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1.  A Regev-Type Fully Homomorphic Encryption Scheme Using Modulus Switching 
The Scientific World Journal  2014;2014:983862.
A critical challenge in a fully homomorphic encryption (FHE) scheme is to manage noise. Modulus switching technique is currently the most efficient noise management technique. When using the modulus switching technique to design and implement a FHE scheme, how to choose concrete parameters is an important step, but to our best knowledge, this step has drawn very little attention to the existing FHE researches in the literature. The contributions of this paper are twofold. On one hand, we propose a function of the lower bound of dimension value in the switching techniques depending on the LWE specific security levels. On the other hand, as a case study, we modify the Brakerski FHE scheme (in Crypto 2012) by using the modulus switching technique. We recommend concrete parameter values of our proposed scheme and provide security analysis. Our result shows that the modified FHE scheme is more efficient than the original Brakerski scheme in the same security level.
doi:10.1155/2014/983862
PMCID: PMC4100376  PMID: 25093212
2.  Life, the Universe, and Everything: An Interview with David Haussler 
PLoS Genetics  2013;9(1):e1003282.
doi:10.1371/journal.pgen.1003282
PMCID: PMC3561096  PMID: 23382705
3.  2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers 
PLoS Computational Biology  2014;10(5):e1003621.
doi:10.1371/journal.pcbi.1003621
PMCID: PMC4031058  PMID: 24853264
4.  Highlights from the ISCB Student Council Symposium 2013 
BMC Bioinformatics  2014;15(Suppl 3):A1.
This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) / European Conference on Computational Biology (ECCB) conference in Berlin, Germany, on July 19, 2013.
doi:10.1186/1471-2105-15-S3-A1
PMCID: PMC4079984  PMID: 25077567
5.  ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus 
PLoS Computational Biology  2015;11(1):e1004087.
Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains as well as 3-D protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature, and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2,000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology [ISMB] 2016, Orlando, Florida).
doi:10.1371/journal.pcbi.1004087
PMCID: PMC4310586  PMID: 25633975
6.  2010 ISCB Overton Prize Awarded to Steven E. Brenner 
PLoS Computational Biology  2010;6(6):e1000831.
doi:10.1371/journal.pcbi.1000831
PMCID: PMC2891695  PMID: 20585610
7.  ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature 
Bioinformatics  2011;27(3):291-294.
doi:10.1093/bioinformatics/btq687
PMCID: PMC3031043  PMID: 21282182
9.  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.
doi:10.1186/1471-2105-12-S13-S1
PMCID: PMC3278825  PMID: 22372736
10.  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.
doi:10.1186/1471-2164-12-S3-S1
PMCID: PMC3333168  PMID: 22369160
11.  A Report of the Curriculum Task Force of the ISCB Education Committee 
PLoS Computational Biology  2012;8(6):e1002570.
doi:10.1371/journal.pcbi.1002570
PMCID: PMC3386154  PMID: 22761560
12.  Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012 
BMC Bioinformatics  2012;13(Suppl 18):A1.
The report summarizes the scientific content of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB) held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference in Long Beach, California on July 13, 2012.
doi:10.1186/1471-2105-13-S18-A1
PMCID: PMC3522031
13.  ISCB Honors Michael S. Waterman and Mathieu Blanchette 
PLoS Computational Biology  2006;2(8):e105.
doi:10.1371/journal.pcbi.0020105
PMCID: PMC1526462
14.  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.
doi:10.1186/1471-2164-14-S2-I1
PMCID: PMC3639071
16.  The Regional Student Group Program of the ISCB Student Council: Stories from the Road 
PLoS Computational Biology  2013;9(9):e1003241.
The International Society for Computational Biology (ISCB) Student Council was launched in 2004 to facilitate interaction between young scientists in the fields of bioinformatics and computational biology. Since then, the Student Council has successfully run events and programs to promote the development of the next generation of computational biologists. However, in its early years, the Student Council faced a major challenge, in that students from different geographical regions had different needs; no single activity or event could address the needs of all students. To overcome this challenge, the Student Council created the Regional Student Group (RSG) program. The program consists of locally organised and run student groups that address the specific needs of students in their region. These groups usually encompass a given country, and, via affiliation with the international Student Council, are provided with financial support, organisational support, and the ability to share information with other RSGs. In the last five years, RSGs have been created all over the world and organised activities that have helped develop dynamic bioinformatics student communities. In this article series, we present common themes emerging from RSG initiatives, explain their goals, and highlight the challenges and rewards through specific examples. This article, the first in the series, introduces the Student Council and provides a high-level overview of RSG activities. Our hope is that the article series will be a valuable source of information and inspiration for initiating similar activities in other regions and scientific communities.
