Science Research Weekly
By Mark R Williamson
Science Research WeeklyApr 22, 2022
Of Cosmic Glitches and Waffle Sketches (Season 3: Episode 18)
Get ready for picky archaeal parasites, a cosmic glitch in gravity, super sticky adhesive, Volume 15/4 of The R Journal, sketchy waffle charts, Super Saiyan Data Skills, and a Department of Defense grant for cancer. Science On.
References:
- Selective lipid recruitment by an archaeal DPANN symbiont from its host
- A cosmic glitch in gravity
- Fibrillar adhesives with unprecedented adhesion strength, switchability and scalability
- The R Journal: Volume 15/4
- Estimate a proportion and a confidence interval in SAS
- R/Medicine is coming June 10-14, 2024 – See Top Five R Medicine Talks from Previous Years
- Guide to Remove Legends in ggplot2 in R Programming
- Sketchy waffle charts in R
- Super Saiyan Data Skills: Mastering Big Data with R
- DoD Peer Reviewed Cancer, Idea Award
R Packages:
- karlen: Real-Time PCR Data Sets by Karlen et al. (2007)
- boggy: Real-Time PCR Data Sets by Boggy et al. (2010)
- SpatGC: Bayesian Modeling of Spatial Count Data
Cnidarian Nightlight (Season 3: Episode 17)
Get ready for friendly giant viruses, the ancient origins of bioluminescence, sneaky bacteria, R codename Puppy Cup, a Super Mario Bros. explanation of R piping, and grants for rare cancer research. Science On.
References:
- A giant virus infecting the amoeboflagellate Naegleria
- Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia
- Burkholderia thailandensis uses a type VI secretion system to lyse protrusions without triggering host cell responses
- [Rd] R 4.4.0 is released
- Navigating the Data Pipes: An R Programming Journey with Mario Bros.
- NIH: Pathway to Independence Award
- NIH: Small Business Transition Grant For Early Career Scientists
- DoD: Rare Cancers, Concept Award
- GenScript Life Science Research Grant Program
R Packages:
- slap: Simplified Error Handling
- RobRegression: Robust Multivariate Regression
- donutsk: Construct Advanced Donut Charts
It’s Raining Antibiotics! (Season 3: Episode 16)
Get ready for umbrella antibiotics, staring into the nanovoid, blue-whale-sized ichthyosaurs (maybe), and astrodynamics knot theory applications. Science On!
References:
- Streptomyces umbrella toxin particles block hyphal growth of competing species
- Beyond nothingness in the formation and functional relevance of voids in polymer films
- The last giants: New evidence for giant Late Triassic (Rhaetian) ichthyosaurs from the UK
- Applications of knot theory to the detection of heteroclinic connections between quasi-periodic orbits
- Distributions with specified skewness and kurtosis
- How to Make Mobile Apps with R Shiny
R Packages:
- filters: A "Snake_case" Filter System for R
- relcircle: Draw Regulatory Relationships Between Genes
Dark Stars and Metastatic Microbiomes (Season 3: Episode 15)
Get ready for the pan-cancer microbiome, auto-parameterizing 3D printing, Bergmann’s rule busted for dinosaurs, and Proca stars made out of dark matter. Science On!
References:
- A pan-cancer analysis of the microbiome in metastatic cancer
- Human brain small extracellular vesicles contain selectively packaged, full-length mRNA
- Online Measurement for Parameter Discovery in Fused Filament Fabrication
- An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments
- Global latitudinal gradients and the evolution of body size in dinosaurs and mammals
- Proca stars with dark photons from spontaneous symmetry breaking of the scalar field dark matter
- Journal of Statistical Software Volume 108
- The Truth About Tidy Wrappers
R Packages:
- IRR2FPR: Computing False Positive Rate from Inter-Rater Reliability
- WayFindR: Computing Graph Structures on WikiPathways
- CARMS: Continuous Time Markov Rate Modeling for Reliability Analysis
The Birds Are Up to Something (Season 3: Episode 14)
Get ready for neoavian phylogenetics, marvelous metafluids, the search for dark photon dark matter, normalization and scaling in R, Highcharts for interactive and animated charts, and a grant on rare diseases. Science On.
References:
- A region of suppressed recombination misleads neoavian phylogenomics
- Shell buckling for programmable metafluids
- First Results from a Broadband Search for Dark Photon Dark Matter in the 44 to 52 μ eV Range with a Coaxial Dish Antenna
- Add a second axis to a SAS graph
- 6 New books added to Big Book of R
- A Practical Guide to Data Normalization in R
- Scaling Your Data to 0-1 in R: Understanding the Range
- R Highcharts: How to Make Animated and Interactive Data Visualizations in R
- NCATS: Preclinical Proof of Concept Studies for Rare Diseases
R Packages:
- CoreMicrobiomeR: Identification of Core Microbiome
- scimo: Extra Recipes Steps for Dealing with Omics Data
Starquaking in My Boots (Season 3: Episode 13)
Get ready for the smallest starquake, migraine risks in young stroke, tardigrade biostasis, too many colors spoiling the graph, Bioconductor Conference 2024, and a subset of Department of Defense grants on human health. Science On.
References:
- Protective effect of PDE4B subtype-specific inhibition in an App knock-in mouse model for Alzheimer’s disease
- Expanding the frontiers of cool-dwarf asteroseismology with ESPRESSO
- Association of Traditional and Nontraditional Risk Factors in the Development of Strokes Among Young Adults by Sex and Age Group: A Retrospective Case-Control Study
- Labile assembly of a tardigrade protein induces biostasis
- CRTFASTGEEPWR: A SAS Macro for Power of Generalized Estimating Equations Analysis of Multi-Period Cluster Randomized Trials with Application to Stepped Wedge Designs
- too many colors spoil the graph
- Bioconductor Conference 2024
- DoD Peer Reviewed Medical, Investigator-Initiated Research Award
- DoD Peer Reviewed Medical, Discovery Award
- AAAAI Foundation Award to Sustain Research Excellence
R Packages:
- CvmortalityMult: Cross-Validation for Multi-Population Mortality Models
- flexOR: Flexible Odds Ratio Curves
- glmMisrep: Generalized Linear Models Adjusting for Misrepresentation
- biopixR: Extracting Insights from Biological Images
Your Brain on Cosmology (Season 3: Episode 12)
Get ready for leafhopper cloaking technology, the question of a dark matter-less universe, life at the extremes of inactive hydrothermal vents, not caring about the Levene’s test, and a grant on brain changes across longer time spans. Science On.
References:
- Geometric design of antireflective leafhopper brochosomes
- Testing CCC+TL Cosmology with Observed Baryon Acoustic Oscillation Features
- Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity
- Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping
- Two-dimensional materials by large-scale computations and chemical exfoliation of layered solids
- assumptions of linear models are about errors, not the response variable
- Here is why I don’t care about the Levene’s test
- NIH: New Approaches for Measuring Brain Changes Across Longer Timespans (R01)
- NIH: New Approaches for Measuring Brain Changes Across Longer Timespans (R21)
R Packages:
- xega: Extended Evolutionary and Genetic Algorithms
- tidyrates: Tidy Epidemiological Rates
- calmr: Canonical Associative Learning Models and their Representations
- ggbrick: Waffle Style Chart with a Brick Layout in 'ggplot2'
Gastronomical Gallivanting (Season 3: Episode 11)
Get ready for bile acid modification, Pizza Pi, pre-print propensity using R, and a grant on misfolding proteins. Science On.
References:
- High-quality semiconductor fibres via mechanical design
- Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes
- The underappreciated diversity of bile acid modifications
- Newsletter March 2024 - Genie Builder Beta Launch - Create Web Apps and Dashboards Easily
- Pizza pi
- My Simple Understanding of Total Effect = Direct Effect + Indirect Effect (via Mediator)
- Mastering Random Sampling in R with the sample() Function
- Pre Self: what fraction of a journal’s papers are preprinted?
- NIH: Exploring Proteogenomic Approaches to Unravel the Mechanisms of Mis-Folded Protein Accumulation in Tauopathies
R Packages:
- glmpermu: Permutation-Based Inference for Generalized Linear Models
- corrmeta: Correlated Meta-Analysis
Vertebrates and Hat Tricks (Season 3: Episode 10)
Get ready for low-oxygen Europa, low-mutational nematode genomes, museum-loads of 3D scanned vertebrates, A Steve’s Data Tips and Tricks hat trick plus one, and a NSF grant on AI and math. Science On.
References:
- Oxygen production from dissociation of Europa’s water-ice surface
- Environmental radiation exposure at Chornobyl has not systematically affected the genomes or chemical mutagen tolerance phenotypes of local worms
- Decoding chromatin states by proteomic profiling of nucleosome readers
- Scientists CT scanned thousands of natural history specimens, which you can access for free
- A Beginner’s Guide to Renaming Data Frame Columns in R
- How to Rename Factor Levels in R (With Examples)
- How to Add New Level to Factor in R
- Filtering Rows in R Where Column Value is Between Two Values
- NSF: Artificial Intelligence, Formal Methods, and Mathematical Reasoning
R Packages:
- DiscreteDatasets: Example Data Sets for Use with Discrete Statistical Tests
- rexer: Random Exercises and Exams Generator
Ask the Genie for Some Cake (Season 3: Episode 9)
Get ready for the brightest quasar of them all, biomolecule chirality mysteries, a Biomedical Engineering roadmap, the release of R’s Angel Food Cake, the release of JuliaHub’s Genie Builder, and Shiny for clinical trial reporting. Science On.
References:
- The accretion of a solar mass per day by a 17-billion solar mass black hole
- Symmetry breaking and chiral amplification in prebiotic ligation reactions
- Grand Challenges at the Interface of Engineering and Medicine
- R 4.3.3 is released
- Unveiling Genie Builder: Create Low-Code Apps on JuliaHub
- On using flexible distributions to fit data
- Using colors to visualize groups in a bar chart in SAS
- What Good is Analysis of Variance?
- Escape the Spreadsheet Inferno: Switch to Shiny for Clinical Trial Reporting
- Demystifying the melt() Function in R
R Packages:
- pctax: Professional Comprehensive Omics Data Analysis
- clusEvol: A Procedure for Cluster Evolution Analytics
- volker: High-Level Functions for Tabulating, Charting and Reporting Survey Data
The Birds and the Beta-amyloids (Season 3: Episode 8)
Get ready for blazing computer processing speeds, a link between fine particulate matter and Alzheimer’s Disease, mammalian gene insertion with bird retrotransposons, experimental confirmation of altermagnets, The Journal of Statistical Software Volume 108, a free R/Shiny eBook, and an NSF grant on acceleration of protein design. Science On.
References:
- Simultaneous and Heterogenous Multithreading
- Association of PM2.5 Exposure and Alzheimer Disease Pathology in Brain Bank Donors—Effect Modification by APOE Genotype
- Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci
- Observation of New Isotopes in the Fragmentation of 198 Pt at FRIB
- Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2
- Journal of Statistical Software Volume 108
- On using the range to estimate the variability of small samples
- measures of model fit for linear regression models
- Level Up Your R/Shiny Team Skills with Our Free Ebook
- Enhancing Your Plots in R: Adding Superscripts & Subscripts
- NSF: Ideas Lab: Use-Inspired Acceleration of Protein Design
- NSF: Plant Genome Research Program
R Packages:
- fluidsynth: Read and Play Digital Music (MIDI)
- aberrance: Detect Aberrant Behavior in Test Data
- ggbrace: Curly Braces for 'ggplot2'
Eeny, Meeny, Mimas, Moe (Season 3: Episode 7)
Get ready for a mini Mimas ocean, microbes for low-cost molecular biology, Ordovician fossils from France, a 3D-printed titanium metamaterial, Emacs for R, and a NASA omnibus funding announcement chock full of opportunity. Science On.
References:
- A recently formed ocean inside Saturn’s moon Mimas
- Efficient natural plasmid transformation of Vibrio natriegens enables zero-capital molecular biology
- The quest for superheavy elements and the limit of the periodic table
- The Cabrières Biota (France) provides insights into Ordovician polar ecosystems
- Pleural macrophages translocate to the lung during infection to promote improved influenza outcomes
- Titanium Multi-Topology Metamaterials with Exceptional Strength
- An exact formula for the sampling distribution of the correlation coefficient
- NIA Career Transition Award
- NASA ROSES: Astrophysics Data Analysis Program
- NASA ROSES: New Frontiers Data Analysis Program
- NASA ROSES: Exobiology
R Packages:
- circlesplot: Visualize Proportions with Circles in a Plot
- multe: Multiple Treatment Effects Regression
- valentine: Spread the Love for R Packages with Poetry
Plankton Power (Season 3: Episode 6)
Get ready for memory B cells that react to allergens, a cosmic chicken and egg questions with black holes and galaxies, the ecological importance of tiny plankton, the spectacular shape of ancient trees, triangular art in Julia, elliptical hearts in SAS, and the 400th entry in the Big Book of R. Science On.
References:
- Type 2–polarized memory B cells hold allergen-specific IgE memory
- Locomotion and the early Mesozoic success of Archosauromorpha
- Which Came First: Supermassive Black Holes or Galaxies? Insights from JWST
- Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides
- The silent majority: Pico- and nanoplankton as ecosystem health indicators for marine policy
- Noninvasive neuromodulation of subregions of the human insula differentially affect pain processing and heart-rate variability: a within-subjects pseudo-randomized trial
- microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
- Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency
- Enigmatic fossil plants with three-dimensional, arborescent-growth architecture from the earliest Carboniferous of New Brunswick, Canada
- Michael Dickey, our guide through the surprising world of liquid metals
- My First Julia Package – TriangulArt.jl
- Newsletter February 2024 - Next Gen Battery Simulation with JuliaSim
- The elliptical heart
- 9 for SAS9 – Top Tips for SAS 9 Programmers Moving to SAS Viya
- How to Check if Date is Between Two Dates in R
- Big Book of R at 400 [New milestone!]
R Packages:
- fastTS: Fast Time Series Modeling with the Sparsity Ranked Lasso
- flowchart: Tidy Flowchart Generator
- mulSEM: Some Multivariate Analyses using Structural Equation Modeling
Great Sharks! (Season 3: Episode 5)
Get ready for a newborn great white shark sighting, an ancient Martian lakebed, a potential new kingdom of viruses, the twin mysteries of correlation and covariance in R, and a clinical trial grant focused on natural products. Science On.
References:
- Novel aerial observations of a possible newborn white shark (Carcharodon carcharias) in Southern California
- Ground penetrating radar observations of the contact between the western delta and the crater floor of Jezero crater, Mars
- Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan
- The name of the variable that contains the largest value in each row
- How to split a large file into smaller chunks using SAS
- Shadow and Substance: Unveiling the Twin Mysteries of Correlation and Covariance
- NCCIH: Natural Product Early Phase Clinical Trial Phased Innovation Award
R Packages:
- NoviceDeveloperResources2: Further Resources to Assist Novice Developers
- fastglmpca: Fast Algorithms for Generalized Principal Component Analysis
- modelfactory: Combine Statistical Models into a Tibble for Comparison
- unigd: Universal Graphics Device
Convergence Research or Bust (Season 3: Episode 4)
Get ready for blockchain for biology, ancient microbe metabolisms, false vacuum decay evidence, angles vs. slopes, and a grant on convergence research. Science On.
