RNATOPS-W: a web server for RNA structure searches of genomes (2009)
Wang, Yingfeng, Huang, Zhibin, Wu, Yong, Malmberg, Russell L., Cai, Liming
Summary: RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile...
Jizhen Zhao, Dongsheng Che, Liming Cai
Template-based comparative analysis is a viable approach to the prediction and annotation of pathways in genomes. Methods based solely on sequence similarity may not be effective enough; functional...
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental...
Parameterized Complexity and Biopolymer Sequence Comparison (2008)
Liming Cai, Xiuzhen Huang, Chunmei Liu, Frances Rosamond, Yinglei Song
The article surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence,...
Learning the Parameters of Stochastic Grammar Models for RNA Structures with Pseudoknots (2008)
Abstract — Stochastic grammar systems have been introduced to model RNA structures with pseudoknots. These grammar systems need to be properly trained to get the accurate probabilistic parameters...
Liming Cai, Michael Fellows, David Juedes, Frances Rosamond
In 1996, Khanna and Motwani [KM96] proposed three logic-based optimization problems constrained by planar structure, and offered the hypothesis that these putatively fundamental problems might...
doi:10.1093/comjnl/bxm035 Parameterized Complexity and Biopolymer Sequence Comparison (2008)
Liming Cai, Xiuzhen Huang, Chunmei Liu, Frances Rosamond, Yinglei Song
The paper surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence,...
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, Liming Cai
doi:10.1093/bioinformatics/btl226 Peptide sequence tag-based blind identification of
Rapid ab initio Prediction of RNA Pseudoknots via Graph Tree Decomposition ∗ (2008)
Jizhen Zhao, Russell L. Malmberg, Liming Cai
The prediction of RNA secondary structure including pseudoknots remains a challenge due to the intractable computation of the sequence conformation from nucleotide interactions under free energy...
Phylogenetic Network Inferences through Efficient (2008)
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai
Abstract. The genotype phasing problem is to determine the haplotypes of diploid individuals from their genotypes where linkage relationships are not known. Based on the model of perfect phylogeny,...
Rapid ab initio RNA Folding Including Pseudoknots via Graph Tree Decomposition (2008)
Jizhen Zhao, Russell L. Malmberg, Liming Cai
Abstract. The prediction of RNA secondary structure including pseudoknots remains a challenge due to the intractable computation of the sequence conformation from intriguing nucleotide interactions....
Jizhen Zhao, Dongsheng Che, Liming Cai
Template-based comparative analysis is a viable approach to the prediction and annotation of pathways in genomes. Methods based solely on sequence similarity may not be effective enough; functional...
Efficient Annotation of Non-coding RNA Structures Including Pseudoknots via Automated Filters (2008)
Chunmei Liu, Yinglei Song, Ping Hu, Russell L. Malmberg, Liming Cai
Computational search of genomes for RNA secondary structure is an important approach to the annotation of non-coding RNAs. The bottleneck of the search is sequence-structure alignment, which is often...
Fast and accurate search for non-coding RNA pseudoknot structures in genomes (2008)
Huang, Zhibin, Wu, Yong, Robertson, Joseph, Feng, Liang, Malmberg, Russell L., Cai, Liming
Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective...
Parameterized Complexity and Biopolymer Sequence Comparison (2008)
Cai, Liming, Huang, Xiuzhen, Liu, Chunmei, Rosamond, Frances, Song, Yinglei
The paper surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence,...
Dongsheng Che, Dongsheng Che, Maureen Grasso, Liming Cai
(Under the direction of Robert W. Robinson) The Web graph is a graph of the World-Wide Web (WWW), with Web pages represented by nodes and hyperlinks represented by directed edges. In the past decade,...
Subexponential Parameterized Algorithms Collapse the (2007)
W -hierarchy, Liming Cai, David Juedes
It is shown that for essentially all MAX SNP-hard optimization problems finding exact solutions in subexponential time is not possible unless W [1] = FPT. In particular, we show that O(2 o(k) p(n))...
Liming Cai, David Juedes, Iyad Kanj
The inapproximability of non NP-hard optimization problems is investigated. Techniques are given to show that problems Log Dominating Set and Log Hypergraph Vertex Cover cannot be approximated to a...
Was There Compression of Disability for Older Americans From 1992 to 2003? (2007)
Demography - Volume 44, Number 3, August 2007
Diehr, Paula, Derleth, Ann, Cai, Liming, Newman, Anne B
Abstract Background Choosing cost-effective strategies for improving the health of the public is difficult because the relative effects of different types of interventions are not well understood....
Permanence and Stability of an Age-Structured Prey-Predator System with Delays (2007)
Liming Cai, Xuezhi Li, Xinyu Song, Jingyuan Yu
An age-structured prey-predator model with delays is proposed and analyzed. Mathematical analyses of the model equations with regard to boundedness of solutions, permanence, and stability are...
Permanence and Stability of an Age-Structured Prey-Predator System with Delays (2007)
Liming Cai, Xuezhi Li, Xinyu Song, Jingyuan Yu
An age-structured prey-predator model with delays is proposed and analyzed. Mathematical analyses of the model equations with regard to boundedness of solutions, permanence, and stability are...
Different Public Health Interventions have Varying Effects (2006)
Diehr, Paula, Newman, Anne B., Cai, Liming, Derleth, Ann
Objective: To compare performance of one-time health interventions to those that change the probability of transitioning from one health state to another. Study Design and Setting: We used...
Different Public Health Interventions have Varying Effects (2006)
Diehr, Paula, Newman, Anne B., Cai, Liming, Derleth, Ann
Objective: To compare performance of one-time health interventions to those that change the probability of transitioning from one health state to another. Study Design and Setting: We used...
