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About Breedbase

The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see RTBbase.org).
Breedbase is striving to be a complete breeding management system, including field management, data collection, crossing utilities, and advanced trial analysis.
Please refer to the Breedbase manual for detailed information about available features.


Lab members 
Staff 
Lukas Mueller Lukas Mueller Director
Naama Menda Naama Menda Postdoc Isaak Y Tecle Isaak Y Tecle Bioinformatics Consultant Tom York Tom York Postdoc
Susan Strickler Susan Strickler Postdoc Noe Fernandez-Pozo Noe Fernandez-Pozo Postdoc Hartmut Foerster Hartmut Foerster MetaCyc curator
Surya Saha Surya Saha Postdoc Guillaume Bauchet Guillaume Bauchet Postdoc Bryan Ellerbrock Bryan Ellerbrock Bioinformatics
Nicolas Morales Nicolas Morales Programmer Alex Agbonna Alex Agbonna Bioinformatics Prashant Hosmani Prashant Hosmani Postdoc
Mirella Flores Mirella Flores Postdoc
Interns 
View more staff & intern photos
Emeritus Staff 
Bioinformatics Analysts
  • Aimin Yan
  • Jeremy Edwards
  • Aureliano Bombarely
  • Anuradha Pujar
  • Robert Buels
  • Joseph Gosselin
  • Jonathan Leto
  • Adri Mills
  • Beth Skwarecki
  • Dean Eckstrom
  • Chris Carpita
  • Marty Kreuter
  • Chenwei Lin
  • John Binns
  • Teri Solow
  • Nicholas Taylor
  • Dan Ilut
  • Robert Ahrens
  • Mark Wright
 Interns
  • Allison Izsak (2015)
  • Jonathan Gomes Selman (2015)
  • Ivana Rodriguez (2015)
  • Angela Zhang (2014)
  • Javon Mullings (2014)
  • Matthew Crum (2013)
  • Amelia Lovelace (2013)
  • Akhil Saji (2013)
  • Kevin Nguyen (2013)
  • Andrew Dunford (2012)
  • Paul Van Eck (2012)
  • Kristin Blacklock (2012)
  • Jessica Jeffrey (2011)
  • Dil Begum (2011)
  • Samuel Moijueh (2011)
  • Benjamin Gordon (2011)
  • Jean Lee (2010)
  • Dean Bobo (2010)
  • Carolyn Ochoa (2010)
  • Mallory Freeberg
  • Carolyn Ochoa
  • Johnathon Schulz
  • Tim Jacobs
  • Sasha Naydich
  • Jessica Reuter
  • Matthew Crumb
  • Bob Albright
  • Emily Hart
  • Scott Bland
  • Amarachukwu Enemuo
  
  • Benjamin Cole
  • Caroline Nyenke
  • Tyler Simmons
  • Evan Herbst
  • Emil Keyder
  • Aseem Kohli
  • Igor Dolgalev
  • Miriam Wallace
  • Jay Gadgil
  • Jennifer Lee
Selected Publications 
  • Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA. The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. (2015) Nucleic Acids Res. Volume 43 (Database issue):D1036-41.
  • Fernandez-Pozo N, Rosli H.G., Martin G.B., Mueller L.A. The SGN VIGS Tool: User-Friendly Software to Design Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics (2015) Molecular Plant, Volume 8, Issue 3, 486-488
  • The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution (2012) Nature 485, 635-641.
  • Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucl. Acids Res. Oct 08, 2010. doi: 10.1093/nar/gkq866.
  • Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA (2010). solQTL: A Tool for QTL analysis, Visualization and Linking to Genomes at SGN Database. BMC Bioinformatics 2010, 11:525.
  • Mueller LA, et al., (2009). A snapshot of the emerging tomato genome sequence. Plant Gen. March 2009 2:78-92; doi:10.3835/plantgenome2008.08.0005.
  • Menda N, Buels RM, Tecle I, Mueller LA (2008). A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol. 2008 Aug;147(4):1788-99 (PMID: 18539779).
  • Mueller LA, Mills AA, Skwarecki B, Buels RM, Menda N, Tanksley SD (2008). The SGN comparative map viewer. Bioinformatics. 2008 Feb 1;24(3):422-3.
  • Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD (2005). The Sol Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond. Plant Physiol 138(3):1310-7.
  • Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006). Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006 Nov;174(3):1407-20.
  • Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD (2005). Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet. 2005 Dec;112(1):114-30.
Funding 
SGN gratefully acknowledges funding from the following funding sources:

National Science Foundation (USA)
  • #0820612 Tomato Chromosome 1 and 10 Sequencing, Coordination and Bioinformatics for the International Solanaceae Genome Initiative
  • #9872617 - Development of Tools for Tomato Functional Genomics
  • #9975866 - Tools for Potato Structural and Functional Genomics
  • #0116076 - Exploitation of Tomato as a Model for Comparative and Functional Genomics
  • #0421634 - Sequence and Annotation of the Euchromatin of Tomato.
  • #0606595 - Characterization of the Tomato Secretome Using Integrated Functional and Computational Strategies


USDA
  • USDA CSREES, grant #2007-02777
  • SolCAP - Solanaceae Coordinated Agricultural Project
 Nestle Corporation
  • SGN gratefully acknowledges a grant from the Nestle Corporation for generation, analysis and integration of Coffea canephora data.




 BARD
  • BARD, grant #FI-370-2005 Bioinformatic links of simple and complex phenotypes with Solanaceae genomes.

Acknowledgments 

Special thanks to the Cornell Biological Services Unit for making their compute clusters available for some of our analyses.

Some data on SGN was obtained from EU-SOL projects. Special thanks to our colleagues at EU-SOL.