Principles for data analysis workflows.

Autor: Sara Stoudt, Váleri N Vásquez, Ciera C Martinez

Publikováno v: PLoS Computational Biology, Vol 17, Iss 3, p e1008770 (2021)

A systematic and reproducible "workflow"-the process that moves a scientific investigation from raw data to coherent research question to insightful contribution-should be a fundamental part of academic data-intensive research practice. In this paper

Externí odkaz: https://doaj.org/article/69081b5ececd439e961766c0c1ab272b

Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences

Autor: Alexander Bucksch, Acheampong Atta-Boateng, Akomian F. Azihou, Dorjsuren Battogtokh, Aly Baumgartner, Brad M. Binder, Siobhan A. Braybrook, Cynthia Chang, Viktoirya Coneva, Thomas J. DeWitt, Alexander G. Fletcher, Malia A. Gehan, Diego Hernan Diaz-Martinez, Lilan Hong, Anjali S. Iyer-Pascuzzi, Laura L. Klein, Samuel Leiboff, Mao Li, Jonathan P. Lynch, Alexis Maizel, Julin N. Maloof, R. J. Cody Markelz, Ciera C. Martinez, Laura A. Miller, Washington Mio, Wojtek Palubicki, Hendrik Poorter, Christophe Pradal, Charles A. Price, Eetu Puttonen, John B. Reese, Rubén Rellán-Álvarez, Edgar P. Spalding, Erin E. Sparks, Christopher N. Topp, Joseph H. Williams, Daniel H. Chitwood

Publikováno v: Frontiers in Plant Science, Vol 8 (2017)

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture w

Externí odkaz: https://doaj.org/article/05ce7f2399df4145ab37ceaddd014118

Ten simple rules on writing clean and reliable open-source scientific software

Autor: Ciera C. Martinez, Alexandre Fioravante de Siqueira, Richard Barnes, Haley Hunter-Zinck, Váleri N. Vásquez

Publikováno v: PLoS computational biology, vol 17, iss 11
PLoS Computational Biology, Vol 17, Iss 11 (2021)
PLoS Computational Biology
PLoS Computational Biology, Vol 17, Iss 11, p e1009481 (2021)

Functional, usable, and maintainable open-source software is increasingly essential to scientific research, but there is a large variation in formal training for software development and maintainability. Here, we propose 10 “rules” centered on 2

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::78d53ae4e60f16c4590a25064a56209e
https://escholarship.org/uc/item/05s3f6dz

Spatial transcriptional signatures define margin morphogenesis along the proximal-distal and medio-lateral axes in tomato (Solanum lycopersicum) leaves

Autor: Ciera C. Martinez, Keiko Sugimoto, Margaret R. Woodhouse, Siyu Li, Neelima Sinha

Publikováno v: The Plant cell. 33(1)

Leaf morphogenesis involves cell division, expansion, and differentiation in the developing leaf, which take place at different rates and at different positions along the medio-lateral and proximal–distal leaf axes. The gene expression changes that

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f28d3474aa225dc6f5cd6c908e957639
https://pubmed.ncbi.nlm.nih.gov/35234944

A sister of PIN1 gene in tomato (Solanum lycopersicum) defines leaf and flower organ initiation patterns by maintaining epidermal auxin flux

Autor: Neelima Sinha, Daniel Koenig, Ciera C. Martinez, Daniel H. Chitwood

Publikováno v: Developmental Biology. 419:85-98

The spatiotemporal localization of the plant hormone auxin acts as a positional cue during early leaf and flower organogenesis. One of the main contributors to auxin localization is the auxin efflux carrier PIN-FORMED1 (PIN1). Phylogenetic analysis h

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c9bf0d87fc0c31b72e93785f26ccd35c
https://doi.org/10.1016/j.ydbio.2016.08.011