Categories
Tag: nu
Postdoc assessing the hazards of nano and micro plastics for humans
Category Research / Academic Location Wageningen Do you want to use your passion to study the possible risks of exposure to nano and microplastics for human health as a Post Doctoral researcher? Are you motivated to work in an team of scientists in an ambitious Dutch research program? Do you…
Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures
Notation Notations used in the ANCOM-BC2 methodology are summarized in Table 1. The overall procedure of the ANCOM-BC2 methodology is summarized in Extended Data Fig. 6. Table 1 Summary of notation ANCOM-BC2 for fixed-effects models Model assumptions Assumption 1 Multiplicative model for observed counts: $${O}_{ij}={S}_{i}{C}_{j}{A}_{ij}{E}_{ij}.$$ Assumption 1 indicates that, in…
Postdoc on Gut Microbiome and Metagenome
Your job Are you the enthusiastic scientist with a PhD, who is experienced with metagenomics data and wants to focus on understanding the function of our microbiome? Are you interested in how microbes can improve the health of babies? We at Wageningen University and Research have a vacancy for a…
Origin and evolution of the triploid cultivated banana genome
Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS PubMed PubMed Central Google Scholar Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…
Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)
Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…
ScRNAseq analysis scran :: quickcluster Error
ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…
Nubank partners with Talos to trim crypto trading costs in Brazil
Nubank, the leading Brazilian digital bank by market value, has announced a partnership with institutional trading technology provider Talos geared toward reducing the cost of trading crypto. “With this partnership, customers who wish to trade crypto assets in Brazilian reais through the Nu app will benefit from reduced costs through…
THE ELECTRONIC SPECTRUM OF AlCl
Abstract New data have been obtained on the electronic transitions of AlCl between 1600{\AA} and 4200{\AA} by both emission and absorption techniques. Studies of the $A^{1}\Pi-X^{1}\sum^{+}$ transition in absorption have yielded rotational structure for the 0-0 band and other low-lying levels, unlike previous studies of the emission spectrum which had…
Assistant/associate professor machine learning in bioinformatics
Your job As an assistant or associate professor, you will play a pivotal role in advancing both research and education within the Bioinformatics Group at Wageningen University. You will set up and maintain a research line on machine-learning-based method development in bioinformatics, with applications in the green life sciences. You…
The Anthropological and historical reasons why Nagas are not Indians and Indians not Nagas | MorungExpress
Kaka D Iralu The following article is made up of excerpts from a paper presented at the international conference on Armed Conflicts in Eastern India held at Shillong from December 1-2, 2006. The original 10-paged paper was entitled, “An anthropological and historical analysis of the Indo-Naga war”. In this just…
Volition Presents at the 5th Annual Congress of the International Liquid Biopsy Society
HENDERSON, Nev, Nov. 17, 2023 /PRNewswire/ — VolitionRx Limited (NYSE AMERICAN: VNRX) (“Volition”), a multi-national epigenetics company, is presenting at the 5th Annual Congress of Liquid Biopsy being held in Madrid, Spain. Lea Payen-Gay, Professor in Toxicology and Biochemistry, University of Lyon I Hospices Civils de Lyon, France and Dr. Jake…
Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding
Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…
Maintenance Ibrutinib Improves Efficacy in MCL
The primary end point for this study was to determine the 3-year PFS rate from the beginning of ibrutinib maintenance treatment. Secondary end points were to analyze toxicity, and assess partial response and CR rates. Results from the phase 2 NU 14H06 study (NCT02242097) demonstrated efficacy in using ibrutinib (Imbruvica)…
Apoptotic stress causes mtDNA release during senescence and drives the SASP – ePrints
Apoptotic stress causes mtDNA release during senescence and drives the SASP Lookup NU author(s): Hanna Salmonowicz, Dr James ChapmanORCiD, George Kelly, Dr Laura Greaves, Professor Derek Mann, Dr Viktor Korolchuk Downloads Full text for this publication is not currently held within this repository….
