scatterbar: an R package for visualizing proportional data across spatially resolved coordinates

Posted by dbos Hopkins

Kavli Affiliate: Jean Fan | Authors: Dee Velazquez and Jean Fan | Summary: Summary: Displaying proportional data across many spatially resolved coordinates is a challenging but important data visualization task, particularly for spatially resolved transcriptomics data. Scatter pie plots are one type of commonly used data visualization for such data but present perceptual challenges that […]


Continue.. scatterbar: an R package for visualizing proportional data across spatially resolved coordinates

Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data

Posted by dbos UCSF

Kavli Affiliate: Robert Edwards | Authors: Bhavya Papudeshi, Michael J. Roach, Vijini Mallawaarachchi, George Bouras, Susanna R Grigson, Sarah K Giles, Clarice M Harker, Abbey L.K Hutton, Anita Tarasenko, Laura K Inglis, Alejandro A Vega, Cole Souza, Lance Boling, Hamza Hajama, Ana Georgina Cobian-Guemes, Anca Segall, Elizabeth A Dinsdale and Robert A Edwards | Summary: […]


Continue.. Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data

Brain-wide representations of prior information in mouse decision-making

Posted by klaurent Columbia

Kavli Affiliate: Liam Paninski | Authors: Charles Findling, Felix Hubert, International Brain Laboratory, Luigi Acerbi, Brandon Benson, Julius Benson, Daniel Birman, Niccolò Bonacchi, Matteo Carandini, Joana A Catarino, Gaelle A Chapuis, Anne K Churchland, Yang Dan, Eric EJ DeWitt, Tatiana A Engel, Michele Fabbri, Mayo Faulkner, Ila Rani Fiete, Laura Freitas-Silva, Berk Gerçek, Kenneth D […]


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ELAVL3 regulates splicing of RNAs encoding synaptic signaling proteins in D1 and D2 striatal medium spiny neurons.

Posted by dbos Rockefeller

Kavli Affiliate: Robert B. Darnell | Authors: Krithi Irmady, Claudia Scheckel, Ruth A Singer, Thomas Carroll and Robert B Darnell | Summary: The neuronal RNA-binding protein (RBP) family nELAVL regulates key neuronal processes by binding directly to target RNA transcripts. In this study, we demonstrate that ELAVL3 is the predominant nELAVL paralog expressed in D1 […]


Continue.. ELAVL3 regulates splicing of RNAs encoding synaptic signaling proteins in D1 and D2 striatal medium spiny neurons.

Inter- and Intrahemispheric Sources of Vestibular Signals to V1

Posted by dbos UCSD / Salk

Kavli Affiliate: Massimo Scanziani | Authors: Guy Bouvier, Alessandro Sanzeni, Elizabeth Hamada, Nicolas Brunel and Massimo Scanziani | Summary: Head movements are sensed by the vestibular organs. Unlike classical senses, signals from vestibular organs are not conveyed to a dedicated cortical area but are broadcast throughout the cortex. Surprisingly, the routes taken by vestibular signals […]


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Quantitative guiding of developmental cell fate transitions using gene-free modelling

Posted by dbos Rockefeller

Kavli Affiliate: Eric D. Siggia | Authors: Ismail Hajji, Eric D Siggia, Francis Corson and Wolfgang Keil | Summary: During development, cells gradually assume specialized fates via changes of transcriptional dynamics in thousands of genes. Terminal cell identities are then stabilized through the convergence of gene regulatory network dynamics and the accumulation of epigenetic DNA […]


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Long-term effects of psilocybin on dynamic and effectivity connectivity of fronto-striatal-thalamic circuits

Posted by dbos UCSF

Kavli Affiliate: Adam Gazzaley | Authors: Lorenzo Pasquini, Jakub Vohryzek, Anira Escrichs, Yonatan Sanz Perl, Adrian Ponce-Alvarez, Sebastian Idesis, Manesh Girn, Leor Roseman, Jennifer M Mitchell, Adam Gazzaley, Morten Kringelbach, David J Nutt, Taylor Lyons, Robin L Carhart-Harris and Gustavo Deco | Summary: Psilocybin has been shown to induce fast and sustained improvements in mental […]


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Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability

Posted by dbos UCSF

Kavli Affiliate: Alex Pollen | Authors: Sara Nolbrant, Jenelle L. Wallace, Jingwen Ding, Tianjia Zhu, Jess L. Sevetson, Janko Kajtez, Isabella A. Baldacci, Emily K. Corrigan, Kaylynn Hoglin, Reed McMullen, Matthew T. Schmitz, Arnar Breevoort, Dani Swope, Fengxia Wu, Bryan J. Pavlovic, Sofie R. Salama, Agnete Kirkeby, Hao Huang, Nathan K. Schaefer and Alex A. […]


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Nuclear DNA replication in Leishmania major relies on a single constitutive origin per chromosome supplemented by thousands of stochastic initiation events

Posted by dbos UCSD / Salk

Kavli Affiliate: Gabriel Silva | Authors: Jeziel D Damasceno, Gabriel LA Silva, Catarina A Marques, Marija Krasilnikova, Craig Lapsley, Dario Beraldi and Richard McCulloch | Summary: Understanding genome duplication requires characterisation of the locations where DNA replication initiates, termed origins. Genome-wide mapping of DNA replication origins has mainly been derived from population-based techniques, with only […]


Continue.. Nuclear DNA replication in Leishmania major relies on a single constitutive origin per chromosome supplemented by thousands of stochastic initiation events

Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction

Posted by dbos Columbia

Kavli Affiliate: Ann McDermott | Authors: Cassandra A Chartier, Virgil A Woods, Yunyao Xu, Anne E van Vlimmeren, Marko Jovanovic, Ann E McDermott, Daniel A Keedy and Neel H Shah | Summary: The rapid identification of protein-protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and proximity-labeling proteomics. […]


Continue.. Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction