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1.  ISCB Honors Michael S. Waterman and Mathieu Blanchette 
PLoS Computational Biology  2006;2(8):e105.
PMCID: PMC1526462
2.  2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research 
BMC Genomics  2010;11(Suppl 3):I1.
Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (, International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) attracted more than 300 papers and 400 researchers and medical doctors world-wide. It was the only inter/multidisciplinary conference aimed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The conference committee was very grateful for the valuable advice and suggestions from honorary chairs, steering committee members and scientific leaders including Dr. Michael S. Waterman (USC, Member of United States National Academy of Sciences), Dr. Chih-Ming Ho (UCLA, Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Wing H. Wong (Stanford, Member of United States National Academy of Sciences), Dr. Ruzena Bajcsy (UC Berkeley, Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Qu Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Andrzej Niemierko (Harvard), Dr. A. Keith Dunker (Indiana), Dr. Brian D. Athey (Michigan), Dr. Weida Tong (FDA, United States Department of Health and Human Services), Dr. Cathy H. Wu (Georgetown), Dr. Dong Xu (Missouri), Drs. Arif Ghafoor and Okan K Ersoy (Purdue), Dr. Mark Borodovsky (Georgia Tech, President of ISIBM), Dr. Hamid R. Arabnia (UGA, Vice-President of ISIBM), and other scientific leaders. The committee presented the 2009 ISIBM Outstanding Achievement Awards to Dr. Joydeep Ghosh (UT Austin), Dr. Aidong Zhang (Buffalo) and Dr. Zhi-Hua Zhou (Nanjing) for their significant contributions to the field of intelligent biological medicine.
PMCID: PMC2999338  PMID: 21143775
3.  ISMB/ECCB 2009 Stockholm 
Bioinformatics  2009;25(12):1570-1573.
The International Society for Computational Biology (ISCB; presents the Seventeenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), organized jointly with the Eighth Annual European Conference on Computational Biology (ECCB;, in Stockholm, Sweden, 27 June to 2 July 2009. The organizers are putting the finishing touches on the year's premier computational biology conference, with an expected attendance of 1400 computer scientists, mathematicians, statisticians, biologists and scientists from other disciplines related to and reliant on this multi-disciplinary science. ISMB/ECCB 2009 ( follows the framework introduced at the ISMB/ECCB 2007 ( in Vienna, and further refined at the ISMB 2008 ( in Toronto; a framework developed to specifically encourage increased participation from often under-represented disciplines at conferences on computational biology. During the main ISMB conference dates of 29 June to 2 July, keynote talks from highly regarded scientists, including ISCB Award winners, are the featured presentations that bring all attendees together twice a day. The remainder of each day offers a carefully balanced selection of parallel sessions to choose from: proceedings papers, special sessions on emerging topics, highlights of the past year's published research, special interest group meetings, technology demonstrations, workshops and several unique sessions of value to the broad audience of students, faculty and industry researchers. Several hundred posters displayed for the duration of the conference has become a standard of the ISMB and ECCB conference series, and an extensive commercial exhibition showcases the latest bioinformatics publications, software, hardware and services available on the market today. The main conference is preceded by 2 days of Special Interest Group (SIG) and Satellite meetings running in parallel to the fifth Student Council Symposium on 27 June, and in parallel to Tutorials on 28 June. All scientific sessions take place at the Stockholmsmässan/Stockholm International Fairs conference and exposition facility.
PMCID: PMC2687994  PMID: 19447790
4.  The International ‘Balint’ Award – a rising opportunity for Romanian Medical Students  
Journal of Medicine and Life  2010;3(1):106-109.
The International ‘Balint’ Award for students, instituted by the Foundation for Psychosomatic and Social Medicine in honor of Michael and Enid Balint, has been a rising opportunity for Romanian medical and psychology students to achieve international fame. Romanian students have been among the winners of this award for the last 10 years, in competition with students from Ivy League and other illustrious universities.
The ‘Ascona model’ case presentation debates the psychological side of a medical case, while keeping in focus the diagnostic, pathology and treatment issues. This article focuses on explaining this type of case presentation in correlation with one of the papers submitted in the contest that has received this award in the 15th International Balint Congress.