Multiple parallel origins of parasitic Marine Alveolates
MALV-II and -IV are closely related to the eleftherids, a new group of free-living heterotrophs We isolated and cultured several strains collectively representing two new species of colorless, eukaryovorous flagellates, which we formally name Eleftheros xomoi (strains Colp-37 and Cur-11, isolated from the surface of a coral in the Caribbean…
Dependencies pymc3 v3.0rc2 – v3
_julian October 29, 2023, 11:38am 1 Hi, I’m trying to install pymc3 v3.0rc2 on Python v2.7 with Anaconda.Since it is a pain to solve all the dependencies with Anaconda, I wanted to ask if somebody knows the dependencies for this pymc3 version. Thank you Hey @_julian, I don’t have immediate…
Volition Presents Breakthrough Liquid Biopsy Blood Test Method for Early-stage Cancer
HENDERSON, Nev., Oct. 23, 2023 /PRNewswire/ —VolitionRX Limited (NYSE AMERICAN: VNRX) (“Volition”), a multi-national epigenetics company, has unveiled what it believes to be an entirely new cancer detection method at ESMO 2023¹, the annual congress of the European Society for Medical Oncology. In early-stage…
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Compagno, L. J. V. Alternative life-history styles of cartilaginous fishes in time and space. Environ. Biol. Fishes 28, 33–75 (1990). Article Google Scholar Kriwet, J., Witzmann, F., Klug, S. & Heidtke, U. H. J. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proc. Biol. Sci….
Volition Presents Three Cancer Detection Abstracts at ESMO 2023
HENDERSON, Nev., Oct. 16, 2023 /PRNewswire/ — VolitionRx Limited (NYSE AMERICAN: VNRX) (“Volition”), a multi-national epigenetics company, is presenting three scientific abstracts at ESMO 2023, the annual congress of the European Society for Medical Oncology. Dr. Jake Micallef, Chief Scientific Officer at Volition, said: “We are delighted to be attending ESMO…
An Intrabody against B-Cell Receptor-Associated Protein 31 (BAP31) Suppresses the Glycosylation of the Epithelial Cell-Adhesion Molecule (EpCAM) via Affecting the Formation of the Sec61-Translocon-Associated Protein (TRAP) Complex
. 2023 Sep 30;24(19):14787. doi: 10.3390/ijms241914787. Affiliations Expand Affiliation 1 College of Life Science and Health, Northeastern University, 195 Chuangxin Road, Hunnan District, Shenyang 110819, China. Item in Clipboard Tianyi Wang et al. Int J Mol Sci. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Sep 30;24(19):14787. doi:…
Integration of phenotypic, qPCR and genome sequencing methodologies for the detection of antimicrobial resistance and virulence in clinical isolates of a tertiary hospital, India
Azimi A, Peymani A, Pour PK (2018) Phenotypic and molecular detection of metallo-β-lactamase-producing Pseudomonas aeruginosa isolates from patients with burns in Tehran. Iran Rev Soc Bras Med Tro 51:610–615. doi.org/10.1590/0037-8682-0174-2017 Article Google Scholar Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology….
DNA damage induced by CDK4 and CDK6 blockade triggers anti-tumor immune responses through cGAS-STING pathway
Patients’ tumor tissues and clinical data This study recruited 125 breast cancer patients for immunohistochemical (IHC) analysis and 10 breast cancer patients for RNA-seq analysis from the Affiliated Tumor Hospital of Nantong University. Tumor tissues collected from surgical patients were fixed with formalin and embedded with paraffin and then examined….
