Ciera C. Martinez, PhD

Berkeley Institute for Data Science

Data Science Research Lead

ciera.martinez@gmail.com

Google Scholar Profile


APPOINTMENTS


Research Lead of Biodiveristy and Enviromental Data Science
July 2020 - present
Berkeley Institute for Data Science (BIDS)
University of California, Berkeley, California

BIDS Postdoctoral Fellow
March 2018 - June 2020
Berkeley Institute for Data Science
University of California, Berkeley, California

NSF Postdoctoral Fellow
Fellow March 2016 - Feb 2018
Molecular and Cell Biology Department
University of California, Berkeley, California



EDUCATION


PhD, Plant Biology, March 2016
Emphasis in Molecular Biology and Genomics
University of California, Davis California

Bachelor of Science, Biology, May 2008
Chemistry Minor
Northeastern Illinois University, Chicago Illinois

PUBLICATIONS

Preprints

Gieger S, and ten other authors including Martinez C. Challenges of doing data-intensive research in teams, labs, and groups:Report from the BIDS best practices in data science series. SocArXIV.

Peer Reviewed

15. Stoudt S*, Valeri V*, Martinez C. Principles for data analysis workflows. 2021. PLOS Computational Biology.
Preprint: arXiv.

14. Martinez C, Li S, Woodhouse M, Sugimoto K, Sinha N.Spatial transcriptional signatures define margin morphogenesis along the proximal-distal and medio-lateral axes in complex leaf species Solanum lycopersicum (tomato). 2021. Plant Cell.
Preprint: BioRxiv

13. Bronski M, Martinez C, Weld H, Eisen M. N. Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses. 2020. G3: Genes, Genomes, Genetics.
Preprint: BioRxiv.

12. Elya C, Lok T, Spencer Q, McCausland H, Martinez C, Eisen M. A fungal pathogen that robustly manipulates the behavior of Drosophila melanogaster in the laboratory. 2018. eLIFE.
Preprint: BioRxiv

11. Bucksch A, 37 authors including Martinez C. Morphological plant modeling: Unleashing geometric and topologic potential within the plant sciences. 2017. Frontiers in Plant Science.
Download: PDF
Preprint: BioRxiv

10. Martinez C*, Chitwood D*, Smith R, Sinha N. Left-right leaf asymmetry in decussate and distichous phyllotactic systems. 2016. Proceedings of the Royal Society B.
Download: PDF
Preprint: BioRxiv

9. Martinez C, Koenig D, Chitwood D, Sinha N. A Sister of PIN1 gene in tomato (Solanum lycopersicum) defines organ initiation patterns by maintaining epidermal auxin flux. 2016.
Developmental Biology.
Download: PDF
Preprint: BioRxiv

8. Chitwood D, Kumar R, Ranjan A, Pelletier J, Townsley B, Ichihashi Y, Martinez C , Zumstein K, Harada J, Maloof J, and Sinha R. Light-induced indeterminacy alters shade avoiding tomato leaf morphology. 2015. Plant Physiology.
Preprint: BioRxiv

7. Chitwood D, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland L, Gallardo EO, Bush S, Carriedo L, Fulop D, Martinez C, Aguilar-Martínez J, Peng J, Maloof J, Sinha N. Resolving distinct genetic regulators of leaf shape within a heteroblastic and ontogenetic context. 2014. Plant Cell.

6. Chitwood D, Ranjan A, Martinez C, Headland L, Thiem T, R Kumar, Covington M, Hatcher T, Naylor D, Zimmerman S, Downs N, Raymundo N, Buckler E, Maloof J, Aradhya M, Prins B, Li L, Myles S, and Sinha N. A modern ampelography: a genetic basis for leaf shape and venation patterning in Vitis vinifera. 2013. Plant Physiology.

5. Martinez C and Sinha N. Genetic Control of Leaf Shape. 2013. Encyclopedia of Life Science (eLS)

4. Ahmad Naz A, Raman S, Martinez C, Neelima S, Schmitz G, Theres K. trifoliate encodes an R2R3 MYB transcription factor that modulates leaf and shoot architecture in tomato. 2013. PNAS.

3. Chitwood D, Headland L, Ranjan A, Martinez C, Braybrook S, Koenig D,Kuhlemeier C, Smith R, and Sinha N. Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. 2012. Plant Cell.

2. Preston J, Martinez C, Hileman L. Gradual disintegration of the floral symmetry gene network is implicated in the evolution of a wind-pollination syndrome. 2011. PNAS.

1. Du J, Miura E, Robischon M, Martinez C, Groover A, 2011 The Populus class III HD ZIP transcription Factor POPCORONA affects cell differentiation during secondary growth of woody stems. 2011. PLoS ONE.


