Bioinformatics Commons^™

Hemo: A Sustainable Multi-Objective Evolutionary Optimization Framework, Jianjun Hu, K. Seo, Z. Fan, R. Rosenberg, E. Goodman

Jianjun Hu

No abstract provided.

Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding, Jianjun Hu, F. Zhang

Jianjun Hu

No abstract provided.

Proteomic Characterization Of Her-2/Neu-Overexpressing Breast Cancer Cells, Hexin Chen, G. Pimienta, Y. Gu, X. Sun, Jianjun Hu, M.-S. Kim, R. Chaerkady, M. Gucek, R. Cole, S. Sukumar, A. Pandey

Jianjun Hu

No abstract provided.

Dnabind: A Hybrid Algorithm For Structure-Based Prediction Of Dna-Binding Residues By Combining Machine Learning- And Template-Based Approaches, R. Liu, Jianjun Hu

Jianjun Hu

No abstract provided.

Computational Identification Of Post-Translational Modification-Based Nuclear Import Regulations By Characterizing Nuclear Localization Signal-Import Receptor Interaction, J.-R. Lin, Z. Liu, Jianjun Hu

Jianjun Hu

No abstract provided.

Subcellular Localization Of Marine Bacterial Alkaline Phosphatases, H. Luo, Ronald Benner, R. Long, Jianjun Hu

Jianjun Hu

Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), …

Integrative Disease Classification Based On Cross-Platform Microarray Data, C.-C. Liu, Jianjun Hu, M. Kalakrishnan, H. Huang, X. Zhou

Jianjun Hu

Background Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generated by different laboratories or with different platforms can not be compared directly due to systematic variations. This issue has severely limited the practical use of microarray-based disease classification. Results In this study, we tested the feasibility of disease classification by integrating the large amount of heterogeneous microarray datasets from the public microarray repositories. Cross-platform data compatibility is created by deriving expression log-rank ratios within datasets. One may then compare vectors of log-rank …

Scored Protein-Protein Interaction To Predict Subcellular Localizations For Yeast Using Diffusion Kernel, A. Mondal, Jianjun Hu

Jianjun Hu

No abstract provided.

Minimalist Ensemble Algorithms For Genome-Wide Protein Localization Prediction, J.-R. Lin, A. Mondal, R. Liu, Jianjun Hu

Jianjun Hu

Background Computational prediction of protein subcellular localization can greatly help to elucidate its functions. Despite the existence of dozens of protein localization prediction algorithms, the prediction accuracy and coverage are still low. Several ensemble algorithms have been proposed to improve the prediction performance, which usually include as many as 10 or more individual localization algorithms. However, their performance is still limited by the running complexity and redundancy among individual prediction algorithms. Results This paper proposed a novel method for rational design of minimalist ensemble algorithms for practical genome-wide protein subcellular localization prediction. The algorithm is based on combining a feature …

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara

Jianjun Hu

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy …

Seqnls: Nuclear Localization Signal Prediction Based On Frequent Pattern Mining And Linear Motif Scoring, J.-R. Lin, Jianjun Hu

Jianjun Hu

Nuclear localization signals (NLSs) are stretches of residues in proteins mediating their importing into the nucleus. NLSs are known to have diverse patterns, of which only a limited number are covered by currently known NLS motifs. Here we propose a sequential pattern mining algorithm SeqNLS to effectively identify potential NLS patterns without being constrained by the limitation of current knowledge of NLSs. The extracted frequent sequential patterns are used to predict NLS candidates which are then filtered by a linear motif-scoring scheme based on predicted sequence disorder and by the relatively local conservation (IRLC) based masking. The experiment results on …

Integrative Missing Value Estimation For Microarray Data, Jianjun Hu, H. Li, M. Waterman, X. Zhou

Jianjun Hu

Background Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. Results We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets …

Robust And Efficient Genetic Algorithms With Hierarchical Niching And A Sustainable Evolutionary Computation Model, Jianjun Hu, E. Goodman

Jianjun Hu

No abstract provided.

Emd: An Ensemble Algorithm For Discovering Regulatory Motifs In Dna Sequences, Jianjun Hu, Y. Yang, D. Kihara

Jianjun Hu

Background Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms. Results We proposed a novel clustering-based ensemble algorithm named EMD for de novo motif discovery by combining multiple predictions from multiple runs of one or more base component algorithms. The ensemble approach is …

Computational Prediction Of Heme-Binding Residues By Exploiting Residue Interaction Network, R. Liu, Jianjun Hu

Jianjun Hu

Computational identification of heme-binding residues is beneficial for predicting and designing novel heme proteins. Here we proposed a novel method for heme-binding residue prediction by exploiting topological properties of these residues in the residue interaction networks derived from three-dimensional structures. Comprehensive analysis showed that key residues located in heme-binding regions are generally associated with the nodes with higher degree, closeness and betweenness, but lower clustering coefficient in the network. HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features. The results showed that incorporation of network-based …

Prediction Of Discontinuous B-Cell Epitopes Using Logistic Regression And Structural Information, R. Liu, Jianjun Hu