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…
Virulence Characteristics of Salmonella Enteritidis
Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…
Post-Doc eDNA bioinformatics – Marine Animal Ecology
Your job Marine Animal Ecology group (MAE) at Wageningen University is looking for a molecular ecology / bioinformatics postdoc, to participate in a project on improving methods for North Sea biodiversity assessment using environmental DNA (eDNA). The position is part of the BeWild project (www.fugro.com/news/business-news/2023/bewild-using-edna-to-measure-biodiversity-at-offshore-wind-farms). This project is funded by…
Mitochondrial DNA damage triggers spread of Parkinson’s disease-like pathology
Lack of IFNβ/IFNAR signaling causes mtDNA oxidization and mutation in a hotspot in complex I respiratory chain subunits mimicking PD brain pathology We analyzed transcriptomic datasets from sPD patients [28] to identify molecular pathways related to the disease pathology. Dysregulated oxidative phosphorylation (OXPHOS) emerged as the top-ranked pathway in sPDD, patients with…
Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits
Swingle, W. T. & Reece, P. C. In The Citrus Industry, History, World Distribution, Botany, and Varieties, Vol. 1 (eds Reuther, W. et al.) 190–143 (Univ. of California Press, 1967). Morton, C. M. & Telmer, C. New subfamily classification for the Rutaceae. Ann. Mo. Bot. Gard. 99, 620–641 (2014). Article …
Age, Height, Net Worth, Wife, Girlfriend, Instagram, Children, Career
Damon Anthony Dash, born on May 3, 1971, popularly known as Damon Dash, He is an American entrepreneur and record executive. He is famous for being the co-founder of Roc-A-Fella. Damon Dash Bio: Full Name: Damon Anthony Dash Date Of Birth: May 3, 1971 Place Of Birth: New York City,…
3 Top Gene-Editing Stocks with Long-Term Potential
The global gene-editing market is projected to skyrocket from US$5 billion in 2021 to US$21.4 billion in 2030, growing 17.3% annually. The increasing prevalence of genetic disorders, leading to a range of diseases, is fuelling demand for personalized medicine and is the driving force behind the sharp rise of the…
One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade
Isolation and microscopy of Mantamonas sphyraenae sp. nov Mantamonas sphyraenae SRT-306 was collected on 26 Sep. 2013 from the surface of a barracuda caught in a lagoon on Iriomote Island, Taketomi, Okinawa Prefecture, Japan (24° 23′ 36.762″ N, 123° 45′ 22.572″ E). It was isolated manually from the rough sample…
Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
Locey, K. J. & Lennon, J. T. Scaling laws predict global microbial diversity. PNAS 113, 5970–5975. doi.org/10.1073/pnas.1521291113 (2016). Article ADS CAS PubMed PubMed Central Google Scholar Hahn, M. W., Koll, U. & Schmidt, J. The Structure and Function of Aquatic Microbial Communities (Springer International Publishing, 2019). Rosenberg, E., DeLong, E….
Canu genome assembly error about low coverage
Canu genome assembly error about low coverage 0 I am assembling a genome using Canu 2.2 with the following commands on a slurm cluster: canu useGrid=false \ -p tf -d tf-pacbio \ genomeSize=164.4m \ -corrected \ corMhapSensitivity=normal \ -pacbio SRR23272336_1_corrected.fastq The input Pacbio fasta file is corrected by LoRDEC. The…
PhD Fully Funded in Bioinformatics: Investigating protein evolution using machine learning at Wageningen University in the Netherlands
Are you looking for a PhD position and interested in research on protein evolution in bacteria? Are you a bioinformatician who wants to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns? Then this PhD vacancy may be of interest to you! Job…
Direct observation of the conformational states of PIEZO1
No statistical methods were used to predetermine sample size. The experiments were not randomized and investigators were not blinded to allocation during experiments and outcome assessment. Expression constructs The coding sequence of mouse PIEZO1 (E2JF22, UniprotKB entry) was codon-optimized, synthesized and cloned into the pcDNA3.1 plasmid. An amber stop codon…
Modeling the dynamics of COVID-19 with real data from Thailand
Analysis of (11) is carried out in this section. Boundedness and positivity of the model system (11) The fractional-order system (11) must be positive because the solutions represent the densities of the populations that interact with each other, and from a biological perspective, the lowest possible value for each population…
