NSF ABI Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing
The University of California, Riverside is awarded a grant to develop a new sequencing protocol for hierarchical (i.e., BAC-by-BAC) genome sequencing of large eukaryotic genomes. At the core of the protocol is the ability to solve a set of hard computational questions, which are the focus of the research plan. The computational challenges require the study of novel combinatorial optimization problems, the development of new time- and space-efficient algorithms, and ultimately the implementation and deployment of user-friendly web-based software tools.
The new combinatorial sequencing protocol is going to be trained first on simulated data and then applied to the cowpea genome. Cowpea Vigna unguiculata, also known as China bean or black-eyed pea, is one of the most important food legume crops in the semi-arid tropics covering Asia, Africa, and Central and South America. A drought-tolerant and warm-weather crop, cowpeas are well-adapted to the drier regions of the tropics, where other food legumes do not perform well. Its modest genome size makes it an excellent candidate to demonstrate the utility of our protocol. We expect the final assembly to provide a sufficient depth of knowledge to support most downstream applications including map-based cloning of trait determinants, development of markers for marker-assisted breeding, microarray development for gene expression studies and analysis of synteny with related species.
- May 2015: paper  accepted and published in Bioinformatics
- May 2015: paper  submitted to WABI 2015
- Apr 2015: paper  accepted and published in BMC Genomics
- Mar 2015: paper  accepted for ISMB/ECCB 2015 in Dublin, Ireland
- Jan 2015: paper  submitted to Bioinformatics (currently on bioRxiv)
- Dec 2014: paper  submitted to BMC Genomics
- 2014: Working on four manuscripts related to this project: an ultra-accurate error-correction method , a divide-and-conquer method to improve decoding and assembly , and a sequence classified to assign BACs to chromosome arms , a new meta-assembler for ultra-deep sequencing data 
- Sep 2013: Denise Duma presented our improved decoding method  based on compressed-sensing at WABI'13 in France
- Aug 2013: Tim Close and I delivered a webinar on our method  via eXtension
- July 2013: Denise Duma presented our work  at ISMB'13 in Berlin, Germany (Highlight Track)
- Apr 2013: Paper  describing the method is available from PLoS Computational Biology
- Mar 2013: Submitted Year 2 progress report (see below)
- Jan 2013: The description of the combinatorial method will be published soon
- Dec 2012: The code of HashFilter is available
- Oct 2012: Our combinatorial sequencing method is used in the barley genome paper  which appears in the journal Nature, the entire team is listed in the authors' list
- Jun 2012: PI Lonardi presents results of this project at UC Irvine
- Apr 2012: PI Lonardi presents results of this project at UC Riverside
- Feb 2012: PI Lonardi invited to present results of this project at the IMA Annual Program Year Workshop: Group Testing Designs, Algorithms, and Applications to Biology (Video of the presentation)
- Jan 2012: Submitted Year 1 progress report (see below)
- Dec 2011: Manuscript draft on the method on barley at ArXiv
- May 1, 2011: Official start of the project
- April 26, 2011: Award is official (see NSF)
- June-September, 2011: Marco and Francesca visiting our lab, worked on the deconvolution algorithm
- January 30, 2012: We have reported to NSF Year 1 progress (see below)
- Prof. Stefano Lonardi (Computer Science)
- Prof. Timothy Close (Botany and Plant Sciences)
- Prof. Gianfranco Ciardo (Computer Science)
- Hamid Mirebrahim (PhD candidate)
- Rachid Ounit (PhD candidate)
- Denisa Duma (PhD candidate)
- Matthew Alpert (undergraduate student)
- Francesca Cordero (Post-doc)
- Marco Beccuti (Post-doc)
- Burair Alsaihati (MS student)
- Yaqin Ma (post-doc)
- Steve Wanamaker (sysadmin and programmer)
-  H. Mirebrahim, T. J. Close, S. Lonardi, "De Novo Meta-Assembly of Ultra-deep Sequencing Data", Bioinformatics, 2015 (to appear).
-  R. Ounit, S. Wanamaker, T. J. Close, S. Lonardi, "CLARK: Fast and Accurate Classification of Metagenomic and Genomic Sequences using Discriminative Kmers", BMC Genomics, 2015
-  D. Duma, F. Cordero, M. Beccuti, G. Ciardo, T. J. Close, S. Lonardi, "Ultra-Accurate Correction of Pooled Sequenced Reads", submitted, 2014.
-  S. Lonardi, H. Mirebrahim, S. Wanamaker, M. Alpert, G. Ciardo, D. Duma, T. J. Close, "When Less is More: 'Slicing' Sequencing Data Improves Read Decoding Accuracy and De Novo Assembly Quality", Bioinformatics, 2014.
-  D. Duma, M. Wootters, A. C. Gilbert, H. Q. Ngo, A. Rudra, M. Alpert, T. J. Close, G. Ciardo and S. Lonardi. "Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing", Proceedings of WABI, 2013.
-  S. Lonardi, D. Duma, M. Alpert, F. Cordero, M. Beccuti, P. R. Bhat, Y. Wu, G. Ciardo, B. Alsaihati, Y. Ma, S. Wanamaker, J. Resnik, S. Bozdag, M-C. Luo, T. J. Close, "Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space", PLoS Computational Biology, 2013.
-  The International Barley Genome Sequencing Consortium, "A physical, genetic and functional sequence assembly of the barley genome", Nature, 2012.