Biological Sciences and Bioengineering
Organization: Sabanci University
The Biological Sciences and Bioengineering Program at Sabancı University have thirteen faculty members who conduct research on modern biological problems. Our laboratories have modern infrastructure and cutting-edge research equipment. We are engaged in research and development projects and collaborate with researchers around the world.
Areas of expertise on this area can be listed as:
Molecular and Cellular Biology - Mammals, including humans, are equipped with various defense mechanisms both at the organismal and cellular levels. Cells ...
Organization: University of California, Irvine (UC Irvine)
Advances in biotechnology have led to the use of "designer" or synthetic genes for many medical, agricultural, and bioindustrial applications. While the use of synthetic genes is now commonplace, current methods for making these genes can limit their utility. For example, one current method for producing a synthetic gene involves making a set oligonucleotides and then ligating the oligonucleotides together in the proper order to create the full length synthetic gene. Depending on the underlying chemical synthesis error rate, approximately 1 ...
Method to Develop Mutant Protein Library
Organization: University of California, Irvine (UC Irvine)
University of California, Irvine researchers have developed a novel method to systematically develop and create a library of mutant proteins that may be optimized for microchip high throughput screening. This new method allows for greater control over the number and type of changes in a mutation library. In particular, this method allows for conditional dependencies among the mutational changes within (but not across) each mutation region of each sequence. Therefore this mutational capability is either inconvenient or impossible with other ...
Finding Functionally Active Mutants In A Mutation Sequence Space Of Biological Or Medical Importance
Organization: University of California, Irvine (UC Irvine)
Combinatorial mutagenesis and directed evolution are vast and important areas of biotechnology. Common practices involve DNA shuffling by exploiting homologous recombination, error-prone PCR, site-directed mutagenesis, and many other strategies. The main disadvantage to overcome was the lack of a systematic method of creating a series of pools of mutant variants that contain all and only a specified number of changes, from one change to two changes three and so forth upward, so that the mutant variants satisfying the selection or screen with ...
Finding Soluble Mutant Variants Of Desired Proteins
Organization: University of California, Irvine (UC Irvine)
Combinatorial mutagenesis and directed evolution are vast and important areas of biotechnology. Common practices involve DNA shuming by exploiting homologous recombination, error-prone PCR, site-directed mutagenesis, and many other strategies. The main disadvantage to overcome was the lack of a systematic method of creating a series of pools of mutant variants that contain all and only a specified number of changes, from one change to two changes to three and so forth upward, so that the mutant variants satisfying the selection or screen ...
Method for Assessing Physiological Response to Drug Target Inhibition
Organization: University of California, San Diego (UC San Diego)
UC San Diego researchers have devised a method for predicting human metabolic physiological response to protein inhibition by drugs. It allows for preliminary testing of drugs, discovery of new uses of existing drugs, and identification of genetic risk factors for drug treatments. The method can be applied to either known or untested protein-ligand interactions. A working prototype exists.
Organization: Boston University
Needle Software for Protein Threading
Organization: Boston University
Organization: Boston University
Organization: University of California, San Diego (UC San Diego)
A Non-Fluorescence based Optical Technique for Biochip Detection
Organization: University of California, Davis (UC Davis)
Measuring subtle change on the atomic level is now possible with a revolutionary technical development from University of California, Davis researchers. This technology permits the quantitative detection of: Molecular binding, Nucleic acid hybridization, Protein interaction with small as well as large molecules, Macromolecular structures changes, or Surface alterations of a few percent of one monomolecular layer. Methods and instruments are provided for measuring differences in fractional reflectivity changes between transverse electric (TE ...
Software for Peptides Identification Using Tandem Mass Spectra of Any Type
Organization: University of California, San Diego (UC San Diego)
UCSD researchers have recently upgraded a previously developed MS/MS database search software tool, MS-GF . It takes tandem mass (MS/MS) spectra and a protein sequence database as an input, and reports a set of Peptide-Spectrum Matches (PSMs) and their E-values as an output. To form the PSMs, it scores the spectra against the theoretical spectra predicted from peptides derived from the protein sequence database and finds the best-scoring peptide for each spectrum. The upgraded MS-GF includes a new scoring model to score PSMs formed by ...
