Tag: HYBRID

Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

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Caribou Biosciences Announces – GuruFocus.com

BERKELEY, Calif., May 11, 2022 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. ( CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, today announced the appointment of David L. Johnson to its board of directors. Mr. Johnson is a seasoned executive with 30 years of commercial and operational experience in the biopharmaceutical…

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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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A new approach produces a 90-fold increase in

Article Highlight | 15-Jun-2022 Researchers leverage viruses identified from worldwide environmental samples to expand knowledge of viral taxa and their role in tree microbiomes DOE/US Department of Energy image: Analysis of metatranscriptome samples with novel viral taxa in Populus. (Top) Graphical abstract of the pipeline. (Bottom) Percentage read classification with novel…

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Novartis announces promising five-year data for leukaemia treatment Kymriah

Novartis has shared long-term, five-year follow-up results from its pivotal clinical phase 2 trial, ELIANA, evaluating Kymriah (tisagenlecleucel), the first-ever approved CAR T-cell therapy, in children and young adult patients with relapsed or refractory (r/r) B-cell acute lymphoblastic leukaemia (ALL). Kymriah is a one-off treatment designed to help patients’ immune…

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RCSB PDB – 7SBA: Structure of type I-D Cascade bound to a dsDNA target

CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems … CRISPR-Cas systems are…

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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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A Standardized, Specification-Driven API Lifecycle

Transcript Lane: I’d like to share with you a high level view of why API specifications matter. How OpenAPI, AsyncAPI, JSON Schema and others are helping us standardize and deliver API lifecycle in a way that the machines understand. Also, allows us humans to better communicate, collaborate, and move forward…

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Microsoft (MSFT) Azure Selected by Meta to Boost AI Innovation

Microsoft MSFT, over the past few years, has almost doubled down on the cloud computing opportunity. Growing demand for the company’s cloud solutions is expected to strengthen its competitive position in the cloud computing market. In the last reported quarter, Microsoft Cloud revenues were up 32% year-over-year, at $23 billion….

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Scientists Genetically Edited Regular Tomatoes To Improve Vitamin D Levels

Scientists have genetically edited tomatoes that are more nutritious in provitamin D3 — a precursor to vitamin D, and they’re as high as two whole eggs or a tablespoon full of tuna. Unsplash Also Read: Tomato Maestros At Heinz Mimicked Mars To Create Alien Ketchup They did so by disabling a…

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Bispecific antibodies | Scientist Live

Bispecific antibodies: rising stars in antibody therapeutics Monoclonal antibodies (mAbs) are important therapeutic agents for the treatment of many human diseases, such as cancer, autoimmune diseases, cardiovascular diseases, asthma, and viral infections. Unlike monospecific mAbs, bispecific antibodies (bsAbs) are antibodies containing two antigen-binding sites and therefore can simultaneously target two…

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Cogent Biosciences Reports Recent Business Highlights and First Quarter 2022 Financial Results

Cogent Biosciences, Inc. Initial bezuclastinib APEX data to be presented at the European Hematology Association (EHA) 2022 Annual Congress Building a portfolio of discovery stage programs, creating potential best-in-class small molecule kinase inhibitors for genetically defined oncology indications and rare diseases Ended 1Q 2022 with $191.0 million in cash, sufficient…

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Administrative Assistant – Director’s Office at European Molecular Biology Laboratory (EMBL)

About the team/job The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations in the world. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Hinxton (UK) and Rome (Italy).  The Director advises and works closely…

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Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar  Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article  Google Scholar  Odland,…

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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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Plant Breeding and CRISPR Plants Market Trends 2022, Global Industry Share, Size, Global Industry Analysis, Key Market Growth Analysis, Segments, Emerging Technologies, Opportunity and Forecast 2027

The “Plant Breeding and CRISPR Plants Market” research report 2021-2027 offering the complete outline of market size, share and growth opportunities, industry segmentation by product type, applications and geographical representation. The report highlights product development along with technological upgrades that can boost the market growth. The Plant Breeding and CRISPR…

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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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Top gru open source projects