doi:10.1371/journal.pcbi.1003241
PMCID: PMC3784494  PMID: 24098107
17.  The ISCB: Growing and Evolving in Step with Science 
PLoS Computational Biology  2005;1(5):e51.
doi:10.1371/journal.pcbi.0010051
PMCID: PMC1274292
18.  ISCB Honors Temple F. Smith and Eran Segal 
PLoS Computational Biology  2007;3(6):e128.
doi:10.1371/journal.pcbi.0030128
PMCID: PMC1904388  PMID: 17604447
19.  One-Year and Cumulative Retention as Predictors of Success in Methadone Maintenance Treatment: A Comparison of Two Clinics in the United States and Israel 
Journal of addictive diseases  2008;27(4):10.1080/10550880802324382.
Outcome predictors between two methadone maintenance treatment clinics in Tel-Aviv, Israel, and Las Vegas, Nevada, were determined by comparing patients’ characteristics. All patients admitted to the two clinics (302 from Las Vegas and 492 from Tel-Aviv) were studied with respect to variables at admission and follow-up. Las Vegas patients were older, contained more females, had more hepatitis C positive markers, and more urine analyses that were positive for cocaine, amphetamines, and tetrahydrocannabinol (THC) on admission than the Tel-Aviv patients. After 1 year, Tel-Aviv patients had higher retention (73.6% vs. 61.6%) and similar opiate abstinence (65.8% vs. 64.9%) compared to Las Vegas patients. Predictors for cumulative retention (Cox regression) for both clinics were higher methadone dosages greater than or equal to 100 mg/day (Tel-Aviv OR [odds ratio] = 2.1, 95% confidence interval [CI] = 1.6–2.9; Las Vegas OR= 1.8, 95% CI = 1.3–2.5). Also, in Tel-Aviv, predictors were no opiate use after 1 year (OR = 1.7, 95% CI = 1.4–2.2) and no benzodiazepine after 1 year, and in Las Vegas no cocaine and no amphetamines after 1 year and age less than or equal to 30 years. The two major predictors in the two clinics were successful in both outcomes: 1 year retention and opiate abstinence.
doi:10.1080/10550880802324382
PMCID: PMC3810137  PMID: 19042587
Methadone maintenance treatment; countries’ differences; Kaplan-Meier analyses; retention; predictors
20.  Clinical Significance of Ryanodine Receptor 1 Gene (RYR1) Variants: Proceedings of the 2013 MHAUS Scientific Conference 
The Malignant Hyperthermia Association of the United States (MHAUS) and the Department of Anesthesia at the University of Toronto sponsored a Scientific Conference on November 1–2, 2013 in Toronto, Canada. The multidisciplinary group of experts, including clinicians, geneticists and physiologists involved in research related to malignant hyperthermia (MH), shared new insights into the pathophysiology of type-1 ryanodine receptor gene (RYR1)-linked diseases, as well as the relationship between MH and “awake MH” conditions, such as exertional rhabdomyolysis (ER) and exertional heat illness (EHI). In addition, the molecular genetics of MH, and clinical issues related to the diagnosis and management of RYR1-linked disorders, were presented. The conference also honored Dr. David H. MacLennan for his contributions to our understanding of the genetics, pathogenesis and treatment of MH and other RYR1-related myopathies. This report represents a summary of the proceedings of this conference.
doi:10.1007/s12630-014-0227-5
PMCID: PMC4276369  PMID: 25189431
21.  Extended-Spectrum Beta-Lactamases among Enterobacter Isolates Obtained in Tel Aviv, Israel 
The extended-spectrum beta-lactamase (ESBL)-producing phenotype is frequent among Enterobacter isolates at the Tel Aviv Sourasky Medical Center, Tel Aviv, Israel. We examined the clonal relatedness and characterized the ESBLs of a collection of these strains. Clonal relatedness was determined by pulsed-field gel electrophoresis. Isoelectric focusing (IEF) and transconjugation experiments were performed. ESBL gene families were screened by colony hybridization and PCR for blaTEM, blaSHV, blaCTX-M, blaIBC, blaPER, blaOXA, blaVEB, and blaSFO; and the PCR products were sequenced. The 17 Enterobacter isolates studied comprised 15 distinct genotypes. All isolates showed at least one IEF band (range, one to five bands) whose appearance was suppressed by addition of clavulanate; pIs ranged from 5.4 to ≥8.2. Colony hybridization identified at least one family of beta-lactamase genes in 11 isolates: 10 harbored blaTEM and 9 harbored blaSHV. PCR screening and sequence analysis of the PCR products for blaTEM, blaSHV, and blaCTX-M identified TEM-1 in 11 isolates, SHV-12 in 7 isolates, SHV-1 in 1 isolate, a CTX-M-2-like gene in 2 isolates, and CTX-M-26 in 1 isolate. In transconjugation experiments with four isolates harboring blaTEM-1 and blaSHV-12, both genes were simultaneously transferred to the recipient strain Escherichia coli HB101. Plasmid mapping, PCR, and Southern analysis with TEM- and SHV-specific probes demonstrated that a single transferred plasmid carried both the TEM-1 and the SHV-12 genes. The widespread presence of ESBLs among Enterobacter isolates in Tel Aviv is likely due not to clonal spread but, rather, to plasmid-mediated transfer, at times simultaneously, of genes encoding several types of enzymes. The dominant ESBL identified was SHV-12.
