Draft of a Japanese worm genome
The first genome draft of a japanese member of the planarians, characterized in collaboration with the Agata lab, has just been published in Zoological Letters. Make sure to check our genome browser for it.
Graph Traversal Edit Distance
Our polynomial time algorithm for graph traversal edit distance appeared at RECOMB 2018. Our algorithm is a Linear Programming relaxation that is guaranteed to yield and integer solution. Since LP has a polynomial-time algorithm (the interior methods), our algorithm has polynomial time complexity.
Principal Variety Analysis
Our method for minimum dimensional algebraic manifold learning, which we call Principal Variety Analysis (PVA), has been accepted at CoRL 2017 and will be published soon.
Role of Clp1 in Yeast
Our work on genomewide analysis of Clp1 function in budding yeast reveals transcription termination and antisense transcription inhibition roles of Clp1. The paper describing our methods and results has been accepted at Scientific Reports and will be published soon.
Structure and function of Protein Disulfide Isomerase
Our work on machine learning and network analysis of molecular dynamics trajectories reveals two chains of Red/Ox-specific residue interactions in Protein Disulfide Isomerase. The paper describing our methods and results has been accepted at Scientific Reports and will be published soon.
Our SNP-Phenotype association corpus extracted from biomedical natural language texts, called SNPPhenA, has been published in the Journal of Biomedical Semantics.
Extraction of drug-drug interaction from literature
Our work on extraction of drug-drug interaction from literature has been published in PLOS One.
New members: Akash Shrestha and Ali Ebrahimpour
We are glad that Akash Shrestha and Ali Ebrahimpour have joined the ABL as graduate students.
New member: Dr. Suzanne Gallagher
We are glad that Dr. Suzanne Gallagher has joined the ABL as a research associate.
Synergistic single-cell genomics
Our work on synergistic co-assembly of multiple related single-cell genomes has been accepted in Frontiers in Bioengineering and Biotechnology, Genomic Assay Technology.
Shedding light on differentiation mechanism in embryogenesis
Ali Sharifi-Zarchi's interesting work on characterization of differentiation mechanism in early embryogenesis has appeared in BMC Systems Biology.
Narjes S. Movahedi Tabrizi's Master's defense
Narjes S. Movahedi Tabrizi successfully defended her master's thesis on co-assembly of single cells.
Paper accepted @ CDC 2014
NUROA, an approximation of the Canny's roadmap using the Lasserre's polynomial optimization method will appear at the 53rd IEEE Conference on Decision and Control (CDC) 2014. For more details, check the preprint here.
Elmirasadat Forouzmand's Master's defense
Elmirasadat Forouzmand successfully defended her master's thesis on learnability of RNA energy from structure.
RCV 2013 proceedings published
Proceedings of the 1st workshop on Robotics Challenges and Vision (RCV2013) held in conjunction with Robotics: Science and Systems in Berlin, Germany is published.
Paper accepted @ RECOMB-seq 2014
Our paper in collaboration with researchers from University of Toronto, University of Maryland, University of Tehran, Royan Institute
for Stem Cell Biology and Technology, and Iranian National Institute of Genetic Engineering and Biotechnology on a new read aligner called ARYANA has been accepted at RECOMB-seq 2014.
Paper accepted @ RECOMB 2014
An exact algorithm for learning RNA energy parameters from structure as well as a necessary and sufficient condition for learnability will appear at RECOMB 2014. The idea is based on computing the Newton polytope of the partition function as a polynomial in the transformed energy parameters. For more details, check the preprint here.
Compressive single-cell genomics
Our paper on compressed sequencing and assembly of all distinct genomes (species) from single cells in a sample has been published in Bioinformatics. This is the first approach to compressive single-cell genomics, to the best of our knowledge. Congratulations to Dr. Zeinab Taghavi for her outstanding work.
The PI Chitsaz has been awarded an NSF ABI research award to pursue the single-cell sequencing and assembly project.
Candidate phylum TM6 genome
The results of our collaborative work with the J. Craig Venter Institute and UCSD on a candidate phylum TM6 genome has been published in the Proceedings of the National Academy of Sciences (PNAS).
Best highlights paper award @ GLBio 2013
'De novo co-assembly of bacterial genomes from multiple single cells' won the best highlights paper award at ISCB Great Lakes Bioinformatics (GLBio) 2013 conference on the CMU campus.
Paper accepted @ ISMB 2013
Our paper on `learnability' of RNA energy parameters as well as an algorithm to assess a necessary condition for it will appear at ISMB 2013. The idea is based on computing the Newton polytope of the partition function as a polynomial in the transformed energy parameters. For more details, check the preprint here.
Paper accepted @ SIAM CT13
Our partial characterization of minimum time trajectories for a car-like robot with one trailer has been accepted at SIAM Control and Its Applications (CT) 2013. Our analysis proves that the robot, on a time optimal path, has to follow a merging curve to straighten up its trailer after a minimum radius turn in order to be able to join a straight line motion.
Robotics Challenges and Vision @ RSS 2013
We are organizing the Robotics Challenges and Vision Workshop at Robotics: Science and Systems 2013 to be held in TU-Berlin, Germany. This is a workshop sponsored by the Computing Community Consortium affiliated with the Computing Research Association, who played a major role in the inception, development, and realization of the National Robotics Initiative. Submission of radical, somewhat controversial, potentially earth-shattering, revolutionary ideas to this workshop are strongly encouraged.
Paper accepted @ JCB
Our algorithm for upper bound on the partition function of nucleic acids has been accepted at Journal of Computational Biology.
RNA meeting in Benasque 2012
Prof. Chitsaz presents their partition function algorithm for RNA-RNA interaction at the 2012 RNA meeting held in Centro de Ciencias de Benasque. Their algorithms piRNA and biRNA compute the partition function, base pairing probabilities, melting temperature, equilibrium concentrations, and binding sites for a pair of RNA sequences.
Co-assembly from multiple single cells
Our paper on de novo co-assembly of bacterial genomes from multiple single cells appeared at IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2012. The co-assembly tool HyDA is currently released in binary.
Single cell genomics
Our single cell assembly paper entitled "Efficient de novo assembly of single-cell bacterial genomes from short-read data sets" has been published in Nature Biotechnology. We modified Velvet to obtain Velvet-SC for MDA single cell data.