Question with manipulating OD gene list when running PCA
Hello, I am using Seurat 4.9.9.905 and Pagoda2 1.0.10 to do sc clustering on an integrated object. I integrated two merged sample sets with var features and normalization applied to each of the two merged objects. I would like to do the clustering in Pagoda. This is my integration script:…
The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards
Grabenstein, K. C. & Taylor, S. A. Breaking barriers: causes, consequences, and experimental utility of human-mediated hybridization. Trends Ecol. Evol. 33, 198–212 (2018). Article PubMed Google Scholar Crispo, E., Moore, J. S., Lee‐Yaw, J. A., Gray, S. M. & Haller, B. C. Broken barriers: human‐induced changes to gene flow and…
Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…
Genome assembly of two diploid and one auto-tetraploid Cyclocarya paliurus genomes
Sample collection, library construction and sequencing Leaves of two diploid C. paliurus (PG-dip and PA-dip) and one auto-tetraploid (PA-tetra) for genome sequencing were collected from plants grown in germplasm bank of C. paliurus, which located in Baima experimental field, Nanjing, Jiangsu province, China. After collecting, tissues were immediately frozen in…
Dynamic RNA profiles in the small intestinal epithelia of cats after Toxoplasma gondii infection | Infectious Diseases of Poverty
Jacobs L. Toxoplasma and toxoplasmosis. Annu Rev Microbiol. 1963;17:429–50. Article CAS PubMed Google Scholar Montoya JG, Liesenfeld O. Toxoplasmosis. The Lancet. 2004;363(9425):1965–76. Article CAS Google Scholar Dubey JP. Duration of immunity to shedding of Toxoplasma gondii oocysts by cats. J Parasitol. 1995;81(3):410–5. Article CAS PubMed Google Scholar Dubey JP, Frenkel…
Pytorch grad issue while using solve in derivatives – Technical Support (Modulus Only)
I have been trying to develop and run a custom model for my physics informed NN, but I don’t understand the issue faced Script: # libraries from sympy import Symbol, Function, exp, Number from modulus.sym.eq.pde import PDE from modulus.sym.node import Node from sympy import Symbol, Eq import numpy as np…
Postdoc Researcher – Single cell RNA-sequencing of plant defences against aphids
Category Research / Academic Location Wageningen Your JobAre you a talented postdoc with a passion for unraveling plant resistance mechanisms against aphids at the cellular level? Do you want to work in a multidisciplinary team along with experienced researchers in collaboration with plant breeding and biocontrol companies? If so, we…
HIV-1 promotes ubiquitination of the amyloidogenic C-terminal fragment of APP to support viral replication
Ethics Statement LifeSource Buffy Coat blood obtained from New York blood center was used for isolation of peripheral blood mononuclear cells using Ficoll-Plaque (GE). Ethical approval for the study was obtained from the Institutional Review Board of Northwestern University and all donors provided their written, informed consent. Cell cultures HEK293T…
nf-core/configs
abims The ABiMS cluster profile slurm adcra CRA HPC profile slurm alice Profile for use on Academic Leiden Interdisciplinary Cluster Environment (ALICE). slurm aws_tower AWS Batch with Tower Profile awsbatch awsbatch AWSBATCH Cloud Profile awsbatch azurebatch Azure BATCH Cloud Profile azurebatch azurebatchdev Azure BATCH Dev Cloud Profile azurebatch bi Boehringer…
New online bioinformatics course designed for INBRE Scholars | Newsroom
A new online course was launched June 16 to help INBRE Scholars understand the world of bioinformatics and how it is utilized in research. Developed with funding from the NE-INBRE program, the seven-module course was created by Babu Guda, PhD, director of the Bioinformatics and Systems Biology Core and professor…
The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation
Billings, W. Adaptations and origins of alpine plants. Arct. Alp. Res. 6, 129–142 (1974). Article Google Scholar Agakhanjanz, O. & Breckle, W. Origin and evolution of the mountain flora in middle Asia and neighbouring mountain regions. in Arctic and Apine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds. Chapin, F. &…
Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor
Crutzen, P. J. The influence of nitrogen oxides on the atmospheric ozone content. Q. J. R. Meteorol. Soc. 96, 320–325 (1970). Article Google Scholar Johnston, H. Reduction of stratospheric ozone by nitrogen oxide catalysts from supersonic transport exhaust. Science 173, 517–522 (1971). Article CAS PubMed Google Scholar Hughes, M. N….
