Correlation of droplet elasticity and volume fraction effects on emulsion dynamics.

The rheological properties of emulsions are of considerable importance in a diverse range of scenarios. Here we describe a superposition of the effects of droplet elasticity and volume fraction on the dynamics of emulsions. The superposition is governed by physical interactions between droplets, and provides a new mechanism for modifying the flow behavior of emulsions, by controlling the elasticity of the dispersed phase.

Controlling orientational order in block copolymers using low-intensity magnetic fields.

The interaction of fields with condensed matter during phase transitions produces a rich variety of physical phenomena. Self-assembly of liquid crystalline block copolymers (LC BCPs) in the presence of a magnetic field, for example, can result in highly oriented microstructures due to the LC BCP's anisotropic magnetic susceptibility. We show that such oriented mesophases can be produced using low-intensity fields (<0.

Dynamics of a thermo-responsive microgel colloid near to the glass transition.

In a previous study, we used diffusing wave spectroscopy (DWS) to investigate the aging signatures of a thermo-sensitive colloidal glass and compared them with those of molecular glasses from the perspective of the Kovacs temperature-jump, volume recovery experiments [X. Di, K. Z.

Evaluation of heterogeneity measures and their relation to the glass transition.

For most phase transitions, dynamic slowdown is accompanied by a static structure change. However, in the case of the supercooled liquid, which is a special liquid state below the melting temperature, one observes pronounced dynamic slowdown, i.e.

Gelation via ion exchange in discotic suspensions.

The phase behavior of charged disk suspensions displays a strong dependence on ionic strengths, as the interplay between excluded volume and electrostatic interactions determines the formation of glasses, gels, and liquid crystal states. The various ions in natural soil or brine, however, could present additional effects, especially considering that most platelet structures bear a momentous ion-exchange capacity. Here we observed how ion exchange modulates and controls the interaction between individual disks and leads to unconventional phase transitions from isotropic gel to nematic gel and finally to nematic liquid crystals.

Signatures of structural recovery in colloidal glasses.

Colloids near the glass concentration are often taken as models for molecular glasses. Yet, an important aspect of the dynamics of molecular glasses, structural recovery, has not been elucidated in colloids. We take advantage of a thermosensitive colloidal suspension to study the structural recovery after concentration jumps by using diffusing wave spectroscopy.

Alternative base calling method for resequencing microarrays.

Analysis of high density oligonucleotide arrays for resequencing requires methods which are highly robust and accurate. We introduce an alternative base calling method built upon ABACUS with the particular advantage of achieving a very low rate for false positive detection of heterozygotes.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Background: DNA copy number alterations are one of the main characteristics of the cancer cell karyotype and can contribute to the complex phenotype of these cells. These alterations can lead to gains in cellular oncogenes as well as losses in tumor suppressor genes and can span small intervals as well as involve entire chromosomes. The ability to accurately detect these changes is central to understanding how they impact the biology of the cell.

Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.

Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.

Motivation: A high density of single nucleotide polymorphism (SNP) coverage on the genome is desirable and often an essential requirement for population genetics studies. Region-specific or chromosome-specific linkage studies also benefit from the availability of as many high quality SNPs as possible. The availability of millions of SNPs from both Perlegen and the public domain and the development of an efficient microarray-based assay for genotyping SNPs has brought up some interesting analytical challenges.

MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays.

We have developed a locus-specific DNA target preparation method for highly multiplexed single nucleotide polymorphism (SNP) genotyping called MARA (Multiplexed Anchored Runoff Amplification). The approach uses a single primer per SNP in conjunction with restriction enzyme digested, adapter-ligated human genomic DNA. Each primer is composed of common sequence at the 5' end followed by locus-specific sequence at the 3' end.

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome.

Algorithms for large-scale genotyping microarrays.

Motivation: Analysis of many thousands of single nucleotide polymorphisms (SNPs) across whole genome is crucial to efficiently map disease genes and understanding susceptibility to diseases, drug efficacy and side effects for different populations and individuals. High density oligonucleotide microarrays provide the possibility for such analysis with reasonable cost. Such analysis requires accurate, reliable methods for feature extraction, classification, statistical modeling and filtering.

Large-scale genotyping of complex DNA.

Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals. Public efforts have so far identified over two million common human SNPs; however, the scoring of these SNPs is labor-intensive and requires a substantial amount of automation. Here we describe a simple but effective approach, termed whole-genome sampling analysis (WGSA), for genotyping thousands of SNPs simultaneously in a complex DNA sample without locus-specific primers or automation.