References:
- Three-dimensional nanoscale metal, metal oxide, and semiconductor frameworks through DNA-programmable assembly and templating
- Emergence of metabolic-like cycles in blockchain-orchestrated reaction networks
- Aspects of the biological carbon cycle in a ca. 3.42-billion-year-old marine ecosystem
- Phylogenomic insights into the first multicellular streptophyte
- False vacuum decay via bubble formation in ferromagnetic superfluids
- Angles vs slopes: The statistics of steepness
- The Art of Estimation in R: Confidence Intervals Demystified
- 6 Benefits of R {targets} for Data Science Workflows
- NSF: Growing Convergence Research
R Packages:
- labeleR: Automate the Production of Custom Labels, Badges, Certificates, and Other Documents
- labelr: Label Data Frames, Variables, and Values
- gbm3: Generalized Boosted Regression Models
- NVAR: Nonlinear Vector Autoregression Models
Science is Coming Up Sixes! (Season 3: Episode 3)
Get ready for an ancient black hole, capturing the complexity of fragile ocean life, the magnetic map of the Milky Way, Six not-so-basic R functions, the Six degrees of Hadley Wickham, and a grant on agricultural genomes to phenomes. Science On.
References:
- A small and vigorous black hole in the early Universe
- Contrast Agent-Free 3D Renal Ultrafast Doppler Imaging Reveals Vascular Dysfunction in Acute and Diabetic Kidney Diseases
- An in situ digital synthesis strategy for the discovery and description of ocean life
- Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration
- Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean
- Tomographic Imaging of the Sagittarius Spiral Arm's Magnetic Field Structure
- charting a path to statistical confidence and mastery
- Six not-so-basic base R functions
- Six degrees of Hadley Wickham: The CRAN co-authorship network
- Creating automatically dozens of calendar notifications (with R)
- USDA: Agricultural Genome to Phenome Initiative
R Packages:
- neonPlantEcology: Process NEON Plant Data for Ecological Analysis
- NGCHM: Next Generation Clustered Heat Maps
- scientific: Elegant Scientific Themed Reporting for 'Markdown'
- MetaNet: Network Analysis for Omics Data
- treestats: Phylogenetic Tree Statistics
- r2fireworks: Enhance Your 'Rmarkdown' and 'shiny' Apps with Dazzling Fireworks Celebrations
Science, Roll Out! (Season 3: Episode 2)
Get ready for rolling ringbots, cancer cannibalizing cells, the R Journal Volume 15/3, a new Bioconductor website, a beginner's guide to probability distributions in R, and an EPA grant to reduce air pollution in schools. Science On.
References:
- New Soft Robots Roll Like Tires, Spin Like Tops and Orbit Like Moons
- Hyperactive Rac stimulates cannibalism of living target cells and enhances CAR-M-mediated cancer cell killing
- Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis
- Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts
- R Journal Volume 15/3
- Blog posts from 2023 that deserve a second look
- Bioconductor
- Retrieving Data From The Bottom Of The Ocean
- Unveiling the Smooth Operator: Rolling Averages in R
- Probably More Than Chance: A Beginner’s Guide to Probability Distributions in R
- Goodbye Complicated Dropdowns: Welcome to the New Era of Human Readable Filters
- Financial Assistance is Available for Your R User Group in 2024!
- EPA: Grant Funding to Address Indoor Air Pollution at Schools
- NSF: Research in Basic Plasma Science and Engineering
R Packages:
- Apoderoides: Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree
- bscui: Build SVG Custom User Interface
- dittoViz: User Friendly Data Visualization
- tidyMC: Monte Carlo Simulations Made Easy and Tidy
- tidyplate: Transform Microplate Data into Tidy Dataframes
Trojan Plants Bearing Vesicles (Season 3: Episode 1)
Get ready for lava-proof ceramics, antibiotic polymers, Trojan horse plant mRNA vesicles, microbiome disturbances in kidney stone formation, Top 10 DO Loop posts from 2023, Mastering Lowess Smoothing in R, and early career grants with no existing preliminary data. Science On.
References:
- Disordered enthalpy–entropy descriptor for high-entropy ceramics discovery
- A giant stem-group chaetognath
- Ring-opening metathesis polymerization of N-methylpyridinium-fused norbornenes to access antibacterial main-chain cationic polymers
- The bacterial replication origin BUS promotes nucleobase capture
- Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection
- Multi-site microbiota alteration is a hallmark of kidney stone formation
- Top 10 posts from The DO Loop in 2023
- Mastering Lowess Smoothing in R: A Step-by-Step Guide
- Four ways to streamline your R workflows
- The 6 steps to finally lose weight (or solve almost any other problem) (with R code)
- NIH: Stephen I. Katz Early Stage Investigator Research Project Grant (clinical trial)
- NIH: Stephen I. Katz Early Stage Investigator Research Project Grant (non-clinical trial)
R Packages:
- allofus: Interface for 'All of Us' Researcher Workbench
- ARGOS: Automatic Regression for Governing Equations (ARGOS)
- MSML: Model Selection Based on Machine Learning (ML)
- surveyexplorer: Quickly Explore Complex Survey Data
Episode 50: Christmas or Break
Get ready for a brief, asynchronous episode today to cover the break over the Christmas holiday. Merry Christmas!
References:
Episode 49: Unnaturally Cool
Get ready for unnatural nucleotides, nutrient-blocking gut microbes, a confluence of newsletters and conferences, Effortless Cool in Data Science, and a grant for long-term ecological research. Science On.
References:
- A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase
- Microbiome diversity protects against pathogens by nutrient blocking
- Registration for useR! 2024
- Python Software Foundation - December 2023 Newsletter
- Julia Newsletter December 2023
- New SAS Training Course: Statistics You Need to Know for Machine Learning
- when the hessian matrix goes wacky
- A three-arm trial using two-step randomization
- A new focus on tidygraph
- Effortless Cool Is A Detailed Process – How To Influence, Tell Better Stories, and Become More Persuasive
- GitHub: Javascript Interview Questions
- NHGRI: Advancing Genomic Technology Development for Research and Clinical Application
- NSF: Long-Term Ecological Research
R Packages:
- AVGAS: A Variable Selection using Genetic Algorithms
- treesliceR: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time
- sfd: Space-Filling Design Library
- explainer: Machine Learning Model Explainer
Episode 48: Diamond Doppelgangers and Distant Oceans
Get ready for Japanese mosasaurs, hard-as-diamond materials, cold ocean exoplanets, polychoric correlation, 15 Academic Research Tools, the 10 most popular R books of 2023, and an NSF grant for Emerging Mathematics in Biology. Science On.
References:
- A new derived mosasaurine (Squamata: Mosasaurinae) from south-western Japan reveals unexpected postcranial diversity among hydropedal mosasaurs
- Synthesis of Ultra-Incompressible and Recoverable Carbon Nitrides Featuring CN4 Tetrahedra
- Prospects for Cryovolcanic Activity on Cold Ocean Planets
- Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype
- What is polychoric correlation?
- what is family-wise error rate?
- Top 15 Academic Research Tools For Scholars And Tutors
- The 10 most popular R books of 2023
- Edge of Tomorrow: Preparing R Functions for the Unexpected
- NSF: Emerging Mathematics in Biology
R Packages:
- DFBA: Distribution-Free Bayesian Analysis
- dunlin: Preprocessing Tools for Clinical Trial Data
- shinyquiz: Create Interactive Quizzes in 'shiny'
- TaxaNorm: Feature-Wise Normalization for Microbiome Sequencing Data
- simtrial: Clinical Trial Simulation
Episode 47: Tis the Season for Better Espresso
Get ready for better expresso, quasi-particle monopoles, crocodilian phylogeny, Anthrobots, SAS tips for creating effective statistical graphics, a Git repo for throwaway code, and excitement over the ExCITe grant. Science On.
