Research Roundup: May 2019

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Research Roundup: May 2019

Here are summaries of a selection of the papers published by GCB faculty in May 2019:

New Tools

Raluca Gordân and team created Quantitative Predictions of TF Binding Changes Due to Sequence Variants (QBiC-Pred), a free web server for predicting quantitative transcription factor binding specificity trained on high-throughput in vitro data. Read more

Andrew Allen was part of a team that created groupedSurv, an R package that enables fast and rigorous genome-wide analysis on the basis of grouped failure time phenotypes at the variant, gene or pathway level. This package is freely available under a public license through the Comprehensive R Archive Network. Read more

Lingchong You was part of a team that created Prophage Hunter, a tool aimed at hunting for active prophages from whole genome assembly of bacteria. Prophage Hunter provides a one-stop free web service to extract prophage genomes from bacterial genomes, evaluate the activity of the prophages, identify phylogenetically related phages, and annotate the function of phage proteins. Read more

Life Cycle

Greg Wray and team, including members of the Proteomic and Metabolomic Shared Resource, used liquid chromatography-tandem mass spectrometry to create proteomic profiles of eggs and early stage larvae from three sea urchin species to identify the developmental and energetic drivers of larval life history evolution. Read more

Jenny Tung was part of a team that tested one of the predictions of Medawar’s mutation accumulation hypothesis: that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Read more

Chronic Kidney Disease

Andrew Allen was part of a team that used exome sequencing and rare-variant collapsing analyses to compare rare genetics variants in over 3,000 cases of chronic kidney disease (CKD). Their findings provide motivation for larger-scale investigation of rare-variant risk contributions across major clinical CKD categories. Read more

DNA

Eukaryotic genomes typically contain large regions of repetitive DNA, referred to as heterochromatin, that are both transcriptionally silent and late replicating. David MacAlpine was part of a team that provided a possible explanation for the association between transcriptional silencing and late replication. Read more

Reviews

Xiling Shen and team reviewed the Compucell3D framework and general workflow for transition from a well-mixed ordinary differential equation model to an agent-based model. Read more

In this review, Charlie Gersbach and Adrian Pickar-Oliver discuss the advances in technology and application of the CRISPR-Cas genome editing systems. Read more

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Weapon of Mass Congestion: Protection from Influenza Virus through Gene Control

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Credit: Pixabay.

DNA Metabarcoding Useful for Analyzing Human Diet

Lawrence David launches new study demonstrating that DNA metabarcoding provides a promising new method for tracking human plant intake, suggesting that similar approaches could be used to characterize the animal and fungal components of human diets.
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Two bacterial colonies that have formed purple rings because of the gene drive that researchers have implanted in them. A new machine learning model greatly speeds up this science by predicting the interaction of dozens of biological variables.

Machine Learning Predicts Behavior of Biological Circuits

Lingchong You has devised a machine learning approach to modeling the interactions between complex variables in engineered bacteria that would otherwise be too cumbersome to predict.
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