The exposed case is that of a 17–year–old boy presenting with apparent stupor encountered by an emergency mobile unit. The patient was suspected of substance abuse and overdose but these suspicions were denied by the clinical exam. Further encounters led to the conclusion that both the boy and his whole family needed psychotherapy counseling and were referred there with great success.
PMCID: PMC3019028  PMID: 20302207
psychotherapy; Balint method; , Ascona model case presentation
5.  SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications 
PLoS ONE  2013;8(12):e82138.
The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not return detailed alignment, or are embedded into other tools. These issues make reusing these efficient Smith-Waterman implementations impractical.
To facilitate easy integration of the fast Single-Instruction-Multiple-Data Smith-Waterman algorithm into third-party software, we wrote a C/C++ library, which extends Farrar’s Striped Smith-Waterman (SSW) to return alignment information in addition to the optimal Smith-Waterman score. In this library we developed a new method to generate the full optimal alignment results and a suboptimal score in linear space at little cost of efficiency. This improvement makes the fast Single-Instruction-Multiple-Data Smith-Waterman become really useful in genomic applications. SSW is available both as a C/C++ software library, as well as a stand-alone alignment tool at:
The SSW library has been used in the primary read mapping tool MOSAIK, the split-read mapping program SCISSORS, the MEI detector TANGRAM, and the read-overlap graph generation program RZMBLR. The speeds of the mentioned software are improved significantly by replacing their ordinary Smith-Waterman or banded Smith-Waterman module with the SSW Library.
PMCID: PMC3852983  PMID: 24324759
6.  InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia 
BMC Genomics  2011;12(Suppl 3):S1.
In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.
PMCID: PMC3333168  PMID: 22369160
7.  Paving the future: finding suitable ISMB venues 
Bioinformatics  2012;28(19):2556-2559.
The International Society for Computational Biology, ISCB, organizes the largest event in the field of computational biology and bioinformatics, namely the annual international conference on Intelligent Systems for Molecular Biology, the ISMB. This year at ISMB 2012 in Long Beach, ISCB celebrated the 20th anniversary of its flagship meeting. ISCB is a young, lean and efficient society that aspires to make a significant impact with only limited resources. Many constraints make the choice of venues for ISMB a tough challenge. Here, we describe those challenges and invite the contribution of ideas for solutions.
PMCID: PMC3463122  PMID: 22796959
8.  Role of connexin-related signalling in hepatic homeostasis and its relevance for liver-based in vitro modelling 
Direct intercellular communication mediated by gap junctions constitutes a major regulatory platform in the control of hepatic homeostasis. Hepatocellular gap junctions are composed of two hemichannels of adjacent cells which are built up by connexin proteins,
in casu Cx32. Mathieu Vinken, Pofessor at the Department of Toxicology of the Free University Brussels-Belgium, was one of the first investigators to demonstrate that hepatic connexin expression is controlled by epigenetic mechanisms. In particular, he found that inhibitors of histone deacetylase enzymes enhance Cx32 production and gap junction activity in cultures of primary hepatocytes, a finding that is of importance for liver-based in vitro modelling. Professor Dr. Mathieu Vinken’s recent work is focussed on the elucidation of the role of connexin proteins and their channels in the hepatocyte life cycle. Specific attention is paid to apoptosis in this context, whereby it has been found that Cx32 hemichannels control the termination of induced cell death in cultures of primary hepatocytes. Overall, Professor Dr. Mathieu Vinken’s research can be considered as an important contribution to the field of hepatic connexin physiology.
PMCID: PMC3196623  PMID: 22013553
Connexin; Hemichannel; Gap junction; Primary hepatocyte; In vitro modelling; Epigenetics; Histone modifications; Cell death; Apoptosis; Hepatotoxicity
9.  Mathieu repair of distal and midshaft hypospadias: risks and benefits of foreskin reconstruction versus circumcision 
The purpose of this study was to compare the risks and benefits of Mathieu repair of hypospadias with or without circumcision in consecutive operated cases.