KPCB_MOUSE – Protein Kinase C Beta, Mouse | ZINC Is Not Commercial
KPCA_MOUSE P20444 CHEMBL2567 Protein Kinase C Alpha, Mouse 27 KPCG_MOUSE P63318 CHEMBL2956 Protein Kinase C Gamma, Mouse 23 KPCD_MOUSE P28867 CHEMBL2560 Protein Kinase C Delta, Mouse 17 KPCL_MOUSE P23298 CHEMBL4992 Protein Kinase C Eta, Mouse 17 KPCA_HUMAN P17252 CHEMBL299 Protein Kinase C Alpha, Human 8 KPCE_HUMAN Q02156 CHEMBL3582 Protein Kinase…
(2023) Damon Dash Net Worth, How Rich Is He?
Damon Dash Net Worth: In this article, we will be here informing you about an American record producer who is also a great entrepreneur and a music executive you might be wondering and getting curious to know about him so he is also considered to be the richest celebrity rapper…
The genome of Acorus deciphers insights into early monocot evolution
Lughadha, E. N. et al. Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates. Phytotaxa 272, 82–88 (2016). Article Google Scholar Group, A. P. An update of the Angiosperm Phylogeny Group classification for…
The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes
Purohit, J., Kumar, A., Hynniewta, M. & Satyawada, R. R. Karyomorphological studies in guar (Cyamopsis tetragonoloba (Linn.) Taub.)—An important gum yielding plant of Rajasthan, India. Cytologia 76(2), 163–169 (2011). Article Google Scholar Gillett, J. B. Indigofera (Microcharis) in tropical Africa with the related genera Cyamopsis and Rhynchotropis. H.M.S.O Kew Bull.,…
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Grimont PAD, W. F. X. Antigenic formulae of the Salmonella serovars, 9th ed. (World health organization collaborating center for reference and research on Salmonella, Insitut Pasteur, 2007). Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ….
Staff scientist Bioinformatics – WUR
Your job Are you our new Staff Scientist Bioinformatics? We seek to hire an expert who is dedicated to implement, support, and develop bioinformatics strategies used in the breath of our research palette. The hiring of a permanent staff scientist in bioinformatics will ensure continued support to our research, and…
deSouza Resigns as Illumina CEO, as Fallout Continues from Icahn Challenge
Activist investor Carl C. Icahn stating his case for change at Illumina on GEN’s “Close to the Edge” video series in April. [GEN] Illumina CEO Francis deSouza has resigned from both his position and his seat on the board, the company said today—just over two weeks after he survived a…
eDNA technology could revolutionise biodiversity monitoring
Choki Wangmo Bhutan could save millions on biodiversity monitoring and assessments if environmental DNA (eDNA) sequencing technology could be used in the country, according to experts. The technology offers cost-effective biodiversity monitoring, potentially saving millions for government and conservation agencies in environmental assessments. It is a collection of mitochondrial DNA…
Vancomycin intermediate-resistant Staphylococcus haemolyticu | IDR
Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…
A case report of cutaneous anthrax diagnosed with mNGS
Yushan Liu,1,2 Gezhi Zheng,1,3 Jing Li,1,3 Nan Yang,1– 4 Juan Li,1,2 Zhengwen Liu,1– 4 Qunying Han,1– 4 Yingren Zhao,1– 4 Fenjing Du,1,3 Yingli He,1,* Taotao Yan1,* 1Department of Infectious Diseases, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China; 2Institution of Hepatology, The First Affiliated…
Contigs to chromosomes annotation
Contigs to chromosomes annotation 0 Hello, I would like to know which is the simplest method to add the names of the chromosomes from D. melanogaster for each contig from a fasta a file of a draft assembly obtained with the Canu application. What tools should I use in order…
A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
Lederberg, J., Cavalli, L. L. & Lederberg, E. M. Sex compatibility in Escherichia Coli. Genetics 37, 720–730 (1952). Article CAS PubMed PubMed Central Google Scholar Elisabeth, G., Günther, M. & Manuel, E. Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301 (2003). Article Google Scholar de la…
Tracking Antibiotic Resistance from the Environment to Human Health
Review doi: 10.1007/978-1-0716-3072-3_15. Affiliations Expand Affiliations 1 Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt. 2 Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt. melhadidi@nu.edu.eg. Item in Clipboard Review Eman Abdelrazik et al. Methods Mol Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID…
The inchworm process failed. Trinity running error.
