Naim Matasci

download pdf | slides

 

 

Manuscripts in preparation

 

Stoltzfus Arlin, Lapp Hilmar, Matasci Naim et al., “Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient,” In prep.

Michels Kurt, Banbury Barbara, Beaulieu Jeremy, Matasci Naim and O’Meara Brian, “Performance of Numerical Optimization Routines in R for Phylogenetic Applications,” In prep.

Matasci Naim, “Tempo and Mode of Primate Protein Expression Evolution,” In prep.

 

Peer-reviewed publications

2013

Matasci Naim and McKay Sheldon J., "Building Large Phylogenetic Trees with iPlant." Submitted.

Boyle Brad, Hopkins Nicole, Lu Zhenyuan, Raygoza Garay Juan Antonio, Mozzherin Dmitry, Rees Tony, Matasci Naim, Narro Martha L., Piel William H., Mckay Sheldon J., Lowry Sonya, Peet Robert K., Freeland Chris and Enquist Brian J., “The Taxonomic Name Resolution Service: an online tool for automated standardization of plant names,” BMC Bioinformatics (2013), 14:16, doi:10.1186/1471-2105-14-16.

2011

Goff Stephen A, Vaughn Matthew, McKay Sheldon, Lyons Eric, Stapleton Ann E, Gessler Damian, Matasci Naim, Wang Liya, Hanlon Matthew, Lenards Andrew, Muir Andy, Merchant Nirav, Lowry Sonya, Mock Stephen, Helmke Matthew, Kubach Adam, Narro Martha, Hopkins Nicole, Micklos David, Hilgert Uwe, Gonzales Michael, Jordan Chris, Skidmore Edwin, Dooley Rion, Cazes John, McLay Robert, Lu Zhenyuan, Pasternak Shiran, Koesterke Lars, Piel William H, Grene Ruth, Noutsos Christos, Gendler Karla, Feng Xin, Tang Chunlao, Lent Monica, Kim Seung-jin, Kvilekval Kristian, Manjunath B.S., Tannen Val, Stamatakis Alexandros, Sanderson Michael, Welch Stephen M, Cranston Karen, Soltis Pamela, Soltis Douglas, O'Meara Brian, Ane Cecile, Brutnell Tom, Kleibenstein Daniel J, White Jeffrey W, Leebens-Mack Jim, Donoghue Michael J, Spalding Edgar P, Vision Todd J, Myers Christopher R, Lowenthal David, Enquist Brian J, Boyle Brad, Akoglu Ali, Andrews Greg, Ram Sudha, Ware Doreen, Stein Lincoln, Stanzione Dan, "The iPlant Collaborative: Cyberinfrastructure for Plant Biology," Frontiers in Plant Science (2011), 2:34, doi: 10.3389/fpls.2011.00034.

Rogowitz Bernice E. and Matasci Naim,"Metadata mapper: A user interface web service for mapping data between independent visual analysis components, guided by perceptual rules," Proceedings of the SPIE Conference on Human Vision and Electronic Imaging (2011), doi: 10.1117/12.881734.

 

Posters & Presentations 

2012

Matasci Naim, Boyle Brad, Lu Zhenyuan, Hopkins Nicole, Piel William H., Raygoza Garay Juan Antonio, Gregory Steven, Lowry Sonya, Mckay Sheldon J., Narro Martha L., Skidmore Edwin, Enquist Brian J., “iPlant’s Taxonomic Name Resolution Service”, Oral presentation, Botany 2012, Columbus, OH

2011

Matasci Naim, Cranston Karen, Donoghue Michael J, Leebens-Mack Jim,  O'Meara Brian, Piel William H, Sanderson Michael, Soltis Douglas, Soltis Pamela, Stamatakis Alexandros, Tannen Val, Vision Todd J, McKay Sheldon, Goff Stephen A, “The iPlant Tree of Life Project and Toolkit: Building a Cyberinfrastructure for Plant Science Research”, Oral presentation, Evolution 2011, Norman, OK