Eighty-six children with midshaft or distal hypospadias were randomly divided into two groups and underwent circumcision (Group A) or preputial reconstruction (Group B) during hypospadias repair. Postoperative complications, outcomes, and parental satisfaction were assessed for circumcised and uncircumcised patients. All patients with midshaft or distal hypospadias with or without minimal chordee were included.
No statistically significant differences in urethral complications were found between the two groups. Meatal stenosis occurred in one case in Group A and one case in Group B. Fistulae occurred in five cases in Group A and six cases in Group B. Urethral dehiscence occurred in no case in either group. No case of phimosis was seen in Group B. After a mean follow-up of 6 months, all parents of Group A cases stated that they were satisfied with the circumcision for religious and/or social reasons, but no parents of Group B cases were satisfied with preputioplasty (P ≤ 0.05). No case of hypospadias repair failure was seen in our operated cases. Finally, no cases in Group B required redo hypospadias surgery.
Mathieu repair with synchronous circumcision is feasible in all patients with distal or midshaft hypospadias with or without minimal chordee, and should be considered in accordance with surgeon preference. In the case of prepuce preservation, parents should be informed that there is a benefit of tissue banking for probable redo hypospadias repair but with an increased risk of complications and a need for another procedure, ie, circumcision.
PMCID: PMC3818950  PMID: 24198642
hypospadias; circumcision; preputioplasty; distal; midshaft; Mathieu repair
10.  Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference 
BMC Bioinformatics  2011;12(Suppl 13):S1.
The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB’s goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.
PMCID: PMC3278825  PMID: 22372736
11.  Summary of talks and papers at ISCB-Asia/SCCG 2012 
BMC Genomics  2013;14(Suppl 2):I1.
The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG).
45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement.
In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.
PMCID: PMC3639071
12.  CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions 
BMC Research Notes  2010;3:93.
Due to its high sensitivity, the Smith-Waterman algorithm is widely used for biological database searches. Unfortunately, the quadratic time complexity of this algorithm makes it highly time-consuming. The exponential growth of biological databases further deteriorates the situation. To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the recently emerging many-core architectures and their associated programming models.
This paper describes the latest release of the CUDASW++ software, CUDASW++ 2.0, which makes new contributions to Smith-Waterman protein database searches using compute unified device architecture (CUDA). A parallel Smith-Waterman algorithm is proposed to further optimize the performance of CUDASW++ 1.0 based on the single instruction, multiple thread (SIMT) abstraction. For the first time, we have investigated a partitioned vectorized Smith-Waterman algorithm using CUDA based on the virtualized single instruction, multiple data (SIMD) abstraction. The optimized SIMT and the partitioned vectorized algorithms were benchmarked, and remarkably, have similar performance characteristics. CUDASW++ 2.0 achieves performance improvement over CUDASW++ 1.0 as much as 1.74 (1.72) times using the optimized SIMT algorithm and up to 1.77 (1.66) times using the partitioned vectorized algorithm, with a performance of up to 17 (30) billion cells update per second (GCUPS) on a single-GPU GeForce GTX 280 (dual-GPU GeForce GTX 295) graphics card.
CUDASW++ 2.0 is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant performance improvement over CUDASW++ 1.0 using either the optimized SIMT algorithm or the partitioned vectorized algorithm for Smith-Waterman protein database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.
PMCID: PMC2907862  PMID: 20370891
The purpose of this study was to review institutional statistics provided in dean's letters and determine the percentage of honors awarded by institution and clerkship specialty.
Institutional and clerkship aggregate data were compiled from a review of dean's letters from 80 United States medical schools. The percentage of honors awarded during 3rd year clerkships during 2005 were collected for analysis. Across clerkship specialties, there were no statistically significant differences between the mean percentage of honors given by the medical schools examined with Internal Medicine (27.6%) the low and Psychiatry (33.5%) the high. However, inter-institutional variability observed within each clerkship was high, with surgery clerkship percentage of honors ranging from 2% to 75% of the students. This suggests some schools may be more lenient and other more stringent in awarding honors to their students. This inter-institutional variability makes it difficult to compare honors received by students from different medical schools and weakens the receipt of honors as a primary tool for evaluating potential incoming residents.