Pytorch Seq2seq Tutorials on implementing a few sequence-to-sequence (seq2seq) models with PyTorch and TorchText. Rnn ctc Recurrent Neural Network and Long Short Term Memory (LSTM) with Connectionist Temporal Classification implemented in Theano. Includes a Toy training example. Haste Haste: a fast, simple, and open RNN library Eeg Dl A Deep…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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AWS Bioinformatics DevOps Engineer – Proven Recruiting

San Diego, California Work Arrangement: Hybrid 2022-04-25 AWS DevOps Engineer – Hybrid Onsite in San Diego If you’re looking for a place where your work really matters and makes a life-changing impact on others… look no further! Our client in the biotech space is looking to bring on a skilled…

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Rat Model Market revenue worth USD 2.3 Billion by 2028,

Selbyville, Delaware, April 26, 2022 (GLOBE NEWSWIRE) — The rat model market value is projected to reach USD 2.3 billion by 2028, according to a new research report by Global Market Insights Inc. Growing consumption of personalized medicine and increasing number of clinical trials is expected to augment the market…

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Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Pair_style smoothed LJ – LAMMPS Beginners

Fatima April 15, 2022, 6:59pm #1 Hello All,I would like to perform a simulation of a system particles interaction via a smoothed LJ potential. the potential has two extra terms compared with the original one. LJ_smooth= 4e((s/r)^12-(s/r)^6) + 4e(c0+c2(r/s)^2) for r<rc I am looking for a pair_style command that let…

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aCGH – Allie: Result by abbreviation

1  array comparative genomic hybridization(1473 times) Neoplasms(306 times) FISH (238 times)CNVs (135 times)MLPA (72 times) 2003 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. 2  array CGH(43 times) Neoplasms(12 times) CNVs (7 times)FISH (3 times)ID (3 times) 2003 Combined array comparative genomic hybridization and…

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LAMMPS run problems – LAMMPS General Discussion

Hi,Recently i use three types of interatomic potential (eam/alloy, eam/fs, bop) for my system (Fe-Cu-H) and perform an energy minimization of the atomic coordinates of the system ,I meet an error that is ‘segmentation fault’. The version of LAMMPS is lammps3Mar20. The system has more than 650000 particles and does…

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What is genetic engineering and how can it benefit healthcare?

Have you heard of purple tomatoes? Or golden rice? If you haven’t, you might be surprised to know that these have actually been created by scientists via genetic engineering. These are genetically modified foods, with purple tomatoes containing 10 times more antioxidants than a normal red tomato. On the other…

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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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H2O.ai brings AI grandmaster-powered NLP to the enterprise

There are about 1200 chess grandmasters in the world, and only 250 AI grandmasters. In chess, as in AI, grandmaster is an accolade reserved for the top tier of professional players. In AI, this accolade is given out to the top-performing data scientists in Kaggle’s progression system. H2O.ai, the AI…

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LAMMPS Patch Release 24 March 2022

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

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[lammps-users] extending of compute centroid/stress/atom command – LAMMPS Mailing List Mirror

Thank you so much for your help. -I’m not sure this calculation makes some physical sense. This idea comes from <Heat conduction in chain polymer liquids: Molecular dynamics study>(doi.org/10.1063/1.3613648). In my system, there are two kinds of materials: A and B. The only connection between A and B is the…

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Sigma-Aldrich Files Opposition to CVC Substantive Preliminary Motion No. 1 to be Accorded Priority Benefit | McDonnell Boehnen Hulbert & Berghoff LLP

On February 18th, Sigma-Aldrich filed its Opposition to Junior Party’s (the University of California, Berkeley; the University of Vienna; and Emmanuelle Charpentier; collectively, “CVC”) Substantive Preliminary Motion No. 1 in Interference No. 106,132, asking the Patent Trial and Appeal Board for benefit of priority to U.S. Provisional Application No. 61/652,086,…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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[slurm-users] Performance with hybrid setup

Hello, I’m performing some tests (CPU-only systems) in order to compare MPI versus hybrid setup. The system is running OpenMPIv4.1.2 so that a job submission reads:       mpirun -np 48 foo.exe or       export OMP_NUM_THREADS=8       mpirun -np 6 foo.exe In our system, the latter runs slightly faster (about 5…