Different Public Health Interventions have Varying Effects (2006)
Diehr, Paula, Newman, Anne B., Cai, Liming, Derleth, Ann
Objective: To compare performance of one-time health interventions to those that change the probability of transitioning from one health state to another. Study Design and Setting: We used...
Different Public Health Interventions have Varying Effects (2006)
Diehr, Paula, Newman, Anne B., Cai, Liming, Derleth, Ann
Objective: To compare performance of one-time health interventions to those that change the probability of transitioning from one health state to another. Study Design and Setting: We used...
12 Protein Structure Prediction by Protein Threading (2006)
Ying Xu, Zhijie Liu, Liming Cai, Dong Xu
protein folding problem ” laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural...
Fixed-parameter approximation: Conceptual framework and approximability results (2006)
Abstract. The notion of fixed-parameter approximation is introduced to investigate the approximability of optimization problems within the framework of fixed-parameter computation. This work...
Liu, Chunmei, Yan, Bo, Song, Yinglei, Xu, Ying, Cai, Liming
An important but difficult problem in proteomics is the identification of post-translational modifications (PTMs) in a protein. In general, the process of PTM identification by aligning experimental...
Is the Number of Sick Persons in a Cohort Constant Over Time? (2005)
Diehr, Paula, Derleth, Ann, Newman, Anne, Cai, Liming
Objectives: To estimate the number of persons in a cohort who are sick, over time.Methods: We calculated the number of sick persons in the Cardiovascular Health Study (CHS), a cohort study of older...
Is the Number of Sick Persons in a Cohort Constant Over Time? (2005)
Diehr, Paula, Derleth, Ann, Newman, Anne, Cai, Liming
Objectives: To estimate the number of persons in a cohort who are sick, over time.Methods: We calculated the number of sick persons in the Cardiovascular Health Study (CHS), a cohort study of older...
Is the Number of Sick Persons in a Cohort Constant Over Time? (2005)
Diehr, Paula, Derleth, Ann, Newman, Anne, Cai, Liming
Objectives: To estimate the number of persons in a cohort who are sick, over time.Methods: We calculated the number of sick persons in the Cardiovascular Health Study (CHS), a cohort study of older...
Is the Number of Sick Persons in a Cohort Constant Over Time? (2005)
Diehr, Paula, Derleth, Ann, Newman, Anne, Cai, Liming
Objectives: To estimate the number of persons in a cohort who are sick, over time.Methods: We calculated the number of sick persons in the Cardiovascular Health Study (CHS), a cohort study of older...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract. Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Profiling and searching for RNA pseudoknot structures (2005)
Chunmei Liu, Yinglei Song, Russell L. Malmberg, Liming Cai
Abstract. We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent...
Tree decomposition based fast search of RNA structures including pseudoknots in genomes (2005)
Yinglei Song, Russell Malmberg, Liming Cai, Chunmei Liu, Fangfang Pan
Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract. Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment (2005)
Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
Abstract—Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify...
BEST: Binding-site Estimation Suite of Tools (2005)
Che, Dongsheng, Jensen, Shane, Cai, Liming, Liu, Jun S.
Summary: The purpose of our Binding-site Estimation Suite of Tools (BEST) is two-fold: to provide a platform for using and comparing different motif-finding programs for transcription factor binding...
BEST: Binding-site Estimation Suite of Tools (2005)
Che, Dongsheng, Jensen, Shane, Cai, Liming, Liu, Jun S.
Summary: The purpose of our Binding-site Estimation Suite of Tools (BEST) is two-fold: to provide a platform for using and comparing different motif-finding programs for transcription factor binding...
Liming Cai, Russell L. Malmberg, Yunzhou Wu
Motivation: Modeling RNA pseudoknotted structures remains challenging. Methods have previously been developed to model RNA stem-loops successfully using stochastic context-free grammars (SCFG)...
Stochastic modeling of RNA pseudoknotted structures: a grammatical approach (2003)
Cai, Liming, Malmberg, Russell L., Wu, Yunzhou
Motivation: Modeling RNA pseudoknotted structures remains challenging. Methods have previously been developed to model RNA stem-loops successfully using stochastic context-free grammars (SCFG)...
The inapproximability of non NP-hard optimization problems (1999)
Liming Cai, David Juedes, Iyad Kanj
The inapproximability of non NP-hard optimization problems is investigated. Techniques are given to show that problems Log Dominating Set and Log Hypergraph Vertex Cover cannot be approximated to a...
Circuit bottom fan-in and computational power (1998)
Liming Cai, Jianer Chen, Johan H Astad
We investigate the relationship between circuit bottom fan-in and circuit size when circuit depth is fixed. We show that in order to compute certain functions, a moderate reduction in circuit bottom...
Circuit Bottom Fan-In And Computational Power (1998)
Liming Cai, Jianer Chen, Johan Håstad, H Astad
. We investigate the relationship between circuit bottom fan-in and circuit size when circuit depth is fixed. We show that in order to compute certain functions, a moderate reduction in circuit...
On The Amount Of Nondeterminism And The Power Of Verifying (1997)
. The relationship between nondeterminism and other computational resources is investigated based on the "guess-then-check" model GC. Systematic techniques are developed to construct...
Applying formal methods to representation of constraints in VLSI design specification / (1994)
Thesis (M.S.)--University of Cincinnati, 1994.
Liming Cai, Nathaniel Schenker, James Lubitz
To analyse functional status transitions in the older population better, we fit a semi-Markov process model to data from the 1992-2002 Medicare Current Beneficiary Survey. We used an analogue of the...
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
Huang, Zhibin, Wu, Yong, Robertson, Joseph, Feng, Liang, Malmberg, Russell L., Cai, Liming
Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective...