MB Kosnik, A Planchart, SW Marvel, DM Reif, CJ Mattingly (2019) Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. Computational Toxicology, 100094
Blog posts : "skylar marvel"
Joint retreat in Oregon with Tanguay + Reif labs
The Tanguay + Reif labs met in Oregon for their second joint retreat.
The retreat started with scientific sessions and lab tours at Oregon State University and the Sinnhuber Aquatic Research Lab (SARL) in Corvallis. We then moved to the Oregon Coast for more scientific sessions, hiking, and int…
ToxPi software updated (v2.2) @ www.toxpi.org
The complete .zip is available for free download at: www.toxpi.org
This update adds flexibility for setting weights, offers improved "zoom" capabilities, updates information included in the saved Results Table object, and fixes issues identified by users.
The updated manual includes a full …
Updated ToxPi version (v 2.1) available at www.toxpi.org
A major update to the ToxPi interface (version 2.1) is now available at:
This update includes major speed improvements (especially noticeable when clustering large datasets), the ability to zoom/pan on cluster dendrograms, as well as other refinements for GUI users.
ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models (2018) BMC Bioinformatics
Marvel SW, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics. 2018 Mar 5;19(1):80. doi: 10.1186/s12859-018-2089-2. PubMed PMID: 29506467.
Flash Report: SEAZIT Ontologies Workshop
A report on the SEAZIT (Systematic Evaluation of the Application of Zebrafish in Toxicology) Ontologies Workshop has been published:
https://ntp.niehs.nih.gov/iccvam/methods/dev-repro/ontologies-wksp-rept-2017.pdf
Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo [a] pyrene in zebrafish (2017) Toxicology and Applied Pharmacology
Knecht AL, Truong L, Marvel SW, Reif DM, Garcia A, Lu C, Simonich MT, Teeguarden JG, Tanguay RL. Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish. Toxicol Appl Pharmacol. 2017 Jun 3;329:148-157. doi: 10.1016/…
Aggregate entropy scoring for quantifying activity across endpoints with irregular correlation structure (2016) Reproductive Toxicology
Zhang G, Marvel S, Truong L, Tanguay RL, Reif DM. Aggregate entropy scoring
for quantifying activity across endpoints with irregular correlation structure.
Reprod Toxicol. 2016 Apr 27;62:92-99. doi: 10.1016/j.reprotox.2016.04.012. [Epub
ahead of print] PubMed PMID: 27132190.
Selected as cov…
Bioinformaticists at the bench
The Reif Lab packed up their laptops and journeyed to Robert Tanguay's lab for a scientific retreat at Oregon State University.
The retreat was packed with scientific presentations, discussion, and socializing. A highlight was seeing the amazing, custom-engineered setup of the laboratory. Li…
12 blog posts