Matasci Naim, Boyle Brad, Lu Zhenyuan, Hopkins Nicole, Piel William H., Raygoza Garay Juan Antonio, Narro Martha L., Lowry Sonya, Mckay Sheldon J., Enquist Brian J., “The TNRS, a Taxonomic Name Resolution Service for Plants”, Oral presentation, iEvoBio 2011, Norman, OK

Matasci Naim, Boyle Brad, Lu Zhenyuan, Hopkins Nicole, Piel William H., Raygoza Garay Juan Antonio, Narro Martha L., Lowry Sonya, Mckay Sheldon J., Enquist Brian J., “Correcting and Standardizing Taxonomic Names with the Taxonomic Name Resolution Service”, Oral presentation, TDWG 2011, New Orleans, LA

Matasci Naim, Cranston Karen, Donoghue Michael J, Leebens-Mack Jim,  O'Meara Brian, Piel William H, Sanderson Michael, Soltis Douglas, Soltis Pamela, Stamatakis Alexandros, Tannen Val, Vision Todd J, McKay Sheldon, Goff Stephen A, “The iPlant Collaborative: a Cyberinfrastructure to Support Next-generation Phylogeny-based Research”, Poster, Plant Genomes and Biotechnology 2011, Cold Spring Harbor, NY

Matasci Naim, Vaughn Matthew, Skidmore Edwin, Merchant Nirav, “Using R to Empower a New Plant Biology”, Poster, UseR! 2011, Warwick, UK

2004-2007

Matasci Naim, “Primate Protein Expression Evolution”, Oral presentation, SMBE 2007, Halifax, Canada.

Matasci Naim, Paavilainen Linda, Wester Kenneth, Pontén Fredrik, Uhlén Mathias, Pääbo Svante, “Evolution of Protein Expression and Localization”, Poster, SMP Proteomics Symposium 2007, Rauischholzhausen, Germany.

Lee Yong Seok, Matasci Naim, Serre David, Wiebe Viktor, Vigilant Linda and Pääbo Svante. “Investigation of some genes putatively under positive selection in humans”. Poster. 16th Annual Meeting, Korean Society for Molecular and Cellular Biology 2004, Seoul, Korea.

 

Invited talks

2011

“The iPlant Collaborative: A Cyberinfrastructure for the Life Sciences”, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ

“What Can iPlant Do for You?”, Department of Plant Sciences, University of Arizona, Tucson, AZ

“The iPlant Tree of Life Project and Toolkit: Building a Cyberinfrastructure for Plant Science Research”, National Museum of Natural History, Washington, DC

“The iPlant Tool Integration Process”, Generation Challenge Program, San Diego, CA

2007

“Protein Evolution and Localization”, University of Maryland, College Park, MD.

 

Workshops

2013

“Phylotastic II”, University of Arizona, Tucson, AZ**

“Tucson Winter Plant Breeding Institute”, University of Arizona, Tucson, AZ*

2012

“Phylotastic Hackathon”, NESCent, Durham, NC

“iPlant Tools and Services”, UC Davis, Davis, CA*

“iPlant Tools and Services”, UC Riverside, Riverside, CA*

“iPlant Tools and Services”, Purdue University, West Lafayette, IN*

“iPlant Tools and Services”, North Carolina State University, Raleigh, NC*

“iPlant Tools and Services”, Botany 2012, Columbus, OH*

“QIIME”, University of Arizona, Tucson, AZ**

“iPlant Tools and Services”, iDigBio's Specimen Digitization Tools and Practices, Columbus OH

2011

“Phylogenetics Workflows Part II: Post-tree Analyses”, Botany 2011, Saint Louis, MO*

“Post Tree Analyses”, NESCent, Durham, NC*

“iPlant Tree of Life”, Plant and Animal Genome 2011, San Diego, CA*

“Phylogenetic Workflows: Tree Building and Post-tree Analyses”, Plant Biology 2011, Minneapolis, MI*

 

*Instructor; **Organizer