References:
- Moisture-controlled triboelectrification during coffee grinding
- Revealing emergent magnetic charge in an antiferromagnet with diamond quantum magnetometry
- Corals and sponges are hotspots of reactive oxygen species in the deep sea
- Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs
- Motile Living Biobots Self-Construct from Adult Human Somatic Progenitor Seed Cells
- Food for all? Wildfire ash fuels growth of diverse eukaryotic plankton
- Fear extinction is regulated by the activity of long noncoding RNAs at the synapse
- Announcing the Release of JuliaHub 6.4 - Package Metrics, Dash.jl Templates, Web App Hosting, and More
- 10 tips for creating effective statistical graphics
- 5 new books added to Big Book of R
- Shiny Express: Blending the Best of Shiny and Streamlit for Dashboard Development
- A Complete Guide to Stepwise Regression in R
- Unveiling the Magic of Polynomial Regression in R: A Step-by-Step Guide
- Get a Git repo where your team can stow their throwaway data science code!
- GitHub: Best-websites-a-programmer-should-visit
- GitHub: Elementor
- NCI: Exploratory Cancer Immunology Projects and Technologies (ExCITe)
- NSF: Mind, Machine and Motor Nexus
R Packages:
- fcp: Function Composition
- survobj: Objects to Simulate Survival Times
- ADTSA: Time Series Analysis
- iperform: Time Series Performance
Episode 46: Good Friends and Bad Graphs
Get ready for the British oral microbiome across history, the catalogue of gamma-ray pulsars, deep mine microbes, the theme() option in ggplot2, friends not letting friends make bad graphs, and a grant on emerging technologies for cancer research. Science On.
References:
- Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain
- The Third Fermi Large Area Telescope Catalog of Gamma-Ray Pulsars
- A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA
- Spatial autocorrelation
- Getting started with theme()
- GitHub: FriendsDontLetFriends
- NIH: Advanced Development and Validation of Emerging Molecular and Cellular Analysis Technologies for Basic and Clinical Cancer Research
R Packages:
- ivo.table: Pretty Contingency Tables and Frequency Tables
- aloom: All Leave-One-Out Models
- revert: Reversion Mutation Identifier for Sequencing Data
Episode 45: Thanks for All the Keystone Species
Get ready for nanoscale protein traps, enigmatic amoeba, keystone microbes, logarithmic regression in R, and project funding for the National Heart, Lung, and Blood Institute. Science On.
References:
Rhabdamoeba marina is a heterotrophic relative of chlorarachnid algae
Identifying keystone species in microbial communities using deep learning
concepts in linear regression to know before learning multilevel models
Logarithmic Regression in R: A Step-by-Step Guide with Prediction Intervals
R lubridate: How To Efficiently Work With Dates and Times in R
NHLBI: Program Project Applications
R Packages:
semidist: Measure Dependence Between Categorical and Continuous Variables
ggScatRidges: Scatter Plot Combined with Ridgelines in 'ggplot2'
air: AI Assistant to Write and Understand R Code
Episode 44: Composite Hands and Mitochondrial Medicine
Get ready for composite 3D robot parts, spotting sugar-protein interactions, MIC for mitochondrial health, the R Journal Volume 15/2, avoiding alphabetical order in SAS, font changes in ggplot2, and an NSF grant for organoid systems. Science On.
References:
- Vision-controlled jetting for composite systems and robots
- Minutes-duration optical flares with supernova luminosities
- Fluorogenic Photo-Crosslinking of Glycan-Binding Protein Recognition Using a Fluorinated Azido-Coumarin Fucoside
- A drug-like molecule engages nuclear hormone receptor DAF-12/FXR to regulate mitophagy and extend lifespan
- The R Journal Volume 15/2
- Tip: Avoid alphabetical order for a categorical axis in a graph
- the difference between standard deviation and standard error
- How to Change Fonts in ggplot2 with Google Fonts
- A classifier that's very accurate (and deep)
- Data Analysis in R for Becoming a Bioscientist
- GitHub: TIL
- NSF: Biocomputing through EnGINeering Organoid Intelligence
R Packages:
- cookiemonster: Your Friendly Solution to Managing Browser Cookies
- PAICE: Phylogeographic Analysis of Island Colonization Events
- BayesGmed: Bayesian Causal Mediation Analysis using 'Stan'
Episode 43: Invasion of the Paleobionics!
Get ready for the new field of Paleobionics, molecular beasts, virus-attaching viruses, Jurassic planets, the 2023 Python Developers Survey, free DataCamp and 365 Data Science courses, and an NSF grant for designing synthetic cells beyond the bounds of evolution. Science On.
References:
- Soft robotics informs how an early echinoderm moved
- Distinctive microfossil supports early Paleoproterozoic rise in complex cellular organisation
- CHARGED “MOLECULAR BEASTS” THE BASIS FOR NEW COMPOUNDS
- Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species
- Oxygen bounty for Earth-like exoplanets: spectra of Earth through the Phanerozoic
- A big step for little particle accelerators
- Join the Python Developers Survey 2023: Share and learn about the community!
- 4 ways to display an inset that contains statistics on a SAS graph
- R Shiny Modules: How to Create Your First R Shiny Module
- How to Make a Data Science Portfolio Website (in Under 15 Minutes with R)
- 365 Data Science courses 100% free until November 20
- Data Camp Free Week
- NIH: Exploratory Clinical Trial Grants in Arthritis and Musculoskeletal and Skin Diseases
- NSF: Incorporating Human Behavior in Epidemiological Models
- NSF: Designing Synthetic Cells Beyond the Bounds of Evolution
R Packages:
- qeML: Quick and Easy Machine Learning Tools
- Spectran: Visual and Non-Visual Spectral Analysis of Light
- SillyPutty: Silly Putty Clustering
Episode 42: Life, the Near Infrared, and Everything
Get ready for the sunken remains of a planet, long-lived fish, near infrared detection on Uranus, R and Bioconductor updates, and NASA grants for life in space. Science On.
References:
- Moon-forming impactor as a source of Earth’s basal mantle anomalies
- Centenarian lifespans of three freshwater fish species in Arizona reveal the exceptional longevity of the buffalofishes (Ictiobus)
- Detection of the infrared aurora at Uranus with Keck-NIRSPEC
- [Rd] R 4.3.2 is released
- Bioconductor 3.18 Released
- Scanning QR codes in R
- Approaches to Calculating Number Needed to Treat (NNT) with Meta-Analysis
- How to Load SAS Files in R: Transitioning from SAS to R with Seamless Data Integration
- NOSI: Using Targeted Degradation of Protein and non-Protein Targets for the Development of Novel Anti-Infectives
- NOSI: Chronic Inflammation of the Oral Cavity - An Agent for Oral Mucosal Disease
- NASA: Established Program to Stimulate Competitive Research (EPSCoR)
- NASA: Transport Phenomena Research at the International Space Station to Benefit Life on Earth
- NASA: NSF/CASIS Collaboration on Tissue Engineering and Mechanobiology on the International Space Station (ISS) to Benefit Life on Earth
R Packages:
- portion: Extracting a Data Portion
- Rnanoflann: Extremely Fast Nearest Neighbor Search
- SurvSparse: Survival Analysis with Sparse Longitudinal Covariates
- tRigon: Toolbox for Integrative Pathomics Analysis
- defineOptions: Define and Parse Command Line Options
Episode 41: Things are Heating Up
Get ready for technosignatures from space, hypertension-reducing gut microbes, DNA nanomachines, molten Martian layers, a RegEx treasure hunt in R, and a radiation medical countermeasures grant. Science On.
