Efficient selection of unique and popular oligos for large EST databases. - Jie Zheng 002; Timothy J. Close; Tao Jiang 001; Stefano Lonardi (Bioinform., 2004)

Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit. - Xinping Cui; Jin Xu; Rehana Asghar; Pascal Condamine; Jan T. Svensson; Steve Wanamaker; Nils Stein; Mikeal Roose; Timothy J. Close (Bioinform., 2005)

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. - Jie Zheng 002; Jan T. Svensson; Kavitha Madishetty; Timothy J. Close; Tao Jiang 001; Stefano Lonardi (BMC Bioinform., 2006)

Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. - Yonghui Wu; Prasanna Bhat; Timothy J. Close; Stefano Lonardi (WABI, 2007)

Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (WABI, 2008)

Deconvoluting BAC-Gene Relationships Using a Physical Map. - Yonghui Wu; Lan Liu 001; Timothy J. Close; Stefano Lonardi (J. Bioinform. Comput. Biol., 2008)

A compartmentalized approach to the assembly of physical maps. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (BMC Bioinform., 2009)

Barcoding-free BAC Pooling Enables Combinatorial Selective Sequencing of the Barley Gene Space - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (CoRR, 2011)

Accurate Construction of Consensus Genetic Maps via Integer Linear Programming. - Yonghui Wu; Timothy J. Close; Stefano Lonardi (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing. - Denisa Duma; Mary Wootters; Anna C. Gilbert; Hung Q. Ngo 001; Atri Rudra; Matthew Alpert; Timothy J. Close; Gianfranco Ciardo; Stefano Lonardi (WABI, 2013)

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. - Stefano Lonardi; Denisa Duma; Matthew Alpert; Francesca Cordero; Marco Beccuti; Prasanna R. Bhat; Yonghui Wu; Gianfranco Ciardo; Burair Alsaihati; Yaqin Ma; Steve Wanamaker; Josh Resnik; et al. (PLoS Comput. Biol., 2013)

A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map. - Serdar Bozdag; Timothy J. Close; Stefano Lonardi (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

De novo assembly of ultra-deep sequencing data. - Seyed Hamid Mirebrahim; Timothy J. Close; Stefano Lonardi (BCB, 2014)

CLARK, accurate and efficient classification of DNA sequences. - Rachid Ounit; Timothy J. Close; Steve Wanamaker; Stefano Lonardi (BCB, 2014)

Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. - Denise Duma; Francesca Cordero; Marco Beccuti; Gianfranco Ciardo; Timothy J. Close; Stefano Lonardi (WABI, 2015)

When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. - Stefano Lonardi; Seyed Hamid Mirebrahim; Steve Wanamaker; Matthew Alpert; Gianfranco Ciardo; Denisa Duma; Timothy J. Close (Bioinform., 2015)

De novo meta-assembly of ultra-deep sequencing data. - Seyed Hamid Mirebrahim; Timothy J. Close; Stefano Lonardi (Bioinform., 2015)