The inchworm process failed. Trinity running error. 0 Hello everyone, I’m trying to perform a de novo transcriptome using Trinity and having many issues. The last time I got the inchworm error attached. ******************************************************************** ** Warning, Trinity cannot determine which version of Java is being used. Version 1.7 is required….
Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
Adamek, M., Spohn, M., Stegmann, E. & Ziemert, N. Mining bacterial genomes for secondary metabolite gene clusters. Methods Mol. Biol. 1520, 23–47 (2017). CAS PubMed Google Scholar Belknap, K. C., Park, C. J., Barth, B. M. & Andam, C. P. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces…
From an unknown person to a “top class”? In-depth interpretation of the past, present and future of circular RNA
foreword Since the circRNA molecule was discovered in the plant virus genome in 1976, after more than 30 years of silence, it finally became a blockbuster in 2012, and quickly became a new generation of star molecules in the following years. In the past ten years, as scientific researchers have…
Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria
Occurrence of prophage sequences in L. casei group genomes The first stage of the analysis involved the identification of prophage-like sequences in 439 genomic sequences of bacterial strains belonging to the following 5 species: L. casei (27), L. paracasei (200), L. rhamnosus (204), L. zeae (6) and L. chiayiensis (2)….
The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae
Elston KM, Leonard SP, Geng P, Bialik SB, Robinson E, Barrick JE. Engineering insects from the endosymbiont out. Trends Microbiol. 2022;30:79–96. Article CAS PubMed Google Scholar Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, et al. Engineered integrative and conjugative elements for efficient and inducible DNA…
A preliminary study of the use of MinION sequencing to specifically detect Shiga toxin-producing Escherichia coli in culture swipes containing multiple serovars of this species
Tarr, P. I., Gordon, C. A. & Chandler, W. L. Shiga toxin-producing Escherichia coli and haemolytic uremic syndrome. Lancet 365, 1073–1086 (2006). Google Scholar Koudelka, G. B., Arnold, J. W. & Chkraborty, D. Evolution of STEC virulence: Insights from the antipredator activities of shiga toxing-producing E. coli. Int. J. Med….
Increasing Demand for Safe and Healthy food is Driving the Food Safety Testing Market
PRESS RELEASE Published May 19, 2023 Food safety testing is the analysis of food samples to detect the presence of harmful contaminants. Contaminants can include bacteria, viruses, toxins, and chemicals. Food safety testing is used to protect consumers from foodborne illness. Food safety testing can be performed on raw ingredients,…
pytorch – Implementing KL-divergence for multivariate t-distribution in Python
I would like to compute KL-divergence of two multivariate t-distributions in python. The distributions have a mean of shape(20480,1) and identity matrix as their covariance matrix. I applied different kl packages on 1000 samples, but the estimation is a large negative value which contradicts with definition of KL. Would you…
Lead Bioinformatics scientist Job in Monument
INFO LEAD BIOINFORMATICS SCIENTIST 90,000 – 120,000 HYBRID (LONDON) COMPANY: We have partnered with a scale-up in the BioTech industry. Our client is using AI/ML to aid in their protein/gene sequencing research. The project areas range from drug discovery to using Mycelium structures for sustainable clothing development! Having secured funding,…
Damon Dash Biography, Birthday, Career, Age, Height and Net Worth
Damon Dash Bio: The American record label administrator, entrepreneur, film producer, director, and actor Damon Dash was born on May 3, 1971. During his tenure at Roc-A-Fella Records, he was in charge of purchasing Armadale Vodka and Pro-Keds. He utilised his musicians and labels to market his other businesses. His…
Bioinformatics scientific software engineer – WUR
Your job As a bioinformatics scientific software engineer in the Wageningen University Bioinformatics Group, you will contribute to the development and dissemination of software tools for -omics data analysis and thereby contribute to scientific research. Your duties and responsibilities include: supporting staff and students in creating robust and sustainable software providing…
Junior lecturer bioinformatics and data science
Your job As a junior lecturer, you will contribute to the Wageningen University Bioinformatics Group’s education efforts. You will help deliver, organize, and innovate our teaching, with room for contributions to research. Your duties and responsibilities will include: teaching a number of existing courses that fit your specific expertise, innovating…
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
Sagan, L. On the origin of mitosing cells. J. Theor. Biol. 14, 225 (1967). Article ADS CAS Google Scholar McBride, H. M., Neuspiel, M. & Wasiak, S. Mitochondria: More than just a powerhouse. Curr. Biol. 16, R551–R560 (2006). Article CAS PubMed Google Scholar Dietrich, M. O., Liu, Z.-W. & Horvath,…
Phenotypic and Genetic Analysis of KPC-49
Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…
An apicomplexan parasite drives the collapse of the bay scallop population in New York
Lafferty, K. D., Porter, J. W. & Ford, S. E. Are diseases increasing in the ocean?. Ann. Rev. Ecol. Evol. Syst. 35, 31–54 (2004). Article Google Scholar Ward, J. R. & Lafferty, K. D. The elusive baseline of marine disease: Are diseases in ocean ecosystems increasing?. PLoS Biol. 2, 542–547…
r – How to calculate the exponential equation in ggplot2?