RESEARCH EXPERIENCE

University of California, Berkeley, March 2016 - July 2020, Advisor: Michael Eisen
University of California, Davis, Jan 2010 - March 2016, Advisor: Neelima Sinha
RIKEN, Yokohama, Japan, Dec 2014 - April 2015, Advisor: Keiko Sugimoto
University of Kansas, Aug 2008 - Aug 2009, Advisors: Lena Hileman and Jill Preston
Chicago Field Museum of Natural History, Sept 2007 - Aug 2008, Advisor: Rick Ree
University of Colorado, Boulder, April - Aug 2007, Advisor: Pamela Diggle
Northeastern Illinois University,
Sept 2006 - May 2008, Advisor: Joel Olfelt


GRANTS, SCHOLARSHIPS, AND FELLOWSHIP AWARDS

2021 Code for Science and Society Grant
2020 Academic Data Science Alliance CDN Seed Grant
2020 The Coaching Fellowship
2018 Mozilla Open Science Fellowship
2017 BIDs Data Science Fellowship
2017 Burroughs Wellcome Postdoctoral Enrichment Grant
2017 Phenome 2017 Travel Scholarship (declined)
2016 Scholarship Summer Institute of Statistical Genetics
2016 NSF Postdoctoral Fellowship
2015 Katherine Esau Summer Graduate Fellowship
2014 NSF Graduate Research Oppurtunities Worldwide (GROW) Fellowship
2014 Walter R. and Roselinde H. Russell Fellowship
2014 ASPB Travel Grant
2013 Elsie Taylor Stocking Fellowship
2013 ASPB Travel Grant
2012 Excellence in Mentorship Award
2012 Elsie Taylor Stocking Fellowship
2012 ASPB Travel Grant
2011 GFRP NSF Predoctoral Fellowship
2009 UC Riverside Travel Grant
2008 PREP Fellow at Kansas University
2007 REU Fellowship at University of Colorado, Boulder


PRESENTATIONS


2021 Data Science Coast to Coast
Talk (invited): Open science in the wild: a guide to train researchers to build reproducible and collaborative workflows

2020 Open Science Symposium, Carnegie Mellon University, Pittsburgh, PA
Talk (invited): Alternative Research Products within the life cycle of data analysis workflows

2020 Academic Data Science Alliance Annual Conference
Talk (selected abstract): Principles for data-intensive research workflows: Guidance for the classroom and the computational laboratory

2020 University of Wyoming, INBRE 2020 Summer of Code
Talk (invited): Bird's Eye View of Reproducibility

2019 Alien CSI, Ljubljana, Slovenia
Talk (plenary): Defining the Usability of Biodiversity Databases - Lessons Learned from Tutorial Creation

2019 Yale, Digital Data Conference, New Haven, CT
Talk (selected abstract): Designing a Synergistic Relationship Between Undergraduate Data Science Education and Usability of Biodiversity Databases

2019 Ropensci Community Call, Online
Talk (invited): Research Applications of rOpenSci Taxonomy and Biodiversity Tools

2019 Lewis & Clark College, Portland OR
Talk (invited): Unleashing the Power of Biodiversity Data with Data Science

2019 OpenCon, Portland OR
Talk: Empowering Computer Scientists to Build Tools and Tutorials for Biodiveristy Data

2018 MSDSE Summit, Park City, Utah
Talk: Reproducibility and Management of Data Science Teams

2018 UC Berkeley Statistics and Genomics Seminar Series
Talk (invited): Data Science and the Evolution of Plant and Animal Morphology

2018 University of San Franscico Biology Seminar Series, San Fransisco CA
Talk (invited): What data science can tell us about organism shape and evolution

2017 University of Kansas EEB Seminar, Lawrence KS
Talk (invited): Evo-Devo in the data science age

2017 Berkeley Institute for Data Science, Berkeley, CA
Talk: How do organisms get their shape?

2017 Enterprise Applications of the R Language (EARL), San Franscisco, CA
Talk (Keynote): R-Ladies: a world-wide organization to promote gender diversity in the R community

2017 58th Annual Drosophila Research Conference, San Diego, CA
Poster: Using comparative genomic approaches to reveal underlying constraints on enhancer sequence divergence

2016 Berkeley Molecular and Cell Biology Colloquim, Asilomar, CA
Poster: Using comparative genomic approaches to reveal underlying constraints on enhancer sequence divergence

2016 Leonardo Art Science Evening Rendezvous
University of California, Davis
Talk (invited): The hidden beauty of plant architecture

2015 1. Nagoya University 2. RIKEN-Kobe 3. NAIST Institute – Nara
Three Talks: Using laser capture micro-dissection and characterization of a Solanum lycopersicum pin1 mutant to understand developmental and cellular differentiation patterns in plants.