DNA-Based Biomarkers For Human Stem Cells And Derivatives
Organization: University of California, Los Angeles (UCLA)
Researchers at UCLA have identified a set of novel DNA methylation signatures to reliably identify and profile both stem cells and normal cells. With this information it is possible to differentiate between embryonic stem cells, induced pluripotent stem cells and somatic cells. Due to the exquisite specificity of this system, it can be used for cell identification, isolation quality control, and molecular diagnosis. This technology has the potential to profoundly impact the fields of stem cell biology, and regenerative medicine.
Novel On-chip Microfluidics Technology
Organization: University of California, Riverside (UCR)
Researchers at UC Riverside have designed a novel operating system for droplet-based LoC’s. The new UC operating system interprets assays dynamically, eliminating costly compilation steps. The operating system enables real-time responses to live-feedback from the LoC, while ensuring that droplets in motion on the LoC do not deadlock. Similar to the popular Java programming language for web applications and Android phones, assays programmed using this system are portable from one droplet-based LoC to another within the same ...
A Novel Method for Predicting Drug-Target Interactions and Its Uses for Drug Repositioning
Organization: Georgetown University
Novel Brain Tumor Model System in the VM Mouse Strain
Organization: Boston College
Organization: Broad Institute
Organization: Broad Institute
Computer Simulation of Biomembranes Using a Coarse Grain Model
Organization: University of Pennsylvania
TechID: O2880 Many key biological processes, including membrane fusion, membrane-protein interaction, and oxidative phosphorylation, occur at the membrane level. The concept of micron size domain formation in membrane (“rafts”) has been used to explain mechanisms involving lateral lipid organization. A broader understanding of the lipid interactions at a mesoscopic level is desirable and can reveal more details in the study of biomembranes. Atomic simulation techniques have been used to model phospholipid ...
Organization: University of Rochester
Applications: This is a genetic method of accurately identifying the clinical risk of patients with genetic mutations or polymorphisms using information from protein and DNA structure. This method of risk stratification has applicability in predicting the severity of the clinical course of disease in a spectrum of conditions in which there is a genetic underpinning. Advantages: This method improves on the clinical risk stratification of cardiac patients as an example but may be applicable to other diseases. It has shown to ...
Quantitative total definition of biologically active sequence elements
Organization: Columbia Tech Ventures
Myoelectrical Control of Multiple Channels Based on Single Muscle Contractions
Organization: University of California, Davis (UC Davis)
Scientists at the University of California have developed a method to produce two or more control signals based on the electrical signals obtained from a sensor(s) mounted on the skin covering a single superficial muscle. Such signals can be used to control multiple aspects of one or more devices. Myoelectric technology uses the electrical signals generated during muscle contractions to generate external control signals1,2. These measured signals are amplified and processed to generate a desired response in an external device(s). Current ...
Atomic Force Microscopy-based Platform for Investigating Single Cell Mechanics
Organization: University of California, Davis (UC Davis)
Researchers at UC Davis have invented a new methodology to measure single cell mechanics. The new method utilizes atomic force microscopy (AFM) to perform single cell compression. Large sphere glued to the end of AFM probe compresses cell with independent displacement and force detection in wide range from 1 nN up to 50 µN. A high-resolution bright field or fluorescent microscopy guides the location of the probe and monitors the deformation of cell and cell organelles during the load cycle. Many previously developed methods probe only ...
A New Tandem-Affinity Tag for Two-Step Protein Purification under Fully Denaturing Conditions
Organization: University of California, Irvine (UC Irvine)
University of California, Irvine researchers have developed a novel tandem-affinity tag that is compatible with two-step purification under fully denaturing conditions such as 8 M urea or 6 M guanidinium. This novel tag serves as a biotinylation signal in vivo. Tagged proteins are efficiently biotinylated in vivo in both yeast and mammalian cells at a specific lysine residue present in the tag. The biotinylated protein can then be sequentially purified by Ni2 -chelate chromatography and binding to streptavidin resins.
