51 Works

Data from: High fidelity detection of crop biomass QTL from low-cost imaging in the field

Darshi Banan, Rachel E. Paul, Max J. Feldman, Mark W. Holmes, Hannah Schlake, Ivan Baxter, Hui Jiang & Andrew D.B. Leakey
Field-based, rapid, and non-destructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype-to-phenotype relationships in next-generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field-grown grass crop. Plant area index (PAI) estimated from below-canopy hemispherical images, as well as a suite of thirteen traits assessed by manual...

Data from: Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

Jessica R. Brandt, Peter J. Van Coeverden De Groot, Kelsey E. Witt, Paige K. Engelbrektsson, Kristofer M. Hegen, Ripan S. Malhi, Oliver A. Ryder, Alfred L. Roca & Kristofer M Helgen
The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D....

Data from: Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

Kranthi Varala, Amy Marshall-Colón, Jacopo Cirrone, Matthew D. Brooks, Angelo V. Pasquino, Sophie Léran, Shipra Mittal, Tara M. Rock, Molly B. Edwards, Grace J. Kim, Sandrine Ruffel, W. Richard McCombie, Dennis Shasha & Gloria M. Coruzzi
This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our “just-in-time” analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated...

Isolated artificial spin ice kinetics

Yuyang Lao & Peter Schiffer
This is the experimental data of isolated nanomagnet islands with or without the presence of large nanomagnet islands. The small islands are made of Permalloy materials with size of 170 nm by 470 nm by 2.5 nm. The systems are measured at a temperature where the small islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the data can be found in the note.txt and Spe_2016.xlsx...

Data from: Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles

Rachel L. Moran, Muchu Zhou, Julian M. Catchen & Rebecca C. Fuller
Behavioral isolation is thought to arise early in speciation due to differential sexual and/or natural selection favoring different preferences and traits in different lineages. Alternatively, behavioral isolation can arise due to reinforcement favoring traits and preferences that prevent maladaptive hybridization. In darters, female preference for male coloration has been hypothesized to drive speciation, because behavioral isolation evolves before F1 inviability. However, as with many long-lived organisms, the fitness of second generation hybrids has not been...

Data from: How large spatially-explicit optimal reserve design models can we solve now? an exploration of current models’ computational efficiency

Yicheng Wang, Hayri Önal & Qiaoling Fang
Spatially-explicit optimal reserve design models select best sites from a set of candidate sites to assemble nature reserves to protect species (or habitats) and these reserves display certain spatial attributes which are desirable for species. These models are formulated with linear 0-1 programming and solved using standard optimization software, but they were run on different platforms, resulting in discrepant or even conflicting messages with regard to their computational efficiency. A fair and accurate comparison of...

Data from: The role of parasite dispersal in shaping a host-parasite system at multiple evolutionary scales

Andrew Sweet & Kevin Johnson
Parasite dispersal can shape host-parasite interactions at both deep and shallow timescales. One approach to understanding the effects of dispersal is to study parasite lineages that differ in dispersal capability but are from the same group of hosts. We compared phylogenetic and population genetic patterns of wing and body lice from ground-doves. Wing lice are more capable of dispersal than body lice. We sequenced full genomes of individual lice for multiple representatives of several wing...

MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide

Vetle I. Torvik
MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide. Prepared by Vetle Torvik 2018-04-05 The dataset comes as a single tab-delimited Latin-1 encoded file (only the City column uses non-ASCII characters), and should be about 3.5GB uncompressed. • How was the dataset created? The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in the first week of October, 2016. Check here for information...

Data from: The origin of the odorant receptor gene family in insects

Philipp Brand, Hugh M. Robertson, Wei Lin, Ratnasri Pothula, William E. Klingeman, Juan Luis Jurat-Fuentes & Brian R. Johnson
The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with the evolution of terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved with an ancestral OR co-receptor (Orco) after the origin of terrestriality and the OR/Orco system is an adaptation to winged flight in insects. We investigated genomes of the Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, and Ephemeroptera, and find ORs present in all insect genomes...

Data from: Verbalizing phylogenomic conflict: representation of node congruence across competing reconstructions of the neoavian explosion

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Yu Shizhuo & Bertram Ludäscher
Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference–such as newly supported clade concepts–have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences....

Data from: The influence of cactus spine surface structure on puncture performance and anchoring ability is tuned for ecology

Stephanie B. Crofts, Philip S.L. Anderson & P. S. L. Anderson
Spines are common morphological features found in almost all major biological groups offering an opportunity to explore large-scale evolutionary convergence across disparate clades. As an example, opuntioid cacti have spines with barbed ornamentation that is remarkably similar in form and scale to that found on porcupine quills, suggesting specific biomechanical convergence across the animal and plant kingdoms. While the mechanics of porcupine quills as defensive mechanisms has been previously tested, the mechanics of cacti spines...

Data for \"Ammonia Flux Measurements above a Corn Canopy using Relaxed Eddy Accumulation and a Flux Gradient System\"

Andrew J Nelson, Nebila Lichiheb, Sotiria Koloutsou-Vakakis, Mark J. Rood, Mark Heuer, LaToya Myles, Eva Joo, Jesse Miller & Carl Bernacchi
Ammonia flux measurement data using flux gradient and relaxed eddy accumulation methods, and ancillary environmental data collected during the 2014 corn-growing season in Central Illinois, USA. This excel file contains two spreadsheets: one README sheet, and one sheet containing all data. These data were used in the development of the manuscript titled "Ammonia Flux Measurements above a Corn Canopy using Relaxed Eddy Accumulation and a Flux Gradient System."

Castilleja coccinea fruit set and seed set data from Illinois Beach State Park

Eun Sun Kim, David N. Zaya, Jeremie B. Fant & Mary V. Ashley
These data include information on a field experiment on Castilleja coccinea (L.) Spreng., scarlet Indian paintbrush (Orobanchaceae). There is intraspecific variation in scarlet Indian paintbrush in the color of the bracts surrounding the flowers. Two bract color morphs were included in this study, the scarlet and yellow morphs. The experiment was conducted at Illinois Beach State Park in 2012. The aim of the work was to compare the color morphs with regard to 1) self-compatibility,...

Data from: Simultaneous radiation of bird and mammal lice following the K-Pg boundary

Kevin P. Johnson, Nam-Phuong Nguyen, Andrew D. Sweet, Bret M. Boyd, Tandy Warnow & Julie M. Allen
The diversification of parasite groups often occurs at the same time as the diversification of their hosts. However, most studies demonstrating this concordance only examine single host-parasite groups. Multiple diverse lineages of ectoparasitic lice occur across both birds and mammals. Here we describe the evolutionary history of lice based on analyses of 1,107 single copy orthologous genes from sequenced genomes of 46 species of lice. We identify three major diverse groups of lice: one exclusively...

Gulf survival capture history

Michael Ward
Data used to estimate the survival of Swainson's Thrushes crossing the Gulf of Mexico.

Data from: The effects of experimental design on mating preferences and reproductive isolation in killifish

Michelle E. St. John & Rebecca C. Fuller
Determining the direction and magnitude of mating preference is fundamental to many questions in evolutionary biology. Unlike the measurement of traits such as body size, the measurement of mating preferences is likely affected by experimental design. Scientists must choose both the behavioral assay in which to measure preference and the metrics that serve as a proxy for preference. The accuracy of these assays and metrics, however, is often unknown and seldom tested. Here, we compared...

Soil organic carbon (SOC) response to soil management practices in the continental United States

Carmen M. Ugarte & Michelle M. Wander
This dataset was compiled between 2010 and 2011 from data published in the scientific literature from articles evaluating the influence of cropping systems and soil management practices on soil organic Carbon. We used the Thomas Reuter Web of Science database and by reviewed the reference sections of key peer-reviewed articles. Articles included in the database presented results from field sites within the continental United States.