Jianjun Hu

Computational prediction of discontinuous B-cell epitopes remains challenging, but it is an important task in vaccine design. In this study, we developed a novel computational method to predict discontinuous epitope residues by combining the logistic regression model with two important structural features, B-factor and relative accessible surface area (RASA). We conducted five-fold cross-validation on a representative dataset composed of antigen structures bound with antibodies and independent testing on Epitome database, respectively. Experimental results indicate that besides the well-known RASA feature, B-factor can also be used to identify discontinuous epitopes. Furthermore, these two features are complementary and their combination can remarkably …

Genome Sequence Of Lactobacillus Pentosus Kca1: Vaginal Isolate From A Healthy Premenopausal Woman, Kingsley Anukam

Kingsley C Anukam

The vaginal microbiota, in particular Lactobacillus species, play an important role in female health through modulation of immunity, countering pathogens and maintaining a pH below 4.7. We report the isolation and genome sequence of Lactobacillus pentosus strain KCA1 (formally known as L. plantarum) from the vagina of a healthy Nigerian woman. The genome was sequenced using Illumina GA II technology. The resulting 16,920,226 paired-end reads were assembled with the Velvet tool. Contigs were annotated using the RAST server, and manually curated. A comparative analysis with the available genomes of L. pentosus IG1 and L. plantarum WCFS1 showed that over 15% …

Bloom-Forming Cyanobacteria And Other Phytoplankton In Northern New Jersey Freshwater Bodies, Tin-Chun Chu, Matthew Rienzo

Tin-Chun Chu, Ph.D.

No abstract provided.

Proteomic Analysis Of 17Β-Estradiol Degradation By Stenotrophomonas Maltophilia, Zhongtian Li

Z Li

Microbial degradation plays a critical role in determining the environmental fate of steroid hormones, such as 17β-estradiol (E2). The molecular mechanisms governing the microbial transformation of E2 and its primary degradation intermediate, estrone (E1), are largely unknown. The objective of this study was to identify metabolism pathways that might be involved in microbial estrogen degradation. To achieve the objective, Stenotrophomonas maltophilia strain ZL1 was used as a model estrogen degrading bacterium and its protein expression level during E2/E1 degradation was studied using quantitative proteomics. During an E2 degradation experiment, strain ZL1 first converted E2 to E1 stoichiometrically. At 16 h …

Removing 17Β-Estradiol From Drinking Water In A Biologically Active Carbon (Bac) Reactor Modified From A Granular Activated Carbon (Gac) Reactor, Zhongtian Li

Z Li

Estrogenic compounds in drinking water sources pose potential threats to human health. Treatment technologies are needed to effectively remove these compounds for the production of safe drinking water. In this study, GAC adsorption was first tested for its ability to remove a model estrogenic compound, 17β-estradiol (E2). Although GAC showed a relatively high adsorption capacity for E2 in isotherm experiments, it appeared to have a long mass transfer zone in a GAC column reactor, causing an early leakage of E2 in the effluent. With an influent E2 concentration of 20 μg/L, the GAC reactor was able to bring down effluent …

Disparities In Combination Drug Therapy Use In Older Adults With Coronary Heart Disease: A Cross-Sectional Time-Series In A Nationally Representative Us Sample, Jennifer Tjia, Becky Briesacher, Dawei Xie, Jason Fu, Robert Goldberg

Jennifer Tjia

BACKGROUND: Despite evidence of effective combination drug therapy for secondary prevention of coronary heart disease (CHD), older adults with this condition remain undertreated.

OBJECTIVE: To describe time trends (1992-2003) in the adoption of combination cardiac drug therapies (beta-blockers [beta-adrenoceptor antagonists], ACE inhibitors or angiotensin II type 1 receptor antagonists [angiotensin receptor blockers; ARBs], and lipid-lowering agents) among older adults in the US with CHD and to identify factors associated with not using combination therapy.

METHODS: The study took the form of a cross-sectional time-series. The study population consisted of a nationally representative sample of adults aged >or=65 years with CHD …

Micrornas Are Independent Predictors Of Outcome In Diffuse Large B-Cell Lymphoma Patients Treated With R-Chop, Goldi Kozloski

Goldi A Kozloski

Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer

Mark R Segal

Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …

Mechanistic And Signaling Analysis Of Muc4-Erbb2 Signaling Module: New Insights Into The Mechanism Of Ligand-Independent Erbb2 Activity, Goldi Kozloski

Goldi A Kozloski

Body Mass Index, Treatment Practices, And Mortality In Patients With Acute Heart Failure, Timothy Fitzgibbons, Olga Hardy, Darleen Lessard, Joel Gore, Jorge Yarzebski, Robert Goldberg

