiting for a Senior Bioinformatics Analyst. The Senior Bioinformatics Analyst provides complex support to Principal Investigator in the Division of Epidemiology and Prevention. The range of duties include, but are not restricted to, designing statistical analysis,…

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How to download data for visualising and analysing in RINalyzer in Cytoscape.

How to download data for visualising and analysing in RINalyzer in Cytoscape. 1 I am new to this plugin in Cytoscape. I want to visualise RIN from pdb and analyze the network. According to the tutorial we can download daat from RIN data websever. But when I am trying to…

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Bioconductor – jmosaics

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see jmosaics. Joint analysis of multiple ChIP-Seq data sets Bioconductor version: 2.12 jmosaics detects enriched regions of ChIP-seq data sets jointly. Author: Xin Zeng Maintainer: Xin Zeng <xinzeng at stat.wisc.edu> Citation (from within R,…

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UCSC knownCanonical hg19 vs. hg38

Hello, We have an FAQ page that covers this topic (genome.ucsc.edu/FAQ/FAQgenes.html#singledownload). As posted by ATpoint, it boils down to different datasets and different approaches. hg19 knownCanonical was last updated in 2013 and built primarily from RefSeq and GenBank sequences and a few other sources. One isoform was identified from each…

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Postdoctoral Fellow Position(s) in Cancer Adoptive Cell Immunotherapy or Bioinformatics

Job Description Dr. Lu’s Lab is seeking motivated, hardworking Post-Doctoral Candidate(s) with a background in immunology and/or cancer biology to take projects focused on understanding to chimeric antigen receptor (CAR) T cell or other cancer immunotherapy resistance. Candidates with a background in bioinformatics are also preferred if they are willing…

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A protein bridging the gap between sea urchin generations

In the second half of the 1800s biologists began to investigate the cellular basis of development. Sea urchins became a favorite material for this endeavor because their gametes can be obtained in vast numbers and fertilization and development are external to the adult body. The first research on fertilization centered…

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Postdoctoral Scientist in Statistical Bioinformatics and Software Development, WEHI, Melbourne, Australia

Research Officer (Statistical Bioinformatics)Bioinformatics Division, WEHI, Australia An opportunity is available for a Research Officer (Statistical Bioinformatics) to join the Bioinformatics Division at Australia’s pre-eminent biomedical research institute. About the position An exciting opportunity exists for a postdoctoral scientist (Research Officer) to join the research laboratory of Professor Gordon Smyth…

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Get rsID for a list of SNPs in an entire GWAS sumstats file

Here is a fairly efficient way to do this; assuming hg38 and BEDOPS and standard Unix tools installed. $ bedmap –echo –echo-map-id –delim ‘t’ <(awk ‘{n=split($0,a,/[:_]/); print “chr”a[1]”t”a[2]”t”a[2]+1″t”a[3]”https://www.biostars.org/”a[4];}’ sumstats.txt | sort-bed -) <(wget -qO- hgdownload.cse.ucsc.edu/goldenPath/hg38/database/snp150.txt.gz | gunzip -c | cut -f2-5 | sort-bed -) > answer.bed This gets around making…

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Bioconductor – pd.feinberg.mm8.me.hx1

    This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see pd.feinberg.mm8.me.hx1. Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Bioconductor version: 2.8 Platform Design Info for NimbleGen feinberg_mm8_me_hx1 Author: Martin Aryee Maintainer: Martin Aryee <aryee at jhu.edu> Citation (from within R, enter citation(“pd.feinberg.mm8.me.hx1”)): Installation To…

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UCSC liftover

UCSC liftover 2 Hi, I’m using UCSC liftover to convert hg19 to hg38. The result came out that I don’t understand. Feb. 2009 (GRCh37/hg19) → Dec. 2013 (GRCh38/hg38) – chr1:120904787 → chr1:143905854 Dec. 2013 (GRCh38/hg38) → Feb. 2009 (GRCh37/hg19) – chr1:143905854 → chr1:149400430 (I didn’t check “Allow multiple output regions”.)…

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How to download GTEx figure from USCS genome browser

How to download GTEx figure from USCS genome browser 1 Hello, Unfortunately the GTEx images are generated on demand then erased later. In case it helps, these are dynamically generated by R from the track data. We can help with finding the exact parameters if you are interested. The temporary…

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A Students’ Guide for Tackling Big Data

Advances in technology have made analyzing large data sets ever more accessible—but there’s still a steep learning curve for students in entomology and other scientific disciplines. (Photo by Christiaan Colen via Flickr, CC BY-SA 2.0) By Victoria Pickens Editor’s Note: This post is part of a series contributed by the…

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Koala killer being passed to joeys from mum – UQ News

A deadly koala virus that can cause immune depletion and cancer, known as koala retrovirus, is being transferred to joeys from their mothers, according to University of Queensland scientists. Associate Professor Keith Chappell, from UQ’s School of Chemistry and Molecular Biosciences, said the virus predisposes koala to chlamydia and other…

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Bioconductor – HarmonizedTCGAData

DOI: 10.18129/B9.bioc.HarmonizedTCGAData     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see HarmonizedTCGAData. Processed Harmonized TCGA Data of Five Selected Cancer Types Bioconductor version: 3.10 This package contains the processed harmonized TCGA data of five cancer types used in “Tianle Ma and Aidong…

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High-throughput DNA sequencing of environmentally insulted latent fingerprints after visualization with nanoscale columnar-thin-film technique

. 2021 Sep;61(5):505-515. doi: 10.1016/j.scijus.2021.06.002. Epub 2021 Jun 7. Affiliations Expand Affiliations 1 Forensic Science Program and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. 2 Department of Psychiatry, Yale University School of Medicine & VA CT Healthcare System, New Haven, CT 06511, USA….

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Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries?

Where is the annotation file if using the GtRNAdb (tRNA SE analysis) for mapping to RNAseq libraries? 0 Hi all, On the GtRNAdb (tRNA-SE analysis) website there is a file containing fasta sequences of different tRNA genes. gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/ I aligned this GtRNAdb database with RNAseq libraries using bowtie2 and got…

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AutoDock Flexible Molecular Docking Tutorial

AutoDock Flexible Molecular Docking Tutorial Autodock is a molecular docking software package, open source and free, the official website is autodock.scripps.edu/, the latest version is AutoDock 4.2.6, including AutoDock and AutoGrid two modules, AutoDock software package download address It is autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/, including Linux, Mac OS and Windows versions…

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BIOINFORMATICS PROGRAMMER

UC San Diego Health BIOINFORMATICS PROGRAMMER Filing Deadline: Thu 9/16/2021, thereafter Open Until filled Salary Range: Commensurate with Experience The UCSD Hemophilia and Thrombosis Treatment Center has a wide-ranging clinical, translational and basic research program, involving genomic and proteomic analysis, in the field of thrombosis and hemostasis. This role involves…

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