doi:10.1128/AAC.49.3.1150-1156.2005
PMCID: PMC549242  PMID: 15728917
22.  DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists 
Nucleic Acids Research  2007;35(Web Server issue):W169-W175.
All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene Functional Classification Tool, the DAVID Functional Annotation Tool, the DAVID Gene ID Conversion Tool, the DAVID Gene Name Viewer and the DAVID NIAID Pathogen Genome Browser. The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bioinformatics databases. For any uploaded gene list, the DAVID Resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more. With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists.
doi:10.1093/nar/gkm415
PMCID: PMC1933169  PMID: 17576678
23.  ARE HONORS RECEIVED DURING SURGERY CLERKSHIPS USEFUL IN THE SELECTION OF INCOMING ORTHOPAEDIC RESIDENTS? 
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
24.  Prevalence of sexually transmitted pathogens among women attending a methadone clinic in Israel. 
Genitourinary Medicine  1991;67(2):133-136.
OBJECTIVE--To assess the prevalence of sexually transmitted pathogens in drug-addicted women in Tel Aviv, Israel. DESIGN--A prospective study conducted between March and July 1987. SETTING--A methadone clinic in Tel Aviv, Israel. SUBJECTS--Sixty four asymptomatic female drug addicts were studied; 38 of them were declared practising prostitutes. METHODS--Cervical specimens were obtained for cultures, and blood samples were drawn for serological tests. Demographic data and sexual histories were obtained using a standard questionnaire. RESULTS--Chlamydia trachomatis was detected in the cervix of 25% of women; 98% had antibody titres (greater than 1:64). Mycoplasma hominis and Ureaplasma urealyticum were isolated in 57% and 65% respectively. Gardnerella vaginalis was detected in 17% of women, and herpes simplex virus was cultured from two prostitutes. Five per cent of women were carriers of HBsAg, while 57% had HBSs and/or HBc antibodies. Only one prostitute had specific treponemal antibodies. In no case were gonococci or group B streptococci isolated, and HIV serology was invariably negative. CONCLUSION--Chlamydia and genital mycoplasmas appear to be the prevailing pathogens in Israeli drug-addicted women, while gonococci and Treponema pallidum occur only rarely.
PMCID: PMC1194648  PMID: 2032707
25.  Modulation of in vitro natural cell-mediated activity against enteropathogenic bacteria by simple sugars. 
Infection and Immunity  1985;47(2):534-539.
Lymphoid cells from mouse Peyer's patches and spleens were tested in a 2-h in vitro assay for their natural activity against the enteropathogenic bacteria Salmonella typhimurium, Salmonella enteritidis, Salmonella tel aviv, and Shigella sp. X16. The antibacterial activity expressed by normal cells was detected against all the bacterial strains tested with the exception of Peyer's patch lymphocytes against S. tel aviv and splenocytes against Shigella sp. X16. To determine whether the different expression of natural antibacterial activity might be due to lectin-like proteins interacting with the saccharidic moieties of the bacterial wall, 11 simple sugars were preincubated with the effector cells before the in vitro assays. We found that some of them could block the natural antibacterial activity as well as induce antibacterial activity when this was not spontaneously expressed. Interestingly, a different panel of sugars among those employed was observed to affect the antibacterial activities for each of the above-mentioned bacterial targets and each effector cell. However, the same panel of sugars was able to block or stimulate the lymphocyte activity when bacteria with the same somatic antigens as two substrains of S. typhimurium and one strain of Salmonella schottmuelleri were employed. To further investigate the interaction between effector cells and bacteria, effector cells or Shigella sp. X16 targets were treated with proteolytic, glycolytic, and lipolytic enzymes before the in vitro assays. Furthermore, EDTA was used to analyze the role of divalent cations in this experimental system. The results obtained suggest that lectin-like proteins playing a role in this interaction are present not only on lymphocytes but also on bacteria and that divalent cations are essential for the expression of in vitro antibacterial activity.
PMCID: PMC263204  PMID: 3967926

Results 1-25 (1045)