References:
- A Simultaneous Dual-site Technosignature Search Using International LOFAR Stations
- Genetically engineered Lactobacillus paracasei rescues colonic angiotensin converting enzyme 2 (ACE2) and attenuates hypertension in female Ace2 knock out rats
- A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower
- Geophysical evidence for an enriched molten silicate layer above Mars’s core
- Weighted Trajectory Analysis and Application to Clinical Outcome Assessment
- mixed models with crossed random factors
- How to Create a Bubble Chart in R using ggplot2
- Unearthing Golden Nuggets of Data: A RegEx Treasure Hunt in R
- 3 (actually 4) neat R functions
- GitHub: MuJoCo
- NIH: Development of Candidate Radiation/Nuclear Medical Countermeasures
R Packages:
- envvar: Make Working with Environment Variables Easier and More Consistent
- multitool: Run Multiverse Style Analyses
- oeli: Utilities for Developing Data Science Software
- mvhtests: Multivariate Hypothesis Tests
- eglhmm: Extended Generalised Linear Hidden Markov Models
Episode 40: Brain Cell Atlas Shrugged
Get ready for polygenic risk score stumbling blocks, million-color-palette miniaturized DNA-based painting, the human brain cell atlas, rogue nanowaves, tiny particle accelerators, a Peanuts Halloween themed R release, the Power of Functional Programming in R, and a grant for developing models of oncoaging in cancer research. Science On.
References:
- Performance of polygenic risk scores in screening, prediction, and risk stratification: secondary analysis of data in the Polygenic Score Catalog
- A Canvas of Spatially Arranged DNA Strands that Can Produce 24-bit Color Depth
- VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities
- Single-cell DNA methylation and 3D genome architecture in the human brain
- Rogue nanowaves: A route to film rupture
- Coherent nanophotonic electron accelerator
- Journal of Statistical Software, Volume 107
- R 4.3.2 scheduled for October 31
- Mastering Interaction Plots in R: Unveiling Hidden Relationships
- Mastering the Art of Drawing Circles in Plots with R
- Releasing collapse 2.0: Blazing Fast Joins, Reshaping, and Enhanced R
- Unlocking the Power of Functional Programming in R (Part 1)
- A brand new GAMLj
- NOSI: Research Projects to Develop Oncoaging Models for Cancer Research
R Packages:
- eglhmm: Extended Generalized Linear Hidden Markov Models
- maplegend: Legends for Maps
- ZIBR: A Zero-Inflated Beta Random Effect Model
- qrlabelr: Generate Machine- And Human-Readable Plot Labels for Experiments
- MicrobiomeSurv: Biomarker Validation for Microbiome-Based Survival Classification and Prediction
- tinycodet: A Few Functions to Help in your Coding Etiquette
Episode 39: Bulking Up on Microbial Dark Matter Proteins
Get ready for X-ray blasted 3D prints, a prehistoric “Pontus” tectonic plate, microbial dark matter protein families, function approximation in SAS, Bionic Reading in R, and a small business grant opportunity for genomic medicine. Science On.
References:
- Dendritic deformation modes in additive manufacturing revealed by operando x-ray diffraction
- Plate tectonic cross-roads: Reconstructing the Panthalassa-Neotethys Junction Region from Philippine Sea Plate and Australasian oceans and orogens
- Unraveling the functional dark matter through global metagenomics
- GMM Estimators for Binary Spatial Models in R
- Approximate functions by using Taylor series and rational functions
- Horizontal Legends in Base R
- Little useless-useful R functions – Function for faster reading with Bionic Reading
- GitHub: Paperless-ngx
- NHGRI: Advancing Genomic Medicine Research through Small Businesses
- NSF: Cognitive Neuroscience
- MSA: Kenneth Downing Postdoctoral Scholarship
R Packages:
- MicrobiomeSurv: Biomarker Validation for Microbiome-Based Survival Classification and Prediction
- samplesizeestimator: Calculate Sample Size for Various Scenarios
- galamm: Generalized Additive Latent and Mixed Models
- wikkitidy: Tidy Analysis of Wikipedia
- mineSweepR: Mine Sweeper Game
Episode 38: Dancing DNA in the Detection Field
Get ready for highly sensitive dancing DNA detection, rare-earth munching bacteria, Python 3.12.0, the Top 9 R packages that every Data Scientist must know, and the Cancer Research Education Grants Program. Science On.
References:
- A New Tissue-Agnostic Microfluidic Device to model physiology and disease: The Lattice Platform
- Nanomechanoelectrical approach to highly sensitive and specific label-free DNA detection
- Genomic characterization of rare earth binding by Shewanella oneidensis
- piRNA processing by a trimeric Schlafen-domain nuclease
- A Candida auris–specific adhesin, Scf1, governs surface association, colonization, and virulence
- Use design matrices to analysis subgroups in SAS IML
- Python 3.12.0 (final) now available
- Top 9 R packages (that every Data Scientist must know)
- Creating typewriter-styled maps in {ggplot2}
- Plotting Decision Trees in R with rpart and rpart.plot
- NIH: Cancer Research Education Grants Program - Courses for Skills Development
- NIH: Cancer Research Education Grants Program - Research Experiences
- NIH: Cancer Research Education Grants Program - Curriculum or Methods Development
- NSF: Trailblazer Engineering Impact Award
- ACSM: Research & Program Grants
R Packages:
- conformalpvalue: Computes Conformal p-Values
- speccurvieR: Easy, Fast, and Pretty Specification Curve Analysis
- syntenyPlotteR: Genome Synteny Visualization
- h3r: Hexagonal Hierarchical Geospatial Indexing System
Episode 37: Code with me, I’m from the Future
Get ready for falling antimatter, water flea waste treatment, super solar distillation, R Journal volume 15/1, future programming languages, how NOT to format time series data, and an Ideas Lab grant for Personalized Engineering Learning. Science On.
References:
- Observation of the effect of gravity on the motion of antimatter
- Harnessing water fleas for water reclamation: A nature-based tertiary wastewater treatment technology
- Delivery of Nematicides Using TMGMV-Derived Spherical Nanoparticles
- A split and inducible adenine base editor for precise in vivo base editing
- Extreme salt-resisting multistage solar distillation with thermohaline convection
- Journal of Statistical Software: Volume 107
- R Journal: Volume 15/1
- 13+ Future Programming Languages 2025-2030 Coders Must Know
- 100+ CGR Micro Project Topics: Unleashing Your Creativity
- How NOT to format time series data
- Mastering Data Visualization with ggplot2: A Guide to Using facet_grid()
- GitHub: Omnivore
- NIAID: Fc-Dependent Mechanisms of Antibody-Mediated Killing
- NSF: Ideas Lab: Personalized Engineering Learning
R Packages:
- Colossus: Risk Model Regression and Analysis with Complex Non-Linear Models
- cloneRate: Estimate Growth Rates from Phylogenetic Trees
- statConfR: Models of Decision Confidence and Metacognition
- chem.databases: Collection of 3 Chemical Databases from Public Sources
Episode 36: Bone Lost in Space
Get ready for bone loss mitigation in space mice, a northern paleo-ocean on Mars, a new deep-sea virus, graphs within graphs in SAS, types of statistical contrasts, and a pediatrics grant from the March of Dimes. Science On.