Jorge L. Yarzebski

OBJECTIVES: Obesity is associated with an increased risk of heart failure (HF). Among patients presenting with acute HF, however, differences in clinical characteristics, treatment regimens, and short-term prognosis of varying weights are largely unknown, particularly from a broader population-based perspective. METHODS: A total of 3722 patients admitted with acute HF to 11 greater Worcester (Massachusetts, USA) hospitals during 1995 and 2000 were categorized as being lean (n = 216), normal weight (n = 1465), overweight (n = 1007), or obese (n = 1034) at the time of hospitalization. RESULTS: Obese patients with decompensated HF were significantly younger (mean age = …

Changes Over Time In The Use Of Aspirin In Patients Hospitalized With Acute Myocardial Infarction (1975 To 1997): A Population-Based Perspective, Elizabeth Jackson, Ramya Sivasubramian, Frederick Spencer, Jorge Yarzebski, Darleen Lessard, Joel Gore, Robert Goldberg

Jorge L. Yarzebski

OBJECTIVE: The purpose of this study was to examine 2 decade-long trends in the use of aspirin and associated outcomes in patients hospitalized with acute myocardial infarction. BACKGROUND: Aspirin has been shown to be beneficial in the secondary prevention of AMI. However, little is known about changes over time in the use of aspirin in patients hospitalized with AMI and associated outcomes, particularly from a more generalizable population-based perspective. METHODS: We examined trends in aspirin use and hospital and long-term outcomes in 9336 metropolitan Worcester, Mass, residents hospitalized with validated AMI in all area hospitals between 1975 and 1997. RESULTS: …

Thirty-Year Trends (1975-2005) In The Magnitude, Patient Characteristics, And Hospital Outcomes Of Patients With Acute Myocardial Infarction Complicated By Ventricular Fibrillation, Robert Goldberg, Jorge Yarzebski, Frederick Spencer, Juan Zevallos, Darleen Lessard, Joel Gore

Jorge L. Yarzebski

Limited contemporary data are available describing the incidence rates, hospital prognosis, and factors associated with the occurrence of ventricular fibrillation (VF) in patients hospitalized with acute myocardial infarction (AMI). The objectives of our study were to examine 3-decade-long trends (1975 to 2005) in the magnitude, predictors, and hospital case-fatality rates associated with VF in residents of a large New England metropolitan area hospitalized at all area medical centers with an uncomplicated AMI. The study population consisted of 7,472 residents of the Worcester (Massachusetts) metropolitan area hospitalized with an uncomplicated AMI in 15 annual periods from 1975 to 2005. The overall …

Temporal Trends (1975 Through 1990) In The Incidence And Case-Fatality Rates Of Primary Ventricular Fibrillation Complicating Acute Myocardial Infarction. A Communitywide Perspective, David Chiriboga, Jorge Yarzebski, Robert Goldberg, Joel Gore, Joseph Alpert

Jorge L. Yarzebski

BACKGROUND: As part of a population-based study of acute myocardial infarction, we examined changes over time in the incidence and in-hospital case-fatality rates of primary ventricular fibrillation complicating acute myocardial infarction. METHODS AND RESULTS: Patients with validated acute myocardial infarction hospitalized at 16 hospitals in the Worcester, Mass, metropolitan area between 1975 and 1990 comprised the study sample. During the 15-year study period, 5.1% of patients developed primary ventricular fibrillation in the setting of uncomplicated acute myocardial infarction, with this rate remaining relatively constant over time. Both age- and multivariable-adjusted analyses showed no significant trend in the incidence rates of …

Temporal Trends And Associated Factors Of Inpatient Cardiac Rehabilitation In Patients With Acute Myocardial Infarction: A Community-Wide Perspective, Frederick Spencer, Bobak Salami, Jorge Yarzebski, Darleen Lessard, Joel Gore, Robert Goldberg

Jorge L. Yarzebski

PURPOSE: Cardiac rehabilitation (CR) has been shown to be an important therapeutic intervention after the development of acute myocardial infarction (AMI), but historically has been underused. Inpatient CR often represents cardiac patients' first exposure to risk factor modification education and acts as a gateway to outpatient programs. METHODS: The authors performed a longitudinal study of the use of inpatient CR in 5204 Worcester residents hospitalized with validated AMI in seven 1-year periods between 1986 and 1997. RESULTS: The overall rate of referral to inpatient CR was 68%, with a slight decline in use to less than 60% in the authors' …

Communitywide Trends In The Use And Outcomes Associated With Beta-Blockers In Patients With Acute Myocardial Infarction: The Worcester Heart Attack Study, Helme Silvet, Frederick Spencer, Jorge Yarzebski, Darleen Lessard, Joel Gore, Robert Goldberg

Jorge L. Yarzebski

BACKGROUND: Despite the benefits associated with beta-blocker therapy in patients with acute myocardial infarction (AMI), limited recent data are available describing the extent of use of this therapy and the associated hospital and long-term outcomes, particularly from the perspective of a population-based study. Data are also limited about the characteristics of patients with AMI who do not receive beta-blockers. This study examines more than 2 decades of trends in the use of beta-blockers in hospitalized patients with AMI. METHODS: Communitywide study of 10,374 patients hospitalized with confirmed AMI in all metropolitan Worcester hospitals during 12 annual periods between 1975 and …