PMCID: PMC2723699  PMID: 19742092
14.  Could shame and honor save cooperation? 
Shame and honor are mechanisms that expose behavior that falls outside the social norm. With recent six-player public goods experiments, we demonstrated that the threat of shame or the promise of honor led to increased cooperation. Participants were told in advance that after ten rounds two participants would be asked to come forward and write their names on the board in front of the fellow group members. In the shame treatment, the least cooperative players were exposed and wrote their names under the sentence “I donated least” while the honored participants wrote their name under “I donated most.” In both the shame and honor treatments, participants contributed approximately 50% more to the public good, as compared with the control treatment in which all players retained their anonymity. Here, we also discuss how shame and honor differ from full transparency, and some of the challenges to understanding how anonymity and exposure modify behavior.
PMCID: PMC3376067  PMID: 22808336
cooperation; honor; public goods game; shame; tragedy of the commons
15.  Density of newly synthesized plasma membrane proteins in intracellular membranes II. Biochemical studies 
The Journal of Cell Biology  1984;98(6):2142-2147.
Using two independent methods, incorporation of radioactive amino-acid and quantitative immunoblotting, we have determined that the rate of synthesis of each of the Semliki Forest virus (SFV) proteins in infected baby hamster kidney (BHK) cells is 1.2 X 10(5) copies/cell/min. Given the absolute surface areas of the endoplasmic reticulum and Golgi complex presented in the companion paper (Griffiths, G., G. Warren, P. Quinn , O. Mathieu - Costello , and A. Hoppeler , 1984, J. Cell Biol. 98:2133-2141), and the approximate time spent in these organelles during their passage to the plasma membrane (Green J., G. Griffiths, D. Louvard , P. Quinn , and G. Warren 1981, J. Mol. Biol. 152:663-698), the mean density of each viral protein in these organelles can be calculated to be 90 and 750 molecules/micron 2 membrane, respectively. In contrast, we have determined that the density of total endogenous integral membrane proteins in these organelles is approximately 30,000 molecules/micron 2 so that the spike proteins constitute only 0.28 and 2.3% of total membrane protein in the endoplasmic reticulum and Golgi, respectively. Quantitative immunoblotting was used to give direct estimates of the concentrations of one of the viral membrane protein precursors (E1) in subcellular fractions; these agreed closely with the calculated values. The data are discussed with respect to the sorting of transported proteins from those endogenous to the intracellular membranes.
PMCID: PMC2113067  PMID: 6563038
16.  Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks 
Bioinformatics  2009;25(19):2617-2618.
Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments.
Availability: Genoscape is an open-source software freely available from the Genoscape webpage ( Installation instructions and tutorial can also be found at this URL.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC2752617  PMID: 19654116
17.  Computing Competition for Light in the GREENLAB Model of Plant Growth: A Contribution to the Study of the Effects of Density on Resource Acquisition and Architectural Development 
Annals of Botany  2007;101(8):1207-1219.
Background and Aims
The dynamical system of plant growth GREENLAB was originally developed for individual plants, without explicitly taking into account interplant competition for light. Inspired by the competition models developed in the context of forest science for mono-specific stands, we propose to adapt the method of crown projection onto the x–y plane to GREENLAB, in order to study the effects of density on resource acquisition and on architectural development.
The empirical production equation of GREENLAB is extrapolated to stands by computing the exposed photosynthetic foliage area of each plant. The computation is based on the combination of Poisson models of leaf distribution for all the neighbouring plants whose crown projection surfaces overlap. To study the effects of density on architectural development, we link the proposed competition model to the model of interaction between functional growth and structural development introduced by Mathieu (2006, PhD Thesis, Ecole Centrale de Paris, France).