2015 International Plant Meeting in Kyoto, Kyoto Sangyo University
Talk (invited): Investigating the molecular mechanisms regulating leaf initiation, morphogenesis, and cellular differentiation in Solanum lycopersicum.

2014 American Society of Plant Biology, Portland, OR
Poster: Global Gene Expression Map of a Complex Leaf

2014 Stanford Carnegie Institution for Science, Palo Alto, CA
Talk (invited): Getting started on making your computational work reproducible.

2013 FASEB Mechanisms in Plant Development, Saxtons River, VT
Talk (selected abstract): Understanding the phylogenetic history and function of members of the PIN-FORMED1 clade using Solanum lycopersicum (tomato)

2013 American Society of Plant Biology, Providence, RD
Poster: Understanding the phylogenetic history and function of members of the PIN-FORMED1 clade using Solanum lycopersicum (tomato)

2012 Plant Biology Graduate Group Fall Colloquium, Davis, CA
Talk: Developing a Global Expression Map of a Developing Leaf

2012 American Society of Plant Biology, Austin, TX
Poster: Exploring the Forgotten Axis of Leaf Development

2011 NAIST Global COE International Symposium, Nara, Japan
Talk: Exploring the Forgotten Axis of Leaf Development

2011 UC Davis Plant Cell Seminar Series, Asilomar, CA
Talk: Auxin’s Influence on the trifoliate Mutant Leaf Phenotype

2008 UC Riverside 25th Symposium in Plant Biology, CA
Poster: Duplication and Divergence of Veronicaceae Floral Symmetry Genes - Implications For The Reduction/Loss of Floral Zygomorphy and Stamen Number

2008 NEIU Research Symposium, Chicago, IL
Talk: Using Chloroplast Genome Regions Trn L-f, Trn T-l, Trn D- psbm2, And Trn D-t to Assess Phylogenetic Relationships of Corydalis

2007 REU Research Symposium, Boulder, CO, Podium
Talk: Fw2.2 Effect On Floral and Fruit Development in Tomato Plants

2007 NEIU Research Symposium, Chicago, IL
Poster: Effects of Gibberellic Acid, Light, and Cold Stratification on Echinacea pallida and Aquilegia canadensis Germination Rates


PROFESSIONAL DEVELOPMENT AND SERVICE



2021 - current Data Science by Design (DSxD) Co-founder, Organizing Committee
2019 - current ADSA CDN Executive Commitee
2017 - current BIDs Best Practices Working Group
2018 - current TextXD Annual Conference Organizing Committee
2019 - current ADSA CDN Executive Commitee
2017 - current BIDs Best Practices Working Group
2017 - 2018 Co-Organizer, RLadies San Franscisco
2016 Reviewer, PLOS One
2016 21st Summer Institute in Statistical Genetics, Seattle, WA
2016 rOpenSci Unconference, San Francisco, CA
2015 NIMBioS Investigative Workshop: Morphological Plant Models
2015 Reviewer, Annals of Botany
2014 Meeting Organizer, Reproducible Science Curriculum
2014 Reviewer, Annals of Botany
2014 Reviewer, New Phytologist
2014 rOpenSci Unconference, San Francisco, CA
2014 Technical Editor, Bioinformatics Data Skills by Vince Buffalo (O'Reilly)
2013 QB3 Python Course
2012 Plant Biology Graduate Group Selection Committee
2011 Reviewer, Molecular Biology and Evolution
2011 Plant Biology Graduate Group Selection Committee
2010 Plant Biology Graduate Collquium and Social Organizer

TEACHING


2020 INBRE 2020 Summer of Code, University of Wyoming
2018 Plant Development, Instructor, Mills College, CA
2017 Evolutionary Development Lab, Instructor, SF Institute of Art, CA
2017 Git and Github Tutorial, Instructor, Berkeley, CA
2016 SOM Clustering Tutorial, Instructor, Davis CA
2015 Reproducible Research Bootcamp, Instructor, Gainsville, FL
2014 BIS 180L Genomics, Teaching Assistant
2014 Introduction to R, Instructor, Woodland Pioneer High School
2014 Software Carpentry Course, Helper, Portland, OR
2014 Software Carpentry Course, Helper, Davis, CA
2013 Bioinformatics and R Tutorial, Instructor
2012 Bioinformatics and R Tutorial, Instructor
2011 PLB 112 Plant Growth and Development, Teaching Assistant
2011 Bioinformatics and R Tutorial, Instructor
2010 Career Development Seminar Series, Coordinator