Tag: nu

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…

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…

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 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…

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…

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. 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….

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…

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 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)….

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…

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….

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,…

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…

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 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…

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…

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…

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,…

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…

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…

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…

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…

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.,…

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 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…

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 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…

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]…

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…

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 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? 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…

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…

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 – Cross Validated …

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 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…

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…

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…

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 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…

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? 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…

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….

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,…

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

Nagpur: A day after Nagpur University administration constituted a panel under a retired judge to probe harassment complaints against its Hindi Department head, the woman guide, who too had labelled accusations against the HOD, has shot off a letter to vice chancellor Subhash Chaudhari, requesting him to remove two members…

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

I’ve found that the following seems to produce reasonable results. I based the priors on this article, and also used it to validate the correlation. All the work is in this notebook. def mad(data, axis=None): return np.median(np.absolute(data – np.median(data, axis)), axis) def covariance(sigma, rho): C = T.alloc(rho, 2, 2) C…

Non-random tissue distribution of mutant mtDNA Lookup NU author(s): Professor Patrick Chinnery, Professor Mark Walker, Professor Robert Taylor, Professor Robert Lightowlers, Professor Laurence Bindoff, Emeritus Professor Doug Turnbull Downloads Full text for this publication is not currently held within this repository. Alternative links…

I have been working with pymc3 for a while and I was observing the several tutorials with examples. However, I am not sure if I am approaching the Bayesian InFerence method correctly. Find below my approach: from pymc3.distributions import Interpolated import numpy as np # import warnings # import sys…

query sequence is input sequence or its reverse complement 0 >sp|O14920.1|IKKB_HUMAN RecName: Full=Inhibitor of nuclear factor kappa-B kinase subunit beta; Short=I-kappa-B-kinase beta; Short=IKK-B; Short=IKK-beta; Short=IkBKB; AltName: Full=I-kappa-B kinase 2; Short=IKK2; AltName: Full=Nuclear factor NF-kappa-B inhibitor kinase beta; Short=NFKBIKB; AltName: Full=Serine/threonine protein kinase IKBKB MSWSPSLTTQTCGAWEMKERLGTGGFGNVIRWHNQETGEQIAIKQCRQELSPRNRERWCLEIQIMRRLTH PNVVAARDVPEGMQNLAPNDLPLLAMEYCQGGDLRKYLNQFENCCGLREGAILTLLSDIASALRYLHENR IIHRDLKPENIVLQQGEQRLIHKIIDLGYAKELDQGSLCTSFVGTLQYLAPELLEQQKYTVTVDYWSFGT LAFECITGFRPFLPNWQPVQWHSKVRQKSEVDIVVSEDLNGTVKFSSSLPYPNNLNSVLAERLEKWLQLM LMWHPRQRGTDPTYGPNGCFKALDDILNLKLVHILNMVTGTIHTYPVTEDESLQSLKARIQQDTGIPEED QELLQEAGLALIPDKPATQCISDGKLNEGHTLDMDLVFLFDNSKITYETQISPRPQPESVSCILQEPKRN LAFFQLRKVWGQVWHSIQTLKEDCNRLQQGQRAAMMNLLRNNSCLSKMKNSMASMSQQLKAKLDFFKTSI…

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

Specific targeting of a DNA-alkylating reagent to mitochondria: Synthesis and characterization of [4-((11aS)-7-methoxy-1,2,3,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4] benzodiazepin-5-on-8-oxy)butyl]-triphenylphosphonium iodide Lookup NU author(s): Professor Robert Lightowlers, Dr Paul Smith Downloads Full text for this publication is not currently held within this repository. Alternative links are provided below where…

Northumbria University is a member of the COVID-19 Genomics UK Consortium (COG-UK).  COG-UK is a pioneer in the use of large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing the COVID-19 pandemic, to understand viral transmission and evolution, and to inform public health responses and vaccine development. We seeking to…

Assembly with repetitive regions 0 Hello all! I am assembling a synthetic genome sequenced with Oxford Nanopore. The problem is that I obtain a very repetitive assembly with all the contigs such as ATATATATATATATATAT. I do not understand why because I have repeated the process with the Acinetobacter pittii genome,…

A new mtDNA point mutation on tRNA Ser(UCN) in a cardiomyopathic patient Lookup NU author(s): Professor Laurence Bindoff, Dr Margaret Johnson, Professor Robert Lightowlers Downloads Full text for this publication is not currently held within this repository. Alternative links are provided below where…

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

Forum:De novo genome assembly 0 Howdy, I have recently been tasked as the ‘bioinformatics guy” in my lab and am having trouble with a de novo genome assembly of Mother of a Thousand. I am working with Nanopore reads and have ran my reads through CANU. I have all of…