References:
- Bisphosphonate conjugation enhances the bone-specificity of NELL-1-based systemic therapy for spaceflight-induced bone loss in mice
- Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit
- Gravity aspects for Mars
- Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m
- Use PROC SGPLOT to embed a graph inside another graph
- six common types of statistical contrasts
- An Educational Stroll With Stan – Part 1
- Histograms with Two or More Variables in R
- MD: Pediatric Scientist Development Program
R Packages:
- LearnSL: Learn Supervised Classification Methods Through Examples and Code
- clustlearn: Learn Clustering Techniques Through Examples and Code
Episode 35: Wi-Fi Reading and Microflying
Get ready for atmospheric water harvesting, entering the lipidome, Wi-Fi reading through walls, electric-producing bacteria, shape-shifting microflyer origami robots, the return of the Journal of Statistical Software, top picks for posit::conf 2023, the TidyTuesday GitHub repository, and a grant to establish a Center for Exposome Research Coordination. Science On.
References:
- Molecularly confined hydration in thermoresponsive hydrogels for efficient atmospheric water harvesting
- Dynamic lipidome alterations associated with human health, disease and ageing
- Analysis of Keller Cones for RF Imaging
- Video of RF Imaging
- An interfacial solar evaporation enabled autonomous double-layered vertical floating solar sea farm
- Extracellular electron transfer pathways to enhance the electroactivity of modified Escherichia coli
- Biofilm formation of Pseudomonas aeruginosa in spaceflight is minimized on lubricant impregnated surfaces
- Senolytic therapy in mild Alzheimer’s disease: a phase 1 feasibility trial
- Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
- Solar-powered shape-changing origami microfliers
- Video of Origami microfliers
- Journal of Statistical Software: Volume 107
- Multi-threading on JuliaHub
- The SG annotation macros in SAS
- Appsilon’s Top 10 Sessions to Check Out at posit::conf 2023
- Creating Population Pyramid Plots in R with ggplot2
- Plotting SVM Decision Boundaries with e1071 in R
- GitHub: TidyTuesday
- NIH: Center for Exposome Research Coordination to Accelerate Precision Environmental Health
- AAN: Clinical Research Training Scholarship in Parkinson's Disease
R Packages:
- DebiasInfer: Efficient Inference on High-Dimensional Linear Model with Missing Outcomes
- biosampleR: Biodiversity Index Calculation and Bootstrap Confidence Interval Estimation
- CohortAlgebra: Use of Interval Algebra to Create New Cohort(s) from Existing Cohorts
- moodlequizR: Easily Create Fully Randomized 'Moodle' Test Questions
- epiCleanr: A Tidy Solution for Epidemiological Data
Episode 34: Ribozyme Samurai
Get ready for distractingly dense planets, SAMURI ribozymes, serious clinical sepsis incidence, jittering in R, the Bioconductor 3.18 release schedule, and the NIH HEAL Initiative. Science On.
References:
- A super-massive Neptune-sized planet
- A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells
- The Rhabdodontidae (Dinosauria, Ornithischia), an enigmatic dinosaur group endemic to the Late Cretaceous European Archipelago
- Estimating Sepsis Incidence Using Administrative Data and Clinical Medical Record Review
- Model data from published summary statistics
- Grants For R Language Infrastructure Projects Available Now!
- When to use Jitter
- Insights on R Package Quality and Validation for Clinical Trials
- Bioconductor 3.18 Release Schedule
- NOSI: Quantum Sensing in Biomedical Applications
- NOSI: Research Supplements to Promote Re-Entry, Re-integration into, and Re-training in Health-Related Research Careers
- NIH: HEAL Initiative
- NSF: Postdoctoral Research Fellowships in Biology
R Packages:
- karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels
- phantSEM: Create Phantom Variables in Structural Equation Models for Sensitivity Analyses
- juicedown: 'juice' + 'markdown': Convert 'R Markdown' into 'HTML' with Inline Styles
- procs: Recreates Some 'SAS®' Procedures in 'R'
- webmap: Create Interactive Web Maps Using 'The National Map' Services
Episode 33: Microbe-Skewering Micro-Spikes
Get ready for allergic disease and the infant gut microbiome, three-eyed arthropods, titanium micro-spikes for killing pathogenic fungus, array thinking in R, and a grant to culture difficult eukaryotic pathogens. Science On.
References:
- Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease
- The early Cambrian Kylinxia zhangi and evolution of the arthropod head
- Apoptosis of Multi-Drug Resistant Candida Species on Microstructured Titanium Surfaces
- Exploring Relationships with Correlation Heatmaps in R
- Plotting Multiple Lines on a Graph in R: A Step-by-Step Guide
- 6 New books added to Big Book of R
- NIH: Research Tools for Difficult to Culture Eukaryotic Pathogens
- NIH: Early-stage Biomedical Data Repositories and Knowledgebases
- Gateway for Cancer Research: Integrative Program
R Packages:
- condensr: Academic Group Website Generator
- ruminate: A Pharmacometrics Data Transformation and Analysis Tool
- phylosem: Phylogenetic Structural Equation Model
Episode 32: The Kirigami Engineers
Get ready for naked-mole rat longevity transfer into mice, kirigami for engineering, a new antibiotic from microbial dark matter, eDNA for vertebrate biomonitoring, Julia cracking the top 20 programming languages, template files with R, and a Predoctoral to Postdoctoral Fellow Transition Award. Science On.
References:
- Increased hyaluronan by naked mole-rat Has2 improves healthspan in mice
- MIT engineers use kirigami to make ultrastrong, lightweight structures
- An antibiotic from an uncultured bacterium binds to an immutable target
- Vertebrate environmental DNA from leaf swabs
- JuliaHub Newsletter August 2023
- Bootstrap predicted means by using PROC GLMSELECT
- Creating template files with R
- Best Practices for Data Cleaning and Preprocessing
- NIH: Predoctoral to Postdoctoral Fellow Transition Award
- NIH: Research Projects to Enhance Applicability of Mammalian Models for Translational Research
- NSF: Ecology and Evolution of Infectious Diseases
R Packages:
- artpack: Creates Generative Art Data
- syllogi: Collection of Data Sets for Teaching Purposes
- rmass2: Repeated Measures with Attrition: Sample Sizes and Power Levels for 2 Groups
- scriptloc: Get the Location of the R Script that is Being Sourced/Executed
Episode 31: Are You Not Entertained?
Get ready the Dinosaur Coliseum, cancer-detecting bioengineer bacteria, embedding Unicode into SAS, a web-crawling Katana, and a Million Dollar Bike ride for rare disease research. Science On.
References:
- Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways
- Vertebrate ichnology and palaeoenvironmental associations of Alaska’s largest known dinosaur tracksite in the Cretaceous Cantwell Formation (Maastrichtian) of Denali National Park and Preserve
- Engineered bacteria detect tumor DNA
- Sustained wet–dry cycling on early Mars
- Add Unicode symbols and format text labels in SAS
- Plot confidence intervals for a regression model in SAS
- Bootstrap confidence intervals for the predicted mean in a regression model
- Mastering Data Visualization: A Guide to Harnessing the Power of R’s par() Function
- GitHub: katana
- NIH/NIA: R43/R44 REDI Award
- NIH/NIA: R41/R42 REDI Award
- NSF: Physics Investigator-Initiated Research Projects
- NSF: Smart Health and Biomedical Research in the Era of Artificial Intelligence and Advanced Data Science
- Air Force: Science and Technology Fellowship
- Marfan Foundation: Innovators Grants
- Million Dollar Bike Ride Pilot Grant Program
- AAI Intersect Fellowship Program
- AHA: AIREA
- McKnight: Scholar Award
R-packages:
- graposas: Graphical Approach Optimal Sample Size
- osmclass: Classify Open Street Map Features
- bulkreadr: The Ultimate Tool for Reading Data in Bulk
- handcodeR: Text Annotation App
- unicol: The Colors of your University
Episode 30: A Bit of a (DNA) Stretch
Get ready for bacterial circadian clocks, a new form of bacterial transduction, the effect of DNA stretches and twists on mutation rates, web development training materials, and a music-based intervention grant. Science On.