Key Results and Conclusions
The model is applied to mono-specific field crops and forest stands. For high-density crops at full cover, the model is shown to be equivalent to the classical equation of field crop production ( Howell and Musick, 1985, in Les besoins en eau des cultures; Paris: INRA Editions). However, our method is more accurate at the early stages of growth (before cover) or in the case of intermediate densities. It may potentially account for local effects, such as uneven spacing, variation in the time of plant emergence or variation in seed biomass. The application of the model to trees illustrates the expression of plant plasticity in response to competition for light. Density strongly impacts on tree architectural development through interactions with the source–sink balances during growth. The effects of density on tree height and radial growth that are commonly observed in real stands appear as emerging properties of the model.
PMCID: PMC2710279  PMID: 18037666
Functional–structural plant models; GREENLAB; competition for light; Beer–Lambert Law; plant plasticity; dynamical system
18.  Analytical Insights on Theta-Gamma Coupled Neural Oscillators 
In this paper, we study the dynamics of a quadratic integrate-and-fire neuron, spiking in the gamma (30–100 Hz) range, coupled to a delta/theta frequency (1–8 Hz) neural oscillator. Using analytical and semianalytical methods, we were able to derive characteristic spiking times for the system in two distinct regimes (depending on parameter values): one regime where the gamma neuron is intrinsically oscillating in the absence of theta input, and a second one in which gamma spiking is directly gated by theta input, i.e., windows of gamma activity alternate with silence periods depending on the underlying theta phase. In the former case, we transform the equations such that the system becomes analogous to the Mathieu differential equation. By solving this equation, we can compute numerically the time to the first gamma spike, and then use singular perturbation theory to find successive spike times. On the other hand, in the excitable condition, we make direct use of singular perturbation theory to obtain an approximation of the time to first gamma spike, and then extend the result to calculate ensuing gamma spikes in a recursive fashion. We thereby give explicit formulas for the onset and offset of gamma spike burst during a theta cycle, and provide an estimation of the total number of spikes per theta cycle both for excitable and oscillator regimes.
PMCID: PMC3848946  PMID: 23945442
Oscillations; PING; Dynamical systems; Geometric singular perturbation theory; Blow-up method; Spike times; Theta-gamma rhythms; Type I neuron; SNIC bifurcation
19.  Beta Value Coupled Wave Theory for Nonslanted Reflection Gratings 
The Scientific World Journal  2014;2014:513734.
We present a modified coupled wave theory to describe the properties of nonslanted reflection volume diffraction gratings. The method is based on the beta value coupled wave theory, which will be corrected by using appropriate boundary conditions. The use of this correction allows predicting the efficiency of the reflected order for nonslanted reflection gratings embedded in two media with different refractive indices. The results obtained by using this method will be compared to those obtained using a matrix method, which gives exact solutions in terms of Mathieu functions, and also to Kogelnik's coupled wave theory. As will be demonstrated, the technique presented in this paper means a significant improvement over Kogelnik's coupled wave theory.
PMCID: PMC3958683  PMID: 24723811
20.  A General Organocatalyzed Michael-Michael Cascade Reaction Generates Functionalized Cyclohexenes 
The Journal of organic chemistry  2011;76(15):6309-6319.
While β-dicarbonyl compounds are regularly employed as Michael donors, intermediates arising from the Michael addition of unsaturated β-ketoesters to α,β-unsaturated aldehydes are susceptible to multiple subsequent reaction pathways. We designed cyclic unsaturated β-ketoester substrates that enabled the development of the first diphenyl prolinol silyl ether-catalyzed Michael-Michael cascade reaction initiated by a β-dicarbonyl Michael donor to form cyclohexene products. The reaction conditions we developed for this Michael-Michael cascade reaction were also amenable to a variety of linear unsaturated β-ketoester substrates, including some of the same linear unsaturated β-ketoester substrates that were previously ineffective in Michael-Michael cascade reactions. These studies thus revealed that a change in simple reaction conditions, such as solvent and additives, enables the same substrate to undergo different cascade reactions, thereby accessing different molecular scaffolds. These studies also culminated in the development of a general organocatalyzed Michael-Michael cascade reaction that generates highly functionalized cyclohexenes with up to four stereocenters, in up to 97% yield, 32:1 dr, and 99% ee, in a single step from a variety of unsaturated β-ketoesters.
PMCID: PMC3198797  PMID: 21714480
21.  Forging Faculty Student Relationships at the College Level Using a Freshman Research Experience 
Journal of chemical education  2008;85(12):1696-1698.