Portable Personal Lung Function Monitor
Organization: University of California, Davis (UC Davis)
Current technology requires patients to visit doctors to test their lung function, or to use devices that are limited to only spirometry analysis (measurements of volume and speed of exhale and inhale). Researchers at the University of California have designed a device which is capable of measuring many important aspects of a patient's lung function, beyond simple spirometry, and transmitting the data not only to the user but also to the supervising physician. The device functions as a spirometer, capable of measuring things like expiratory ...
String Matching in Hardware using the FM-Index
Organization: University of California, Riverside (UCR)
String matching algorithms (or string searching algorithms) are ubiquitously used in a wide range of computer science applications such as packet routing, intrusion detection, web querying, and genome analysis. The FM-Index is a search substring that contains the Burrows-Wheeler Transform (BWT) of the text to be searched in the form of a set of numerical arrays. In software, FM-Index has successfully been used for string matching at speeds comparable to large text indices, but with the significant advantage of space ...
Organization: University of California, Davis (UC Davis)
The device operates as an ion mobility-based sensor, designed to discern individual compounds in a mixture or establish the composition of complex mixtures by measuring gas-phase ionized chemical species without any additional sample preparation. The device separates any gas-phase ionized chemical species. The miniature drift tube and sensing component are manufactured using microfabrication techniques, and the ion source in interfaced to the microfabricated device. A spatially-alternating electric field with varying ...
Organization: University of California, Irvine (UC Irvine)
Researchers at the University of California, Irvine, have developed a method for the computational optimization of DNA sequences that encode their own correct self-assembly. Scores of short overlapping synthetic oligonucleotides are designed to hybridize correctly with great efficiency at a high temperature, while all competing nonproductive hybridization events are identified and disfavored. Sequence properties are optimized using a formal heuristic search. Long strings of mixed coding, regulatory, and intergenic regions may be hybridized ...
Organization: University of California, Davis (UC Davis)
Cell cultures can be an effective and efficient model for drug discovery, but there is a need for culture-based methods to assess drug effects on a cellular system as a surrogate for a complex tissue. Researchers at the University of California, Davis have invented a method for analyzing the volatile and non-volatile biomarker profile(s) released from cell line cultures in situ in order to link changes in biomarkers to alterations of certain metabolic pathways. In more advanced versions, cell line mixtures (co-cultures) can be created that ...
Flexible And Tunable Plasmonic Nanostructures
Organization: University of California, Davis (UC Davis)
Researchers at the University of California Davis have developed a novel method for preparation of flexible and tunable plasmonic nanostructures.Structure properties of these bowl-shaped nano-voids were characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM).Plasmonic properties were characterized via UV/Vis absorption spectroscopy, dark field microscopy, and surface-enhanced Raman spectroscopy (SERS). Two plasmonic absorption maximawere observed for all nanostructures corresponding to surface plasmons of the ...
Organization: University of California, San Diego (UC San Diego)
This invention provides a new approach for fabricating high-density nano-arrays for bio-molecules. Researchers used glass slides derivatized with functional groups, then coated them with a thin layer of photo-resist. Conventional photolithography is then used to create high-density wells of sub-micron dimension into which nano-particles conjugated to a single DNA clone are allowed to self-assemble. The small size of the wells prevents more than one molecule from attaching in any given well. The nano-particles remain fixed in their wells ...
Methods and Systems for Direct Sequencing of Single DNA Molecules
Organization: University of California, San Diego (UC San Diego)
Scientists at UC San Diego have discovered a method for the direct sequencing of single DNA molecules by monitoring the dynamic conformational changes of the DNA or RNA polymerase when each base is incorporated into the extending primer hybridized to the DNA template in the DNA synthesis or RNA transcription process. The method enables direct real-time sequencing of single DNA molecules from genomic DNA at the speed and accuracy of the natural DNA polymerases using native nucleotides. The method is called READS Genome Technology (READS: ...
Gene Knockout And Replacement In Stem Cells
Organization: University of California, Irvine (UC Irvine)
It is often advantageous to ascertain the biological purpose of a gene product by "knocking out" that gene and observing the phenotypic consequence(s). This is most often accomplished in whole animal experiments that are costly and take long periods of time related to the gestation period of the animal system. Here we divulge a system where this goal can be accomplished in a short period of time in laboratory cultured animal cells. This method is enabled by the fact that every sequence region of a gene optimized using UCI’s proprietary ...
