Bioinformatics

Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been...

A pseudo-testcross pedigree is widely used for mapping quantitative trait loci (QTL) in outcrossing species, but the model for analyzing pseudo-testcross data borrowed from the inbred backcross design can only detect those QTLs that are heterozygous only in one parent. In this study, an intercross model that incorporates the high...

Bacterial autotransporters represent a diverse family of proteins that autonomously translocate across the inner membrane of Gram-negative bacteria via the Sec complex and across the outer bacterial membrane. They often possess exceptionally long N-terminal signal sequences. We analyzed 90 long signal sequences of bacterial autotransporters and members of the two-partner...

A signal transduction pathway (STP) is a cascade composed of a series of signal transferring steps, which often activate one or more transcription factors (TFs) to control the transcription of target genes. Understanding signaling pathways is important to our understanding of the molecular mechanisms of disease. Many condition-annotated pathways have...

The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here,...

Studies investigating possible associations between cytochrome P4501B1 (CYP1B1) polymorphisms and breast cancer risk have been inconsistent. We set out to ascertain whether there might be an association between polymorphisms in exon 2 (codon 119, G→T) and exon 3 (codon 432, G→C) of CYP1B1 and breast cancer in a Chinese Han...

The purpose of this analysis was to evaluate if serum levels of potential tumor markers for the diagnosis of malignant mesothelioma and lung cancer are affected by confounding factors in a surveillance cohort of workers formerly exposed to asbestos. SMRP, CA125, and CYFRA21-1 concentrations were determined in about 1,700 serum...

This study was designed to discover blood biomarkers of cancer susceptibility using invasive multiple (n = 21), single primary breast cancer (n = 21), and control subjects (n = 20). Heparinized whole blood was incubated at 37 °C for 2 hours after 0–10 Gy of radiation, then cell cycle arrest...

A variety of post-translational protein modifications (PTMs) are known to be altered as a result of cancer development. Thus, these PTMs are potentially useful biomarkers for breast cancer. Mass spectrometry, antibody microarrays and immunohistochemistry techniques have shown promise for identifying changes in PTMs. In this review, we summarize the current...

Around 80% of acute myeloid leukemia (AML) patients achieve a complete remission, however many will relapse and ultimately die of their disease. The association between karyotype and prognosis has been studied extensively and identified patient cohorts as having favourable [e.g. t(8; 21), inv (16)/t(16; 16), t(15; 17)], intermediate [e.g. cytogenetically...

Prostate cancer is the second most common cancer and the second leading cause of cancer death in men. However, prostate cancer can be effectively treated and cured, if it is diagnosed in its early stages when the tumor is still confined to the prostate. Combined with the digital rectal examination,...

No abstract provided.

Motivation: Whole genome microarrays are increasingly becoming the method of choice to study responses in model organisms to disease, stressors or other stimuli. However, whole genome sequences are available for only some model organisms, and there are still many species whose genome sequences are not yet available. Cross-species studies, where...

Automated disease surveillance systems are becoming widely used by the public health community. However, communication among non-collocated and widely dispersed users still needs improvement. A web-based software tool for enhancing user communications was completely integrated into an existing automated disease surveillance system and was tested during two simulated exercises and...

This article describes the process of developing an advanced pharmacogenetics clinical decision support at one of the United States’ leading pediatric academic medical centers. This system, called CHRISTINE, combines clinical and genetic data to identify the optimal drug therapy when treating patients with epilepsy or Attention Deficit Hyperactivity Disorder. In...

Laurence Alpay1, John Verhoef1,2, Bo Xie3, Dov Te’eni4 and J.H.M. Zwetsloot-Schonk11Clinical Informatics Group, Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre (LUMC), Leiden, The Netherlands. 2Department of Physical Therapy, Leiden University Medical Centre (LUMC), Leiden, The Netherlands. 3College of Information Studies, University of Maryland, College Park, U.S.A. 4Faculty...

David E. Axelrod1, Naomi Miller2 and Judith-Anne W. Chapman31Department of Genetics and Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854-8082 U.S.A. 2Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, Ontario, Canada, M5G 2C4. 3NCIC Clinical Trials Group, Queen’s...

Cancer is a disease associated with the deregulation of multiple gene networks. Microarray data has permitted researchers to identify gene panel markers for diagnosis or prognosis of cancer but these are not sufficient to make specific mechanistic assertions about phenotype switches. We propose a strategy to identify putative mechanisms of...

When confronted with a small sample, feature-selection algorithms often fail to find good feature sets, a problem exacerbated for high-dimensional data and large feature sets. The problem is compounded by the fact that, if one obtains a feature set with a low error estimate, the estimate is unreliable because training-data-based...

When confronted with a small sample, feature-selection algorithms often fail to find good feature sets, a problem exacerbated for high-dimensional data and large feature sets. The problem is compounded by the fact that, if one obtains a feature set with a low error estimate, the estimate is unreliable because training-data-based...

Multi-class cancer classification based on microarray data is described. A generalized output-coding scheme based on One Versus One (OVO) combined with Latent Variable Model (LVM) is used. Results from the proposed One Versus One (OVO) output- coding strategy is compared with the results obtained from the generalized One Versus All...

The recently published article by Wang, and commented on by Ertel in this journal, describes development of a method, named the Bimodality Index, to objectively identify and rank meaningful and reliable bimodal patterns from large-scale gene expression datasets. This is an important step because genes with a bimodal distribution may...

Certain species of the fungal genus Trichoderma are potent mycoparasites and are used for biological control of fungal diseases on agricultural crops. In Trichoderma, whole-genome sequencing reveal between 20 and 36 different genes encoding chitinases, hydrolytic enzymes that are involved in the mycoparasitic attack. Sequences of Trichoderma chitinase genes chi18-5,...

The sizes of the protein databases are growing rapidly nowadays, thus it becomes increasingly important to cluster protein sequences only based on sequence information. In this paper we improve the similarity measure proposed by Kelil et al, then cluster sequences using the Affinity propagation (AP) algorithm and provide a method...

Achievement of the best balance between the accuracy and efficiency is always an important issue when searching a tree space of large data sets. In the 5th issue in 2009, Rodrigo et al used bootstrapped topologies as fixed genealogies to distribute an MCMC analysis across a cluster of computers, resulting...

The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155...

The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155...

A method has been developed whereby diffusion and exchange in micro cellular structures in the human brain are correlated to produce a new type of image contrast leading to determination of water exchange rates in vivo. The diffusion method relies on differential apparent diffusion coefficients as detectable nuclei exchange between...

A. Huda1,2, R.K. Gupta3, N. Rajakumar2 and M.A. Thomas21Department of Physics, California State University, Fresno, CA 93740. 2Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095. 3Department of Radiology, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, India.AbstractA spectrum of neuropsychiatric abnormalities caused...

Marc Dhenain1,2,3 1CEA, DSV, I2BM, SHFJ, MIRCen Program, 4 Place du Général Leclerc, 91401 OrsayCedex, France. 2CNRS, URA 2210, 4 Place du Général Leclerc, 91401 Orsay Cedex, France. 3CEA, DSV, I2BM, NEUROSPIN, Centre CEA de Saclay, Bât. 145, 91191 Gif sur Yvette, France. Abstract Alzheimer’s disease is...

Uma Sharma, Rani Gupta Sah and Naranamangalam R. Jagannathan Department of NMR and MRI Facility, All India Institute of Medical Sciences, New Delhi—110029, India. Abstract Breast cancer is a major health problem in women and early detection is of prime importance. Breast magnetic resonance imaging (MRI) provides...