References:
- The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems
- Dual pathogenicity island transfer by piggybacking lateral transduction
- Structural underpinnings of mutation rate variations in the human genome
- Enhance Your Plots with the text() Function in R
- GitHub: Web-Dev-For-Beginners
- NIH: Music-based Interventions Toolkit for Brain Disorders of Aging
- NSF: Artic Research Opportunities
- AHA: Institutional Research Enhancement Award
R Packages:
- none
Episode 29: Greengenes 2, This Time, It’s Personal
Get ready for ancient, icy nematodes, renewable plastics, Greengenes volume 2, linear model transformations in R, and Gut-Brain Communication in Parkinson’s grants. Science On.
References:
- A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva
- Exploring the relationship between social jetlag with gut microbial composition, diet and cardiometabolic health, in the ZOE PREDICT 1 cohort
- Biorenewable and circular polydiketoenamine plastics
- Greengenes2 unifies microbial data in a single reference tree
- SatRdays London 2023 – Recordings
- One Weird Trick to Make Ggplot2 Columns the Same Width
- Linear model and Transformations
- GitHub: ClickHouse
- NIH: Secondary Analysis and Integration of Existing Data to Elucidate Cancer Risk and Related Outcomes (R01)
- NIH: Secondary Analysis and Integration of Existing Data to Elucidate Cancer Risk and Related Outcomes (R21)
- NIH: A Consortium for Gut-Brain Communication in Parkinson’s Disease (U01)
- NIH: A Consortium for Gut-Brain Communication in Parkinson’s Disease (U24)
- McKnight Foundation: Neurobiology of Brain Disorders Award
- ASCO: Young Investigator Award
R Packages:
- none
Episode 28: Fungal Enlightenment
Get ready for fungal genome mining, new R books, and a cancer nanotechnology grant. Science On.
References:
- Size Dependence of the Bouncing Barrier in Protoplanetary Dust Growth
- Near-Infrared Fluorescent Biosensors Based on Covalent DNA Anchors
- Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters
- what is a randomized complete block design?
- Simplify Your Code with R’s Powerful Functions: with() and within()
- 7 New books added to Big Book of R
- GitHub: Cal.com
- NOSI: Lymphatic System in Health and Disease
- NCI: Innovative Research in Cancer Nanotechnology
R Packages:
- MultiClassROC: ROC Curves for Multi-Class Analysis
- UpDown: Detecting Group Disturbances from Longitudinal Observations
Episode 27: Dog Bites Dinosaur
Get ready for DNA origami, an Elvis-impersonator pterodactyl, self-healing metal, a dinosaur-chomping mammal, the case of the missing dark matter, a lazier way to use Docker, and a grant for theoretical physics hubs. Science On.
References:
- DNA-origami-directed virus capsid polymorphism
- Petrodactyle wellnhoferi gen. et sp. nov.: A new and large ctenochasmatid pterosaur from the Late Jurassic of Germany
- Autonomous healing of fatigue cracks via cold welding
- An extraordinary fossil captures the struggle for existence during the Mesozoic
- The massive relic galaxy NGC 1277 is dark matter deficient
- Dates and location for useR! 2024
- JuliaHub Newsletter July 2023
- Standardize regression coefficients for models that include categorical variables
- GitHub: lazydocker
- GitHub: how-web-works
- NSF: Focused Research Hubs in Theoretical Physics
R Packages:
- badgen: Fast and Simple Badge Generator
- forestly: Interactive Forest Plot
- quickcode: A Compilation of Some Frequently Used R Functions
Episode 26: Living Cameras and Old Universes
Get ready for weird whales, bacterial sample collection via lollipop, hints at life on Mars, living digital cameras, a much older universe, free training on 67 programming languages, and a Housing and Urban Development grant for radon detection and mitigation. Science On.
References:
- Convergent evolution of skim feeding in baleen whales
- At-Home Saliva Sampling in Healthy Adults Using CandyCollect, a Lollipop-Inspired Device
- Microeukaryotic predators shape the wastewater microbiome
- The effects of board games on math skills in children attending prekindergarten and kindergarten: A systematic review
- Oncogene-like addiction to aneuploidy in human cancers
- A mid-Cambrian tunicate and the deep origin of the ascidiacean body plan
- Diverse organic-mineral associations in Jezero crater, Mars
- A biological camera that captures and stores images directly into DNA
- JWST early Universe observations and ΛCDM cosmology
- datasetR – R package for creating datasets
- Unveiling a New Era in Molecular Visualization: Introducing shiny.molstar for Large Molecular Structures Visualization in R
- Array Languages: R vs APL
- exercism
- HUD: Radon Testing and Mitigation Demonstration for Public Housing
- DOD: Toxic Exposures
R Packages:
- grpnet: Group Elastic Net Regularized GLM
- bbmix: Bayesian Model for Genotyping using RNA-Seq
- TOmicsVis: Transcriptome Visualization Process Scheme
Episode 25: Top Transposon, Maverick
Get ready for metallic 3D prints, Cambrian predators that skipped appendage-day at the gym, the mechanisms of chemical gardens, the mysteries of virus-like transposon ‘Mavericks’, coding cheat sheets, and a rare disease grant. Science On.
References:
- Remote detection of a lunar granitic batholith at Compton–Belkovich
- Metallic gels for conductive 3D and 4D printing
- Raptorial appendages of the Cambrian apex predator Anomalocaris canadensis are built for soft prey and speed
- Pattern selection by material aging: Modeling chemical gardens in two and three dimensions
- Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities
- An Easy Way to Customize Your Shiny App Theme
- CheatSheet for coding in R, Python and Julia
- GitHub: Tkinter-Designer
- NIH: Preclinical Proof of Concept Studies for Rare Diseases
- NIH: Cellular and Molecular Biology of Complex Brain Disorders (R01)
- NIH: Cellular and Molecular Biology of Complex Brain Disorders (R21)
- Jonathan F. Reichert Foundation: ALPhA Immersions Support
- AABB Foundation: Early-Career Scientific Research Grants Program
R Packages:
- esem: Exploratory Structural Equation Modeling ESEM
- protHMM: Protein Feature Extraction from Profile Hidden Markov Models
- ZooID: Load, Segment and Classify Zooplankton Images
Episode 24: My Chemical Sequence
Get ready for extinct avian genomes, stellar smashing, chemical needles in the haystack, the last Top 40 New CRAN Packages, and career awards at the scientific interface. Science On.
References:
- Genomes of the extinct Bachman’s warbler show high divergence and no evidence of admixture with other extant Vermivora warblers
- A long-duration gamma-ray burst of dynamical origin from the nucleus of an ancient galaxy
- BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences
- Therapeutic efficacy of 211At-radiolabeled 2,6-diisopropylphenyl azide in mouse models of human lung cancer
- A Dual-Gated Structures for Lossless Ion Manipulations-Ion Mobility Orbitrap Mass Spectrometry Platform for Combined Ultra-High-Resolution Molecular Analysis
- Newsletter June 2023 - Julia 2023 User & Developer Survey - Closing Soon!
- two types of effect size statistic: standardized and unstandardized
- May 2023: “Top 40” New CRAN Packages
- ggplotting power curves from simr package
- GitHub: Svelte
- NOSI: Advancing Biomedical Research in Pulmonary Non-Tuberculous Mycobacterial Infections
- NOSI: Using Targeted Degradation of Protein and non-Protein Targets for the Development of Novel Anti-Infectives
- North Carolina Biotechnology Center Translational Research Grant
- American Roentgen Ray Society Scholarship
- BWF Career Awards at the Scientific Interface
R Packages:
- New CRAN packages that deserve to bask in the light of a new day:
- flashlighttext: Flashlight Text R Interface
- GRCRegression: Modified Poisson Regression of Grouped and Right-Censored Counts
- otargen: Access Open Target Genetics
- tree3d: 3D Tree Models
Episode 23: Sir Ankylosaurus, I Presume?