Converting Genomic Protein Sequences into Music
Organization: University of California, Los Angeles (UCLA)
Researchers at UCLA have developed a method of converting amino acid sequences into musical notes in a way that avoids the awkward sounds resulting from a simple 20 note scale in which each amino acid is assigned to one of 20 notes. This new method involves a reduced 13 note scale based on hydrophobicity and pairing of like amino acids, and using three-note chords to differentiate between members of amino acid pairs. Rhythm was added according to the codon distribution used in the genome-encoded protein sequence, allowing each amino acid to ...
Software Method for Optimization of Protein Production Rates
Organization: University of California, San Francisco (UCSF)
Ultrasensitive Surface Plasmon Biosensing
Organization: University of California, Irvine (UC Irvine)
Researchers in UCI’s Chemistry Department have developed a novel detection method that utilizes a combination of gold nanoparticles and surface plasmon coupled gold gratings to create an ultra sensitive surface bioaffinity sensor. By combining the opticaloptical properties of gold nanoparticles that are adsorbed onto the grating surface in the presence of a biomolecule target and the optical properties of planar surface Plasmon polaritons generated on micron-scale gold gratings they have achieved enhanced sensitivity that is over 100 ...
REGULATION OF GENE EXPRESSION IN PLANTS USING ALTERNATIVE SPLICING
Organization: University of California, Berkeley (UC Berkeley)
METHOD FOR EXTENSION OF READ LENGTHS FOR ULTRA HIGH-THROUGHPUT SEQUENCING
Organization: University of California, San Francisco (UCSF)
Organization: University of California, Los Angeles (UCLA)
The invention provides a novel way to determine the variables and the specific state of each variable that altogether exert a desirable and optimal effect on a system, such as a population of cells, without having to investigate the details of the internal process of this system (e.g., how each variable affects cellular behavior). This approach, therefore, obviates the need to run a large number of tests, thereby reducing the amount of time and resources required for this goal. Specifically, the physical device that embodies the inventive ...
Non-invasive Assessment Of Intracranial Pressure
Organization: University of California, Los Angeles (UCLA)
Researchers at UCLA have developed a novel, non-invasive protocol for the measurement of ICP. It makes use of current transcranial Doppler (TCD) devices to measure cerebral blood flow velocity (CBFV). CBF information is gathered and used in conjunction with a database and proprietary algorithm to assess ICP, non-invasively. The algorithm used in the invention improves upon current non-invasive ICP protocols and can potentially complement them as well.Advantageously, existing manufacturing processes for TCD equipment do not need to be altered. ...
HESA: Hepatic Encephalopathy Screening Algorithm
Organization: University of California, San Diego (UC San Diego)
This is a unique algorithm presented on a Grading Sheet which can be used to calculate the hepatic encephalopathy grade. The clinical assessments of the patients are performed according to commonly available clinical grading tables and the results are recorded on the HESA Grading Sheet. Next, the neuropsychological assessments are administered and the cognitive results recorded. To determine the final HE grade, one starts at the top of the grading sheet and proceeds downward until the appropriate grade is found.
Method for Identifying Drug Targets Using Sequence Data
Organization: University of California, San Diego (UC San Diego)
Horizontal gene transfer is defined as the movement of genetic material between phylogenetically unrelated organisms by mechanisms other than parent to progeny inheritance. Any biological advantage provided to the recipient organism by the transferred DNA creates selective pressure for its retention in the host genome. Horizontal transmission is now considered a major factor in the process of environmental adaptation, for both individual species and entire microbial populations. These adaptations can include acquisition of ...
Organization: University of California, San Diego (UC San Diego)
This approach abandons the classical "overlap - layout - consensus" approach in favor of a new graph approach that, for the first time, resolves the problem of repeats in fragment assembly. The graph approach, in contrast to the Celera assembler, does not mask repeats but uses them instead as a powerful fragment assembly tool. The software also works with 454 contigs. For general information about the EULER project see Pevzner, et al, PNAS, 98, 2001 and http://nbcr.sdsc.edu/euler/. Site License.