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BTG2 gene predicts poor outcome in PT-DLBCL

Introduction Primary testicular diffuse large B-cell lymphoma (PT-DLBCL) is a rare and aggressive form of mature B-cell lymphoma.1–3 PT-DLBCL was the most common type of testicular tumor in men aged over 60 and characterized by painless uni- or bilateral testicular masses with infrequent constitutional symptoms.4–6 PT-DLBCL shows significant extranodal tropism,…

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Next Generation Sequencing (NGS) Leader Nick McCooke Joins Genomics Company RevoluGen as Strategic Advisor

LONDON, March 10, 2022–(BUSINESS WIRE)–UK genomics company, RevoluGen Ltd. (RevoluGen or the Company), today announces that Nick McCooke, widely recognised leader in the next generation sequencing (NGS) field, has been appointed as Strategic Advisor. This press release features multimedia. View the full release here: www.businesswire.com/news/home/20220310005076/en/ Nick McCooke, NGS Expert and…

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Business News | IIIT Hyderabad’s Annual R&D Showcase to Be Presented for the First Time in Metaverse

Hyderabad (Telangana) [India], March 8 (ANI/PR Newswire): IIITH’s annual R&D Showcase will be held this year on Saturday 12 March 2022 in a hybrid model – physically on campus for students and in the metaverse for visitors. The Showcase will be hosted on the metaverse by NextMeetLive, one of CIE…

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CEFAS22-11 Next Generation Sequencing Services Framework: | Construction Tenders

Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Tender Details Reference ocds-h6vhtk-031eee Common Procurement Vocabulary Technical analysis or consultancy services Procurement Method Open procedure Value £500,000 Section I: Contracting authority I.1) Name and addresses CEFAS Pakefield Road Lowestoft NR33 0HT…

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rstudio::conf(2022) is open for registration!

rstudio::conf, the conference for all things R and RStudio, will take place July 25-28 in National Harbor, DC! As usual, we’ll have two days of workshops followed by two days of talks. If you’ve attended before and already know you want to attend, register now! Otherwise, read on to learn…

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Caribou Biosciences to Present at Upcoming Investor Conferences

Get instant alerts when news breaks on your stocks. Claim your 1-week free trial to StreetInsider Premium here. BERKELEY, Calif., March 07, 2022 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq: CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today that Rachel Haurwitz, Ph.D., Caribou’s president and chief executive officer,…

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The Ribosomal Protein RpL22 Interacts In Vitro with 5′-UTR Sequences Found in Some Drosophila melanogaster Transposons

Mobility of eukaryotic transposable elements (TEs) are finely regulated to avoid an excessive mutational load caused by their movement. The transposition of retrotransposons is usually regulated through the interaction of host- and TE-encoded proteins, with non-coding regions (LTR and 5′-UTR) of the transposon. Examples of new potent cis-acting sequences, identified…

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Dublin, Ireland | Bioinformatics Research Fellow: Understanding the production of CAR-T cell therapies

Job:Dublin, Ireland | Bioinformatics Research Fellow: Understanding the production of CAR-T cell therapies 0 Cell therapy is the transfer of intact, live cells into a patient to treat or cure a disease. Cell-based immunotherapy and in particular, modified-cell immunotherapy such as CAR-T, has been delivering spectacular results for cancer patients…

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Secondary succession of bacterial communities and co-occurrence of phylotypes in oil-polluted Populus rhizosphere

doi.org/10.1016/j.soilbio.2012.11.018Get rights and content Abstract Oil pollution can be considered as a driver for bacterial secondary succession. A greenhouse study was conducted using forest mineral soil contaminated by heavy fuel oil and planted with hybrid aspen. The aim was to compare the bacterial succession in oil- and plant-amended ecosystems. Samples…

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Post-doctoral Research Fellow job with KINGS COLLEGE LONDON

Job description We are seeking an enthusiastic and experience postgraduate researcher with a PhD in psychiatric genetics or a related field, to work with the Biomarkers and Genomics theme of the NIHR Maudsley BRC.  In this role, you will lead on development of collaborative genetic projects in the BRC, including…

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Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