I am trying to fit the exponential line to the points. It is working. But the linear formula appears in the diagram. I would appreciate someone telling me how to make the exponential formula in the plot. Nu treat pH Cd 1 Soil 6.1 0.28 2 Soil 6.1 0.29 3…
Casino and Gaming Market May See a Big Move
PRESS RELEASE Published April 18, 2023 Advance Market Analytics added research publication document on Worldwide Casino and Gaming Market breaking major business segments and highlighting wider level geographies to get deep dive analysis on market data. The study is a perfect balance bridging both qualitative and quantitative information of Worldwide…
Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia
Burger, G., Gray, M. W. & Lang, B. F. Mitochondrial genomes: Anything goes. Trends Genet. 19, 709–716 (2003). Article CAS PubMed Google Scholar Hawksworth, D. L. & Lücking, R. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spectr. 5, 5–4 (2017). Article Google Scholar Theelen, B., Christinaki, A. C.,…
PUREE: accurate pan-cancer tumor purity estimation from gene expression data
Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…
Recommendation for de novo scaffolder
Recommendation for de novo scaffolder 0 Hi, I performed de novo assembly using Canu following a hybrid method. I have both Illumina (PE) and Oxford Nanopore reads. I performed reference guided scaffolding using ragtag before, but now, I want to see if doing the scaffolding de novo has any impact…
Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species
Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS PubMed PubMed Central Google Scholar Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS PubMed Google Scholar Peralta, I. E., Spooner, D. M. & Knapp, S….
Biochemist Jennifer Doudna receives Kimberly Prize
Biochemist Jennifer Doudna received the inaugural Kimberly Prize in Biochemistry and Molecular Genetics at the Robert H. Lurie Medical Research Center on Tuesday. The prize will be awarded annually to a scientist who has made “outstanding research contributions into the molecular basis of life with a direct demonstrated link of…
KEGG ENZYME: 1.3.99.39
Entry EC 1.3.99.39 Enzyme Name carotenoid phi-ring synthase;crtU (gene name) (ambiguous) Class Oxidoreductases;Acting on the CH-CH group of donors;With unknown physiological acceptorsBRITE hierarchy Sysname carotenoid beta-ring:acceptor oxidoreductase/methyltranferase (phi-ring-forming) Reaction(IUBMB) carotenoid beta-end group + 2 acceptor = carotenoid phi-end group + 2 reduced acceptor [RN:R12115] Reaction(KEGG) Substrate carotenoid beta-end group [CPD:C21915]; acceptor [CPD:C00028]…
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
Bradley, B. A. et al. Cheatgrass (Bromus tectorum) distribution in the intermountain western United States and its relationship to fire frequency, seasonality, and ignitions. Biol. Invasions 20, 1493–1506 (2018). Article Google Scholar Balch, J. K., Bradley, B. A., D’Antonio, C. M. & Gomez-Dans, J. Introduced annual grass increases regional fire…
Friend or foe: role of pathological tau in neuronal death
Bredesen DE, Rao RV, Mehlen P. Cell death in the nervous system. Nature. 2006;443:796–802. Article CAS PubMed PubMed Central Google Scholar Fricker M, Tolkovsky AM, Borutaite V, Coleman M, Brown GC. Neuronal cell death. Physiol Rev. 2018;98:813–80. Article CAS PubMed PubMed Central Google Scholar West MJ, Coleman PD, Flood DG,…
The Biostar Herald for Monday, March 13, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding? 9 Is there a simple tool I can use to quickly find out if a FASTQ file is in Sanger or Phred64 encoding? Ideally something that tells me ‘Encoding XX’ somewhere the terminal output. fastq tools • 46k…
Advances in the detection, characterization, and monitoring of cancer in pets