Organization: University of California, San Diego (UC San Diego)
Researchers at UCSD have produced bioinformatics middleware for working with protein and nucleic acid macromolecular structure data stored in the new standard mmCIF format now being supported by the Protein Data Bank. The software will be very useful to researchers in basic and applied research in biology, biochemistry, pharmacology, medical research, molecular biology and protein ...
Organization: University of California, San Diego (UC San Diego)
Researchers at UCSD have come up with efficient software for data mining and statistical modeling of biodiversity data. This new technique for interrogating large datasets is scalable, parallelizable, and easily adaptable to other fields of use. See also http://biodi.sdsc.edu/ww_home.html and http://biodi.sdsc.edu/Visual/ww_poster.pdf
New Method for Similarity Search with Well-Characterized Statistics
Organization: University of California, San Diego (UC San Diego)
Similarity search methods are important for data mining in many fields, such as biology, finance, and artificial intelligence. In molecular biology, for example, computer-assisted sequence comparison is widely recognized as an essential analytical tool. The quality of an alignment is usually characterized by an alignment score. Statistical significance (e.g., a p-or E- value) needs ...
The Equalizer: DNA Array Analysis Software for Data Normalization
Organization: University of California, San Diego (UC San Diego)
The equalizer is a custom application that uses rank-order similarity in gene expression intensity to construct non-linear equalization vectors that are then used to linerize the data matrix to a consistent slope of 1. In addition, the equalizer rationally eliminates "negative" values of expression seen in Affymetrix data. Use of the equalizer greatly facilitates downstream data analysis. This software has been used for Affymetrix chip analysis but has applications to other microarray systems as well. See also: Robert O. Stuart, Kevin ...
Family Pairwise Search v1.0 Software
Organization: University of California, San Diego (UC San Diego)
Family Pairwise Search (FPS) is a method for scoring a single biological sequence against a family of sequences. FPS compares pairs of sequences and then combines the pairwise scores into an overall score for the match of the single sequence to the family of sequences. FPS operates in two modes. In the single-sequence mode, FPS compares a single query sequence to a library of ...
Organization: University of California, San Diego (UC San Diego)
A software toolkit for building motif-based hidden Markov models ("HMM") of families of related DNA or protein sequences. It combines multiple motif models created by MEME into a single HMM. This HMM can be trained (by the software) via expectation-maximization, and the resulting trained model can be used to produce a motif based multiple ...
Predictive Markers Of Response to Dasatinib in Human Colon Cancer
Organization: University of California, Los Angeles (UCLA)
Investigators at the UCLA David Geffen School of Medicine have identified predictive markers that can identify human colon cancer cell lines that are likely to respond to dasatinib or to other similar kinase inhibitors. A group of genes have been identified whose expression is higher in cell lines that are sensitive to dasatinib than in those who are resistant.
High-sensitivity Angular Interferometer
Organization: University of California, Berkeley (UC Berkeley)
A Drift-Corrected, High-Resolution Optical Trap
Organization: University of California, Berkeley (UC Berkeley)
Organization: University of California, San Diego (UC San Diego)
UC San Diego inventors have developed an approach for the construction of dynamic genome-scale mathematical models and their governing equations, which can be used to build and analyze dynamic models of biological networks and to predict responses to environmental and genetic perturbations.
Genome-Scale Reconstruction Of Human Metabolism
Organization: University of California, San Diego (UC San Diego)
Human genomic information (NCI Build 35) and over 50 years of legacy data were manually reconstructed to yield a global human metabolic network, which was mathematically represented as an in silico model. This was used to compute allowable network states under governing chemical and genetic constraints. The product of this endeavor (“Recon 1”) is a comprehensive reconstruction of human metabolism, which was validated by five iterative rounds of reconstruction and simulation of 288 known metabolic functions found in a variety ...
Methods for High Sensitivity Detection of Deletions from Genomic DNA
Organization: University of California, San Diego (UC San Diego)
Researchers at the UC San Diego have developed a proprietary method to detect chromosomal gene deletions and map their breakpoints in biological samples. This method is based on the fact that a positive PCR signal can be obtained when DNA fragments otherwise too distant in the genome are brought close together by loss of nucleotides from a chromosomal region. Genomic DNA obtained from biopsy tissue is amplified by multiplex PCR and specific breakpoints can be identified by analyzing the PCR product(s) obtained. Advantages of this simple and ...