This protocol presents a complete experimental workflow for studying RNA-protein interactions using optical tweezers. Several possible experimental setups are outlined including the combination of optical tweezers with confocal microscopy. The overall goal of the following method article is to demonstrate a protocol useful to study RNA interactions with proteins or…

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[lammps-users] On hybrid REAX FF – LAMMPS Mailing List Mirror

Hello, I am simulating a bilayer system with REAX FF comprising 2 surfaces. Surface #1 comprises C, H, O, and N; surface #2 is composed of C, H, O, and V. I have two REAX force field files for each surface. I am using hybrid pair_style to simulate the surfaces…

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HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd

Bioinformatics Scientist 2 Hours: 37.5 hours per week Salary: Competitive Ref No: HRJOB7442 Business Unit: Diagnostic Services Location: Craigavon or Manchester Open To: Internal and External Applicants The Company Almac Diagnostic Services is a leading stratified medicine business, specialising in biomarker-driven clinical trials. We are incredibly proud to be involved…

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UMD Genome group

An email was successfully sent. MaSuRCA assembler MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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Katia Feve – Academia.edu

Katia Feve – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. 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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H2O brings AI grandmaster-powered NLP to the enterprise

There are about 1200 chess grandmasters on the earth, and solely 250 AI grandmasters. In chess, as in AI, grandmaster is an accolade reserved for the highest tier {of professional} gamers. In AI, this accolade is given out by the top-performing knowledge scientists in Kaggle’s development system. H2O.ai, the AI…

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Lammps stop running on hpc cluster but it can run on my own computer – LAMMPS General Discussion

Hi there, I am recently want to try running an oxidation process.Here is my codes and report from the cluster.it can run the minimize part. After the minimization,it seems that it stop after printing” setting up verlet run”.Can you help me? Thank you So much!package omp 4 neigh no#newton onunits…

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CAMBREEN-WEEDER-BIOMOBY 3geonames

CAMBREEN-WEEDER-BIOMOBY Pick a Random location anywhere API Pick a Random location proximal to Land 78.489530, 17.759360, 0 Source Code Perl5 Geo::Code::XYZ README Reverse Geocode.xyz Near Philippbreen Svalbard Spitsbergen SJ Elevation: 632 metres TimeZone: Arctic/Longyearbyen Points of Interest around 78.489530,17.759360 Results from Reverse Geocoder Lite api.3geonames.org/78.489530,17.759360 Geocode.xyz/78.489530,17.759360 N6D2H5UWRW CAMBREEN-TKH5B0 🇸🇯 Nearby…

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The epigenetic dimension of protein structure

References [1] Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, et al. Highly accurate protein structure prediction for the human proteome. Nature. 2021;596:590–6.10.1038/s41586-021-03828-1Search in Google Scholar [2] Hardy J, Allsop D. Amyloid deposition as the central event in the aetiology of Alzheimer’s disease. Trends Pharmacol Sci….

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Help regarding LAMMPS HMC using C – LAMMPS Development

Hello I am working on creating a Hybrid Monte Carlo (HMC) code in LAMMPS using C programming language for running a NPT system.I have a working HMC code for a NVT system. I am trying to make it into a NPT system but am facing difficulty in passing the changed…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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A kolmogorov/crespi/full LAMMPS question (from a mathematician) – LAMMPS Development

Dear Colleagues, We are developing a discrete-to-continuum procedure that will allow to model a graphene bilayer as a continuum sheet. We are able to compare continuum and discrete simulations results for fake simple systems (e.g., in-plane harmonic extensional, torsional, and dihedral springs + LJ or kolmogorov/crespi/z interactions between the layers)…

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Materials Science Community Discourse

Sign Up Log In Log In Popular FireworksFireWorks Using fix GCMC to plot adsorption isothermsLAMMPS General Discussion Topic of the Month: What are your favorite pre- and postprocessing toolsLAMMPS Why is My lattice size increasing during the initial NPT run for equilibrating Si diamond crystal?LAMMPS General Discussion About fix smdLAMMPS…

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Spatial components of molecular tissue biology

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

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Caribou Biosciences to Present at the SVB Leerink 11th Annual Global Healthcare Conference

