Zhen-Yu Yan

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We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted FFLs by their explanatory power to(More)
We perform molecular dynamics simulations to investigate the relationship between structural order and waterlike dynamic and thermodynamic anomalies in spherically symmetric potentials having either one or two characteristic length scales. Structural order is characterized by translational and orientational order parameters. We find that (i) dynamic and(More)
BACKGROUND Immune activation is a strong predictor of disease progression in HIV infection. Combinatorial plasma biomarker signatures that represent surrogate markers of immune activation in both viremic and aviremic HIV patients on combination antiretroviral therapy (cART) have not been defined. Here, we identify a plasma inflammatory biomarker signature(More)
We investigate the equation of state, diffusion coefficient, and structural order of a family of spherically symmetric potentials consisting of a hard core and a linear repulsive ramp. This generic potential has two characteristic length scales: the hard and soft core diameters. The family of potentials is generated by varying their ratio, lambda. We find(More)
We perform molecular dynamics simulations of water using the five-site transferable interaction potential (TIP5P) model to quantify structural order in both the first shell (defined by four nearest neighbors) and second shell (defined by twelve next-nearest neighbors) of a central water molecule. We find that the anomalous decrease of orientational order(More)
Using the five-site transferable intermolecular potential (TIP5P) we perform molecular dynamics simulations to investigate the relationship between the excess entropy and anomalies of water. We find that the two-body excess entropy is an ideal quantity to predict the regions of structural, dynamic, and thermodynamic anomalies of water in its(More)
BACKGROUND & OBJECTIVE Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium. Consequently, there is(More)
Multiple myeloma is a hematological cancer of plasma B cells and remains incurable. Two major subtypes of myeloma, hyperdiploid MM (HMM) and non-hyperdiploid MM (NHMM), have distinct chromosomal alterations and different survival outcomes. Transcription factors (TrFs) have been implicated in myeloma oncogenesis, but their dysregulation in myeloma subtypes(More)
Nodose ganglia are composed of A-, Ah- and C-type neurons. Despite their important roles in regulating visceral afferent function, including cardiovascular, pulmonary, and gastrointestinal homeostasis, information about subtype-specific expression, molecular identity, and function of individual ion transporting proteins is scarce. Although experiments(More)
In the present study, human umbilical cord blood mesenchymal stem cells were injected into a rat model of traumatic brain injury via the tail vein. Results showed that 5-bromodeoxyuridine-labeled cells aggregated around the injury site, surviving up to 4 weeks post-transplantation. In addition, transplantation-related death did not occur, and neurological(More)