Data from: Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

Therese A. Catanach, Andrew D. Sweet, Nam-Phuong D. Nguyen, Rhiannon M. Peery, Andrew H. Debevec, Andrea K. Thomer, Amanda C. Owings, Bret M. Boyd, Aron D. Katz, Felipe N. Soto-Adames & Julie M. Allen
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However,...

Data from: Classical Topological Order in the Kinetics of Artificial Spin Ice

Yuyang Lao, Francesco Caravelli, Mohammed Sheikh, Joseph Sklenar, Daniel Gardeazabal, Justin D. Watts, Alan M. Albrecht, Andreas Scholl, Karin Dahmen, Cristiano Nisoli & Peter Schiffer
The dataset includes the data used in the study of Classical Topological Order in the Kinetics of Artificial Spin Ice. This includes the photoemission electron microscopy intensity measurement of artificial spin ice at different temperatures as a function of time. The data includes the raw data, the metadata, and the data cookbook. Please refer to the data cookbook for more information. Note: vertex_population.xlsx file in the meta_data_code folder can be disregarded.

Data from: Agonistic character displacement of genetically based male colour patterns across darters

Rachel L. Moran & Rebecca C. Fuller
Agonistic character displacement (ACD) occurs when selection to avoid maladaptive interspecific aggression leads to the evolution of agonistic signals and/or associated behavioural biases in sympatry. Here we test for a pattern consistent with ACD in male colour pattern in darters (Percidae: Etheostoma). Male colour pattern has been shown to function in male-male competition rather than female mating preferences in several darter species. Additionally, males bias their aggression towards conspecific over heterospecific males in sympatry but...

Dataset: Ultra-sensitivity of Numerical Landscape Evolution Models to their Initial Conditions

Jeffrey Kwang & Gary Parker
This dataset contains experimental measurements used in the paper, "Ultra-sensitivity of Numerical Landscape Evolution Models to their Initial Conditions." (to be submitted). The data is taken from experimental runs in a miniature landscape model named the eXperimental Landscape Evolution (XLE) facility. In this facility, we complete five >24hr runs at 5 minute temporal resolution. Every five minutes, an planform image was capture, and a digital elevation model (DEM) was generated. For each run, images and...

CyberGIS-Jupyter HAND Example Notebook

Dandong Yin & Shaowen Wang
The dataset contains a complete example (inputs, outputs, codes, intermediate results, visualization webpage) of executing Height Above Nearest Drainage HAND workflow with CyberGIS-Jupyter.

Author-Linked data for Author-ity 2009

Vetle I. Torvik
Provides links to Author-ity 2009, including records from principal investigators (on NIH and NSF grants), inventors on USPTO patents, and students/advisors on ProQuest dissertations. Note that NIH and NSF differ in the type of fields they record and standards used (e.g., institution names). Typically an NSF grant spanning multiple years is associated with one record, while an NIH grant occurs in multiple records, for each fiscal year, sub-projects/supplements, possibly with different principal investigators. The prior...

Author-ity 2009 - PubMed author name disambiguated dataset

Vetle I. Torvik & Neil R. Smalheiser
Author-ity 2009 baseline dataset. Prepared by Vetle Torvik 2009-12-03 The dataset comes in the form of 18 compressed (.gz) linux text files named authority2009.part00.gz - authority2009.part17.gz. The total size should be ~17.4GB uncompressed. • How was the dataset created? The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in July 2009. A total of 19,011,985 Article records and 61,658,514 author name instances. Each instance of an author name...

Data from: Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets

Michael Nute, Ehsan Saleh & Tandy Warnow
The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Illinois at Urbana Champaign
  • University of Illinois
  • University of Michigan-Ann Arbor
  • Indiana University Bloomington
  • University of Sheffield
  • Rice University
  • University of Notre Dame
  • University of Georgia
  • Johns Hopkins University
  • State University of New York