BERKELEY, Calif., Feb. 07, 2022 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq:CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today that Rachel Haurwitz, Ph.D., Caribou’s president and chief executive officer, will participate in a fireside chat at the SVB Leerink 11th Annual Global Healthcare Conference on Thursday, February 17th,…

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Bioinformatics Scientist Job Opening in Seattle, WA at Alpine Immune Sciences

Job Posting for Bioinformatics Scientist at Alpine Immune Sciences Alpine Immune Sciences is applying our platform discovery technology to bring innovative new therapies to people living with serious or life-threatening illnesses or conditions, such as cancer and autoimmune/inflammatory diseases. Exciting challenges lie ahead—guided by our core values, we’ll…

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Data Scientist – Molecular Biology job with SRG

Data Scientist London (hybrid, some remote working is possible) Permanent Up to £40k per annum I’m partnering with an exciting and revolutionary MedTech organisation based in London who are hiring for a Data Scientist to join their assay development team. The organisation has developed unique wearable, personalised technology to inform…

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Transverse Sectioning of Mature Rice (Oryza sativa L.) Kernels for Scanning Electron Microscopy Imaging Using Pipette Tips as Immobilization Support

This protocol allows for the preparation of transverse sections of cereal seeds (e.g., rice) for the analysis of endosperm and starch granule morphology using scanning electron microscopy. This protocol allows seeds to be sliced intact so they don’t crumble, permitting visualization of starch granules in any seed that can fit…

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Pair_write with eam/alloy – error – LAMMPS General Discussion

Dear LAMMPS Users, I encountered a problem while trying to use pair_write command with an eam/alloy potential. pair_style hybrid eam/alloy table spline 100000 zbl 1.0 4.0pair_coeff * * eam/alloy Be_Agrawal.eam.alloy Be NULLpair_coeff 1 2 table DBe.potential-table DFT_DBEpair_coeff 2 2 zbl 1.0 1.0pair_write 1 1 100 r 1.0 6.0 table.txt metal…

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A cell-based phenotypic library selection and screening approach for the de novo discovery of novel functional chimeric antigen receptors

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

Continue Reading A cell-based phenotypic library selection and screening approach for the de novo discovery of novel functional chimeric antigen receptors

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

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

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

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

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Using Minimap2 with FMLRC2

Using Minimap2 with FMLRC2 1 Hello all, I am using FMLRC2 (github.com/HudsonAlpha/rust-fmlrc) to correct PacBio reads with Illumina reads for hybrid genome assembly. Since FMLRC2 only corrects reads (does not do any assembly) another program is needed. In the paper published on FMLRC minimap (now succeeded by minimap2, github.com/lh3/minimap2) was…

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Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

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Addressing the Challenges of AAV Production

Adeno-associated virus (AAV) vectors are a versatile and appealing gene therapy delivery platform, capable of targeting a wide range of cell types. However, AAV must be produced in a living system, and issues with scalability and high production costs have so far limited the widespread adoption of the technology. Technology…

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Caribou Biosciences to Present at 40th Annual J.P. Morgan Healthcare Conference

BERKELEY, Calif., Jan. 04, 2022 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq:CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today that Rachel Haurwitz, Ph.D., Caribou’s president and chief executive officer, will present a corporate update at the 40th Annual J.P. Morgan Healthcare Conference on Thursday, January 13, 2022 at…

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RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

Abstract Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However,…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

doi: 10.3389/fgene.2021.772557. eCollection 2021. Chun Huang  1 , Fei Ge  1 , Xiaoming Ma  1 , Rongfeng Dai  1 , Renqing Dingkao  2 , Zhuoma Zhaxi  3 , Getu Burenchao  3 , Pengjia Bao  1 , Xiaoyun Wu  1 , Xian Guo  1 , Min Chu  1 , Ping Yan  1 , Chunnian Liang  1 Affiliations Expand Affiliations 1 Key Laboratory of…

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48 Postdoctoral and Academic Positions at The European Molecular Biology Laboratory, Germany

Postdoctoral and Academic Positions at The European Molecular Biology Laboratory (EMBL), a molecular biology research institution, Germany Scientific Officer – Protein Expression and Purification Core Facility Staff Member at EMBL Heidelberg Closes 14 February 2022 |  Grading: Grading: 4, 5 or 6; depending on experience and qualifications (monthly salary starting from 3.1k – 3.8k EUR…

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Scientists Say They Could Bring Back Woolly Mammoths. But Maybe They Shouldn’t | THE DAILY TRIBUNE

Agencies | Washington The Daily Tribune – www.newsofbahrain.com Using recovered DNA to “genetically resurrect” an extinct species — the central idea behind the Jurassic Park films — may be moving closer to reality with the creation this week of a new company that aims to bring back woolly mammoths thousands of years…

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Where Do Species Come From?