Content sponsored by Blue Buffalo. Historically, physicians have identified cancer in humans and animals through the appearance of an obvious mass/lump or the development of clinical signs that typically occur when a tumor is advanced (weight loss, vomiting, coughing, etc). Over the past few decades, technologies have improved substantially to…
Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae
Crous, P. et al. Fungal planet description sheets: 107–127. Pers. Mol. Phylogeny Evol. Fungi 28, 138–182. doi.org/10.3767/003158512X652633 (2012). Article CAS Google Scholar Visentin, I. et al. Gnomoniopsis castanea sp. nov. (Gnomoniaceae, Diaporthales) as the causal agent of nut rot in sweet chestnut. J. Plant Pathol. 94, 411–419. doi.org/10.4454/JPP.FA.2012.045 (2012). Article …
pymc3 – PyMC: fixing model function with real function
pymc3 – PyMC: fixing model function with real function – Cross Validated …
Switch them off or not: selective rRNA gene repression in grasses: Trends in Plant Science
Nucleolar dominance: 90 years ago to present A nucleolus (see Glossary) is formed in the vicinity of the chromosomal locus whose tandemly repeated 35-48S rDNA is transcribed (Figure 1) [ 1. Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids. , 2. Nucleolar dominance: a ‘David and…
The Biostar Herald for Monday, February 06, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
Dealing with missing (NA) values in my 450K methylation array dataset
I am looking to analyse some pre-processed infinium 450k methylation data (GSE65820) – values have been normalised and undergone QC and removal of batch effects. I have used GEOquery to download the series matrix file GSE65820 <- getGEO(“GSE65820”, GSEMatrix=TRUE) From this I have extracted metadata about the samples using the…
Draft genomes of Blastocystis subtypes from human samples of Colombia | Parasites & Vectors
Andersen LO, Bonde I, Nielsen HB, Stensvold CR. A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiol Ecol. 2015. doi.org/10.1093/femsec/fiv072. Article Google Scholar Audebert C, Even G, Cian A, Loywick A, Merlin S, Viscogliosi E, et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human…
Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients
doi: 10.1038/s41397-023-00299-7. Online ahead of print. Affiliations Expand Affiliations 1 Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA. 2 Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA. 3 Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA. amye@unc.edu….
Mapping a small number of contigs to a reference subsequence
Mapping a small number of contigs to a reference subsequence 1 Hello, Is there a method or a tool to align/map a small number of contigs (obtained with Canu) to a subsequence extracted from a reference genome ? For example,in a similar way to reads to reference assembly (using bwa…
Postdoc Communication Science
Category Research / Academic Location Amsterdam Do you enjoy Engaging in cutting-edge research on disinformation, as part of the European Digital Media Observatory EDMO; Participatingin groupsof internationally renowned scholars, and join peer networks, with many opportunities to engage and develop your career; Being part of a state-of-the-art research, innovative in…
minimap2, before or after assembly?
minimap2, before or after assembly? 1 Dear all, I feel confused because I saw someone uses the minimap2 after demultiplexing, but before proceeding with the assembly (CANU) [case 1], and someone using the minimap2/samfile/BFCTools/medaka after assembly (always CANU) [case 2]. In case 1, the reference file used to align against…
The genus Serratia revisited by genomics
Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….
N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research
Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…