Get ready for English ankylosaurs, video game mechanics for brain cell monitoring, microbial dark oxygen, pangolin robots, sampling in R, code editing for Macs, and a pangenome informatics grant. Science On.
References:
- Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons
- Vectipelta barretti, a new ankylosaurian dinosaur from the Lower Cretaceous Wessex Formation of the Isle of Wight, UK
- Super-resolved trajectory-derived nanoclustering analysis using spatiotemporal indexing
- Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems
- Pangolin-inspired untethered magnetic robot for on-demand biomedical heating applications
- R 4.3.1 is released
- Python 3.12.0 beta 3 released
- Summary of Julia Plotting Packages
- Use built-in ODS templates to display SAS tables
- Unleashing the Power of Sampling in R: Exploring the Versatile sample() Function
- GitHub: CodeEdit
- NHGRI: Informatics Tools for the Pangenome
- NHGRI: High Quality Reference Genomes
- NSF: Cellular and Biochemical Engineering
- NSF: Engineering of Biomedical Systems
R Packages:
- ppRep: Analysis of Replication Studies using Power Priors
- CIfinder: Estimate the Confidence Intervals for Predictive Values
- pivotea: Create Pivot Table Easily
Episode 22: Of Vikings and Tokamaks
Get ready for phosphates in an icy moon’s ocean, Neanderthals and Vikings disease, compact fusion reactors, the difficulties of effect size, Bayesian SEM, and Neuropsychiatric Symptoms grant funding. Science On.
References:
- Detection of phosphates originating from Enceladus’s ocean
- Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals
- Achievement of ion temperatures in excess of 100 million degrees Kelvin in the compact high-field spherical tokamak ST40
- the effect size: the most difficult step in calculating sample size estimates
- Mojo Programming Language: A Beginner’s Guide
- Top 37+ Exciting Website Project Ideas to Ignite Creativity
- Bayesian structural equation model tutorial
- GitHub: astro
- NIH: Novel Mechanism Research on Neuropsychiatric Symptoms (NPS) in Alzheimer's Dementia
- NOSI: Applications of Data Science in Translational Dental, Oral, and Craniofacial Research
R Packages:
- DDPM: Data Sets for Discrete Probability Models
- boxly: Interactive Box Plot
- ggaligner: Visualizing Sequence Alignment by Generating Publication-Ready Plots
- pcutils: Some Useful Functions for Statistics and Visualization
- STAREG: An Empirical Bayes Approach for Replicability Analysis Across Two Studies
- tdata: Prepare Your Time-Series Data for Further Analysis
- epiworldR: Fast Agent-Based Epi Models
- GGoutlieR: Identify Individuals with Unusual Geo-Genetic Patterns
Episode 21: Eukaryote Fell Down and Broke Its Crown
Get ready for air-quality environmental DNA, multiple British spinosaurids, a lost branch of the eukaryotic family tree, bioinks for space, GLM proselytizing, and Small Business Innovation Research grants. Science On.
References:
- Air-quality networks collect environmental DNA with the potential to measure biodiversity at continental scales
- Buckling Metamaterials for Extreme Vibration Damping
- Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes
- Isolated tooth reveals hidden spinosaurid dinosaur diversity in the British Wealden Supergroup (Lower Cretaceous)
- Lost world of complex life and the late rise of the eukaryotic crown
- Bioinks for Space Missions: The Influence of Long-Term Storage of Alginate-Methylcellulose-Based Bioinks on Printability as well as Cell Viability and Function
- Python 3.11.4, 3.10.12, 3.9.17, 3.8.17, 3.7.17, and 3.12.0 beta 2 are now available
- Visualize the Spearman rank correlation
- Update to Data Science Software Popularity
- Why GLMs should be a priority when teaching statistics
- How to improve your storytelling with R
- Simulating confounders, colliders and mediators by @ellis2013nz
- NIAID: New Innovators Awards
- USDA: 2023 SPSD Collaborative Soil Science Research
- NSF: Small Business Innovation Research/ Small Business Technology Transfer Program Phase I
R Packages:
- ami: Checks for Various Computing Environments
- rtms: R Toolkit for Mass Spectrometry
- gptzeror: Identify Text Written by Large Language Models using 'GPTZero'
Episode 20: Tintin and the Rare-Earth Elements
Get ready for rare-earth element binding proteins, single atom X-ray signals, Beagle Scouts on the march, the 2023 Python Language Summit, embedding code into SAS programs, ggplots with Tintin, and Gateway for Cancer Research funding opportunities. Science On.
References:
- Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer
- Characterization of just one atom using synchrotron X-rays
- Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor
- R 4.3.1 scheduled for June 16
- The Python Language Summit 2023
- Julia Newsletter May 2023
- Embedding any code anywhere into SAS programs
- Demystifying Regular Expressions: A Programmer’s Guide for Beginners
- Introducing standby
- April 2023: “Top 40” New CRAN Packages
- ‘ggplot2’ Palettes From Tintin Comic Books
- GitHub: grype
- CIDR: High Throughput Sequencing and Genotyping Resource Access
- AAS-EPD Mini-Grant Program
- Gateway for Cancer Research
R packages:
- intrinsicKappa: Sample Size Planning Based on Intrinsic Kappa Value
- WeibullR.plotly: Interactive Weibull Probability Plots with 'WeibullR'
- dmetatools: Computational Tools for Meta-Analysis of Diagnostic Accuracy Test
- HDMFA: High-Dimensional Matrix Factor Analysis
- siftr: Fuzzily Search a Dataframe to Find Relevant Columns
Episode 19: Small Things Considered
Get ready for non-natural amino acids, screwdriver-toothed mosasaurs, bubble-powered microbots, SAS Hackathon breakthroughs, Amazing Biochemistry Project Topics, and funding support from a little giraffe. Science On.
References:
- A platform for distributed production of synthetic nitrated proteins in live bacteria
- Stelladens mysteriosus: A Strange New Mosasaurid (Squamata) from the Maastrichtian (Late Cretaceous) of Morocco
- High-throughput printing of combinatorial materials from aerosols
- Bubble-Based Microrobots with Rapid Circular Motions for Epithelial Pinning and Drug Delivery
- Generic Air-Gen Effect in Nanoporous Materials for Sustainable Energy Harvesting from Air Humidity
- Macromolecular Engineering: From Precise Macromolecular Inks to 3D Printed Microstructures
- Python 3.12.0 beta 1 released
- How does PROC SGPLOT position labels for polygons?
- Unleashing brilliance: 3 innovative solutions to real-world problems at the SAS Hackathon
- the difference between clustered, longitudinal, and repeated measures data
- 35+ Amazing Biochemistry Project Topics To Boost Your Skills
- Why learning Python is hard (but important) for Data Scientists that use R
- R Consortium-Funded R Package “matter” Helps Solve Larger-Than-Memory Issues
- GitHub: rembg
- NSF: Geoinformatics
- DOD: Neurofibromatosis New Investigator Award
- 2023 Neonatal Research Initiative - Request for Proposals
- Hirshberg Foundation Seed Grant Program
- 2023 Kaggle AI Report
- HuBMAP - Hacking the Human Vasculature
R packages:
- BIDistances: Bioinformatic Distances
- cstidy: Helpful Functions for Cleaning Surveillance Data
- ggautomap: Create Maps from a Column of Place Names
- JUMP: Replicability Analysis of High-Throughput Experiments