The evolutionary biologist Jochen Wolf was working from home when we first spoke, in April, 2020. Germany was under lockdown, and his lab, at Ludwig Maximilian University, in Munich, had been closed for weeks. Still, a reminder of his research had followed him from the office. “I have a crow…

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Kaggle Jane Street competition

1 introduction Kaggle There are a lot of competitions sponsored by hedge funds , It may have become a new type of inner roll , Or maybe you really want to start from Kaggler Get some idea.This time we’re here to learn what has just ended Jane Street Sponsored competition…

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Micromotor-based localized electroporation and gene transfection of mammalian cells [Engineering],Proceedings of the National Academy of Sciences of the United States of America

Herein, we studied localized electroporation and gene transfection of mammalian cells using a metallodielectric hybrid micromotor that is magnetically and electrically powered. Much like nanochannel-based, local electroporation of single cells, the presented micromotor was expected to increase reversible electroporation yield, relative to standard electroporation, as only a small portion of…

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De-extinction Could Reverse Species Loss. But Should We Do It?

THE MOST BELOVED BIRD IN HISTORY may very well have been a 29-year-old pigeon by the name of Martha. It was the early 1900s, shortly before the United States entered the First World War, and Martha was at the height of her fame. Perched on her humble roost at the Cincinnati…

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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The Problem With the Idea To Bring Back Woolly Mammoths

An illustrated recreation of a woolly mammoth, on display at the Royal Victoria Museum, British Columbia. Credit: Thomas Quine/Flickr, CC BY 2.0 Like Sergey Zimov’s ‘Pleistocene Park’, George Church’s company Colossal plans to repopulate the Arctic tundra with woolly mammoths. Church, a genetic engineering expert, plans to splice mammoth genes…

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[lammps-users] Define different intramolecular and intermolecular forces – #2 by akohlmey – LAMMPS Mailing List Mirror

Groups are a dead end, since there is no way to restrict or differentiate pairwise interactions by groups. Thus I think the only way that you can currently realize such a model would be to have different atom types for each molecule and then use the hybrid pair style. So…

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Micromotor-based localized electroporation and gene transfection of mammalian cells

Significance A metallodielectric Janus particle–based micromotor system for local electroporation and gene transfection of a single mammalian cell is studied. This hybrid micromotor is magnetically and electrically propelled with magnetic steering to approach and contact a targeted cell. The targeted cell is then locally electroporated at its contact point with…

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Jennifer Doudna’s CRISPR startup Mammoth Biosciences goes unicorn

The gene-editing tool CRISPR is moving toward the market, promising better tests, disease cures — and maybe even a woolly mammoth. The big picture: CRISPR is already a historic scientific achievement, but we’re just now entering the moment when it will begin to impact patients and possibly the planet. Driving…

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My symmetry-equivalent sites don’t have the same energy

Hello! Help, my symmetry-equivalent sites don’t have the same energy! __The problem:__ My system is insulating and antiferromagnetic Cr2O3 with a positive interstitial H in a hexagonal supercell. There are 6 equivalent* sites in a ‘doughnut’ around a large interstitial region. When I compute the total energy of these sites…

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Scientists say they could bring back woolly mammoths, but maybe they shouldn’t

Artist’s impression of a woolly mammoth in a snow-covered environment. Leonello Calvetti/Stocktrek Imag / Getty Images/Stocktrek Images Using recovered DNA to “genetically resurrect” an extinct species — the central idea behind the Jurassic Park films — may be moving closer to reality with the creation this week of a new…

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scarlet star plant propagation

Humidity – high, Air Plants, Bromeliads, Flowering Plants, Foliage Plants, Garden Plants, Indoor Plants Keep geraniums in winter. For medium sized aquariums it is much better placed as a midground plant only use as a background plant in smaller aquariums. Another nice aspect of . In their natural habitat, most…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange

Significance A great challenge for humanity is feeding its growing population while minimizing ecosystem damage and climate change. Here, we uncover the global benefits arising from the introduction of one wild species accession to peanut-breeding programs decades ago. This work emphasizes the importance of biodiversity to crop improvement: peanut cultivars…

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Mammoth-elephant hybrids could be created within the decade. Should they be?