Coupling the scholarly activities of the chemistry research faculty with that of the freshman Honors general chemistry class has resulted in a rise of productivity within the Department. For seven years, freshman Honors students enrolled in the Honors general chemistry laboratory sections have been assigned to work in the labs of the research active faculty within the Department of Chemistry. Approximately a quarter of those enrolled in the Honors general chemistry laboratory sections elect to continue their research experience. The continued and sustained research experience has resulted in a research journal paper for six participants. For the past four years, four papers have been accepted for publication because of the research activities conducted as freshman stemming from this program. Each paper has had at least one co-author as an undergraduate at the sophomore or freshman level.
PMCID: PMC2691711  PMID: 19503760
Curriculum; Inquiry-Based / Discovery Learning; Problem Solving / Decision Making; Undergraduate Research
22.  PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology 
Nucleic Acids Research  2005;33(Web Server issue):W535-W539.
PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith–Waterman and ParAlign. The ParAlign algorithm is similar to Smith–Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at , where the major public databases can be searched. The software can also be downloaded free of charge for academic use.
PMCID: PMC1160184  PMID: 15980529
23.  Testing statistical significance scores of sequence comparison methods with structure similarity 
BMC Bioinformatics  2006;7:444.
In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences.
All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores.
The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.
PMCID: PMC1618413  PMID: 17038163
24.  CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment 
BMC Bioinformatics  2008;9(Suppl 2):S10.
Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic programming approach that explores all the possible alignments between two sequences; as a result it returns the optimal local alignment. Unfortunately, the computational cost is very high, requiring a number of operations proportional to the product of the length of two sequences. Furthermore, the exponential growth of protein and DNA databases makes the Smith-Waterman algorithm unrealistic for searching similarities in large sets of sequences. For these reasons heuristic approaches such as those implemented in FASTA and BLAST tend to be preferred, allowing faster execution times at the cost of reduced sensitivity. The main motivation of our work is to exploit the huge computational power of commonly available graphic cards, to develop high performance solutions for sequence alignment.
In this paper we present what we believe is the fastest solution of the exact Smith-Waterman algorithm running on commodity hardware. It is implemented in the recently released CUDA programming environment by NVidia. CUDA allows direct access to the hardware primitives of the last-generation Graphics Processing Units (GPU) G80. Speeds of more than 3.5 GCUPS (Giga Cell Updates Per Second) are achieved on a workstation running two GeForce 8800 GTX. Exhaustive tests have been done to compare our implementation to SSEARCH and BLAST, running on a 3 GHz Intel Pentium IV processor. Our solution was also compared to a recently published GPU implementation and to a Single Instruction Multiple Data (SIMD) solution. These tests show that our implementation performs from 2 to 30 times faster than any other previous attempt available on commodity hardware.
The results show that graphic cards are now sufficiently advanced to be used as efficient hardware accelerators for sequence alignment. Their performance is better than any alternative available on commodity hardware platforms. The solution presented in this paper allows large scale alignments to be performed at low cost, using the exact Smith-Waterman algorithm instead of the largely adopted heuristic approaches.
PMCID: PMC2323659  PMID: 18387198
25.  SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 
BMC Research Notes  2008;1:107.
We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and compares its performances with several other implementations.
Our benchmarking results show that swps3 is currently the fastest implementation of a vectorized Smith-Waterman on the Cell/BE, outperforming the only other known implementation by a factor of at least 4: on a Playstation 3, it achieves up to 8.0 billion cell-updates per second (GCUPS). Using the SSE2 instruction set, a quad-core Intel Pentium can reach 15.7 GCUPS. We also show that swps3 on this CPU is faster than a recent GPU implementation. Finally, we note that under some circumstances, alignments are computed at roughly the same speed as BLAST, a heuristic method.
The Cell/BE can be a powerful platform to align biological sequences. Besides, the performance gap between exact and heuristic methods has almost disappeared, especially for long protein sequences.
PMCID: PMC2615776  PMID: 18959793

Results 1-25 (790)