![]() |
![]() |
|
|
Projects |
|
Modeling Fluid Mixing in Microfluidic Grids This is an application to model fluid mixing in grid-based microfluidic chips. It provides a fast approximation of velocity and concentration at outlets for given grid-based chip designs. | Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) is a method that permits the identification of arrayed ribosomal RNA genes (rDNA)through a series of hybridizaition experiments using small DNA probes. It provides a cost effective means to extensively analyze microbial communities and should have application in medicine, biotechnology and ecosystem studies. This project is funded by NSF DBI. |
PRImer Selector (PRISE) is an interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3' end of the primers - a property that is crucial for sequence selectivity / specificity. | OligoSpawn is an efficient software for selecting two types of oligos, namely unique and popular oligos, from large unigene databases. |
MSOAR is a high-throughput system for ortholog assignment on a genome scale. | Two Sample Logo is a procedure for discovery of statistically significant position-specific differences in residue compositions between two multiple sequence alignments, as well as for graphical representation of those differences. |
BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer. BRAT supports single-end and pair-end short reads mapping and allows alignment of different length reads/mates. | Composition Profiler is a web-based tool that automates detection of enrichment or depletion patterns of individual amino acids or groups of amino acids classified by several physico-chemical and structural properties. |
FLowgram Alignment Tool (FLAT) is a method for probabilistic matching of small RNA flowgrams against the reference genome. | LRTag is an efficient software tool for selecting a minimum set of TagSNPs across multiple populations via the linkage disequilibrium criteria. |
MSTmap is a genetic mapping tool which constructs the initial genetic map from the minimum spanning tree (MST) of a graph. It is able to detect genotyping errors and can handle various mapping populations including DH, Hap, BC, and RIL. | MergeMap is software tool for merging individual genetic linkage maps into a consensus map. When there are conflicts among the individual maps, MergeMap is able to produce a graph which highlights the possible problematic marker occurrences. |
Graphlet kernel is a supervised learning framework for annotating functional residues in protein structures. Each residue is represented as a vector of counts of labeled nonâisomorphic subgraphs (called graphlets) in the protein contact graph, and a similarity measure between two vertices is expressed as the inner product of their respective count vectors. |
Faculty |
|
![]() Marek Chrobak Office: Bourns Hall A159C Design and analysis of algorithms; data structures; theory of computation; combinatorial optimization; computational geometry; automata theory; graph theory; on-line algorithms; graph drawing algorithms; algorithms in discrete tomography. |
![]() Tao Jiang Office: WCH 336 My research has been focused on the design and analysis of algorithms of either theoretical or practical importance. Some of my past work includes approximation algorithms, average-case analysis, computational complexity, and computational learning. My current work is mostly concerned with algorithmic and machine learning problems in bioinformatics and biomedical informatics. |
![]() Stefano Lonardi Office: WCH 325 Research interests: computational molecular biology, bioinformatics, design of algorithms, machine learning and data mining. |
![]() Yihan Sun Office: TBD Broad topics in the theory and practice of parallel computing, including algorithms, data structures, frameworks, implementations, and their applications. My work involves improving asymptotical theoretical bounds, simplifying algorithms and proofs, and developing efficient solutions to real-world problems. |
![]() Amey Bhangale Office: TBD My research interests lie in Complexity Theory. More specifically, I am interested in topics related to approximation algorithms, constraint satisfaction problems, analysis of Boolean functions and probabilistically checkable proofs. |
![]() Yan Gu Office: TBD My current research interest is design efficient (usually parallel) algorithms for large-scale data with good performance in practice. |
![]() Silas Richelson Office: Bourns Hall A159 My research interests are in Cryptography, Computer Security and Complexity Theory. |
Students and postdocs |
||
Md. Abid Hasan Ph.D. candidate, Computer Science |
Abbas Roayaei Ph.D. candidate, Computer Science |
Qihua Liang Ph.D. candidate, GGB |
Dipankar Ranjan Baisya Ph.D. candidate, Computer Science |
Huong Luu Ph.D. candidate, Computer Science |
Hao Chen Ph.D. candidate, Computer Science |
Dipan Shaw Ph.D. candidate, Computer Science |
Jiaqi Hao MS, Computer Science |
Parker Newton PhD candidate, Computer Science |
Irem Ergun Ph.D. student, Computer Science |
Sourya Roy Ph.D. candidate, Computer Science |
Yugarshi Shashwat Ph.D. student, Computer Science, Computer Science |
Alumni |
||
Miguel Coviello Ph.D. Computer Science (2019) |
Xin Zhang Ph.D. Computer Science |
Yu-Ting Huang Ph.D. Computer Science |
Weihua Pan Ph.D. Computer Science (2019) |
Hind Alhakami Ph.D. Computer Science (2017) |
Rachid Ounit Ph.D. Computer Science (2017) |
Wei-Bung Wang Ph.D. Computer Science |
Guanqun Shi Ph.D. Computer Science |
Yang Yang Visiting researcher |
Monik Khare Ph.D. Computer Science |
Arman Yousefi Ph.D. student, Computer Science |
Elena Harris Ph.D. Computer Science (2010) |
Christos Koufogiannakis Ph.D. Computer Science (2009) |
Vladimir Vacic Ph.D. Computer Science (2008) |
YongHui Wu Ph.D. Computer Science (2008) |
Serdar Bozdag Ph.D. Computer Science (2008) |
Zhaocheng Fan Visiting researcher |
Qi Fu Ph.D. Computer Science (2007) |
Zheng Fu Ph.D. Computer Science (2007) |
Lan Liu Ph.D. Computer Science (2007) |
Mathilde Hurand Visiting researcher |
Zheng Liu Ph.D. Computer Science (2006) |
Jie Zheng Ph.D. Computer Science (2006) |
Wojciech Jawor Ph.D. Computer Science (2006) |
Qiaofeng Yang Ph.D. Bioinformatics (2006) M.S. Computer Science (2006) |
Chuhu Yang Ph.D. Bioinformatics (2005) |
Xin Chen Postdoc (2005) |
Haifeng Li Ph.D. Computer Science (2005) |
Petr Kolman Postdoc (2004) |
Jing Li Ph.D. Computer Science (2004) |
Andres Figeuroa Ph.D. Computer Science (2004) |
Ashraful Arefeen Ph.D. Computer Science |