The park’s vision of bringing back ancient grasslands is “an exciting hypothesis,” says University of Maine palaeoecologist Jacquelyn Gill, based on the effects that today’s elephants have on their habitats. However, she cautions that researchers still don’t know the full details of how woolly mammoths’ ecosystems functioned, which complicates efforts…

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A startup wants to bring mammoths back to the Arctic

It’s almost been a decade since Harvard geneticist George Church first talked about using synthetic biology to bring woolly mammoths back to life. Now, his idea to reverse history is pressing forward.  Today, Church and software entrepreneur Ben Lamm announced the launch of their biotech startup, Colossal, with seed funding…

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Strata Oncology Trial Data Support Robustness of NGS Assay for Challenging Samples

NEW YORK – Research from Strata Oncology on a large cohort of cancer patients has shown that the firm’s amplification-based sequencing assay can handle samples that don’t meet the usual requirements for comprehensive genomic profiling (CGP). The company also believes that assays like StrataNGS that only need little tumor tissue…

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Cisco targets net-zero by 2040, Illumina by 2050

Tech giant Cisco has pledged to reach net-zero emissions for operations by 2025 and the supply chain by 2040, while healthcare research and solutions firm Illumina has set a 2050 target. Cisco’s new targets involve reaching net-zero for Scope 1 (direct)…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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GALAXY Workflow for Bacterial Next-Generation Sequencing De Novo Assembly and Annotation

Whole-genome sequencing of prokaryotes is now readily available and affordable on next-generation sequencing platforms. However, the process of de novo assembly can be complicated and tedious for those without a background in computational biology, bioinformatics, or UNIX. Licenses for commercial bioinformatics software may be costly and limited in flexibility. GALAXY…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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chloramphenicol resistance

Using these strains, it is possible to integrate plasmids that carry the complementary ΦC31 att site onto the chromosome (attP, in this figure). Because the mtDNA codes for key OXPHOS polypeptides, genetic alterations in the mtDNA will affect energy metabolism. Proc Natl Acad Sci U S A. 1969 Jun;98(3):1248-57 eCollection…

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Satellite DNA-mediated diversification of a sex-ratio meiotic drive gene family in Drosophila

1. Sandler, L. & Novitski, E. Meiotic drive as an evolutionary force. Am. Nat. 91, 105–110 (1957). Article  Google Scholar  2. Lindholm, A. K. et al. The ecology and evolutionary dynamics of meiotic drive. Trends Ecol. Evol. 31, 315–326 (2016). Article  PubMed  Google Scholar  3. Lyttle, T. W. Segregation distorters….

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Caribou Biosciences Announces Publication of Data Demonstrating High Specificity Genome Editing with its Proprietary chRDNA Technology

Data published in Molecular Cell provide a mechanistic framework to explain the enhanced specificity and key differentiation of Caribou’s proprietary chRDNA technology for therapeutic applications BERKELEY, Calif., Sept. 02, 2021 (GLOBE NEWSWIRE) — Caribou Biosciences, Inc. (Nasdaq:CRBU), a leading clinical-stage CRISPR genome-editing biopharmaceutical company, announced today the publication of data…

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PROPER-Seq Uses NGS to ID Undiscovered Protein-Protein Interactions

NEW YORK – A new method for profiling protein-protein interactions (PPIs) using next-generation sequencing as a readout has the potential to reveal thousands of previously undiscovered combinations in human cells. The method, called PROPER-seq (protein-protein interaction sequencing), tags proteins with RNA barcodes that form chimeric sequences when brought into proximity with…

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