Tag: DECIPHER

Molecular biologists: let’s reconnect with nature

Charles Darwin’s voyage on HMS Beagle led to a treasure trove of observations: the behaviour of cuttlefish, a parasitic ichneumon wasp feasting inside live caterpillars, fossils of extinct giant sloths and ‘mastodons’. The result, of course, was his theory of natural selection. Darwin needed the complex natural world to inspire…

Continue Reading Molecular biologists: let’s reconnect with nature

Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

Continue Reading Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

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…

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

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

Continue Reading GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

BioSpace hiring Bioinformatics Scientist in Bethesda, Maryland, United States

We are currently searching for a Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the Center for Alzheimer’s and Related Dementias, National Institute on Aging. The primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it…

Continue Reading BioSpace hiring Bioinformatics Scientist in Bethesda, Maryland, United States

Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

Continue Reading Establishment of sunitinib-resistant CDX model of ccRCC

Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

Continue Reading Classifiers for predicting coronary artery disease

Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators

volume 103, issue 52, P19635-19640 2006 J. Ju, D. H. Kim, L. Bi, Q. Meng, X. Bai, Z. Li, X. Li, M. S. Marma, S. Shi, J. Wu, J. R. Edwards, A. Romu, N. J. Turro Abstract: DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction offers…

Continue Reading Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators

Sequenced quoll genome a new tool for conservation

European colonists mistakenly labelled quolls as “native cats” when in fact they are among Australia’s last living carnivorous marsupials. Often overshadowed by their better-known cousins the Tasmanian Devils and the extinct Tasmanian Tiger (thylacine), quolls have a 15 million year history in Australia, successfully balancing shifting ecosystems by suppressing prey…

Continue Reading Sequenced quoll genome a new tool for conservation

Rare barley mutation with potential

Seven-day-old barley roots of mutant egt2: It grows strictly downwards (hypergravitropic). Credit: Gwendolyn Kirschner The importance of the root system for agricultural yields is often underestimated. Whether roots can access water and nutrients effectively also determines the resilience of important crops to drought and climate change. Researchers from the Universities…

Continue Reading Rare barley mutation with potential

Predicting and characterizing a cancer dependency map of tumors with deep learning

INTRODUCTION The development of novel cancer therapies requires knowledge of specific biological pathways to target individual tumors and eradicate cancer cells. Toward this goal, the landscape of genetic vulnerabilities of cancer, or the cancer dependency map, is being systematically profiled. Using RNA interference (RNAi) loss-of-function screens, Marcotte et al. (1),…

Continue Reading Predicting and characterizing a cancer dependency map of tumors with deep learning

Finding sequence family specific primers using DECIPHER

Hello, I am trying to find PCR primers that are specific to a family of repetitive elements in the human genome. For this, I found the R package DECIPHER, which seemingly can do exactly this using its TileSeqs and DesignPrimers functions as described in one of their vignettes. After getting…

Continue Reading Finding sequence family specific primers using DECIPHER

Why do I get a big log fold change but small mean change in b value when plotting differential methylation?

Why do I get a big log fold change but small mean change in b value when plotting differential methylation? 0 Hello I am doing differential methylation analysis using limma. I use the m values for testing and b values for plotting. I plotted a volcano plot visualizing the p…

Continue Reading Why do I get a big log fold change but small mean change in b value when plotting differential methylation?