Privacy Preserving Genomic Mobile Device Computational Infrastructure
Organization: University of California, Irvine (UC Irvine)
UCI researchers have developed a novel infrastructure where human genomes can be safe stored in a database or cloud in a secure and private manner which can later be downloaded to mobile devices enabling individuals to perform a variety of genetic based tests. In the medical realm users can interact with points of health care ranging from hospitals to pharmacies to personal physicians. While in the social realm private and secure peer-to-peer transactions include paternity testing, relatedness (are you my 3rd cousin?) and other genetic ...
Second Harmonic Optical Coherence Tomography
Organization: University of California, Irvine (UC Irvine)
Optical coherence tomography (OCT) is an emerging imaging technology that provides in-vivo high-resolution, cross-sectional images of biological tissues. Using coherence gating technique, OCT is capable of detecting the backscattered light from highly scattering tissues at depths of 2-3 mm. OCT imaging contrast originates from the inhomogeneities of sample scattering properties that are linearly dependent on sample refractive indices. In many instances such as pathological processes in tissue, changes in sample linear scattering properties ...
<h2>Small Molecules That Test Positive For P53 "Cancer Rescue" Activity</h2>
Organization: University of California, Irvine (UC Irvine)
UC Irvine biologists, chemists and computer scientists have identified an elusive pocket on the surface of the p53 protein that can be targeted by cancer-fighting drugs. The finding heralds a new treatment approach, as mutant forms of this protein are implicated in nearly 40 percent of diagnosed cases of cancer, which kills more than half a million Americans each year. In a study published online this week in Nature Communications, the UC Irvine researchers describe how they employed a computational method to capture the various shapes of the ...
Inclined Single Plane Imaging Microscope Box (iSPIM Box)
Organization: University of California, Irvine (UC Irvine)
iSPIM Box is intended for imaging biological samples with a fast volumetric acquisition and offers numerous advantages over existing technologies, such as the confocal microscope principle which has been combined with spinning disk technology and very fast laser scanning microscopes to yield 3D microscopy images, but results in problems with photo-bleaching and energy load. Light-sheet microscopy techniques decrease the photo-bleaching and energy load problems inherent in confocal microscopes, but introduce new disadvantages. Specifically, ...
System And Method For Capturing Vital Vascular Fingerprint
Organization: University of California, Irvine (UC Irvine)
Regular morphology fingerprinting is heavily relied upon for identification purposes, but is an imperfect method of identification, which can be obstructed by an ordinary finger scar. It is further vulnerable to fabrication and cannot verify that the fingerprint belongs to a live person. There have been attempts to remedy the shortcomings of fingerprint technology using the technique of finger vein authentication which uses LED to capture large veins in the finger. However, this reveals a vein vascular pattern which is different from a ...
A New Approach to Medical Diagnostics and Therapeutics
Organization: University of California, San Diego (UC San Diego)
UCSD inventors have come up with an approach to patient selection and assessment of response to therapy that is very different from traditional pharmacogenomic approaches. This novel approach allows doctors to make various health prognosis tailored to individuals. It can also be used to estimate the life span, predisposition to diseases, and reaction to various chemotherapies in a variety of patient groupings. This invention would allow a company to profitably leverage the large sets of genome data soon to be available.
A Web-Based Insulin Infusion Calculator (IIC)
Organization: University of California, San Diego (UC San Diego)
UC San Diego researchers and physicians have developed a software system—an insulin infusion calculator (IIC)—to improve insulin compliance and to reduce the number of calculation errors. To briefly summarize, the invention is a hospital-tested software system designed to achieve desirable blood glucose control and minimize hypoglycemia by automating the calculation for the appropriate insulin dosage for intravenous infusion. The computerized insulin calculator works by prompting onsite glucose measurements and calculating an ...
A Method to Generate Novel Bioactive Molecules
Organization: University of California, San Diego (UC San Diego)
UC San Diego inventors have invented a very general method to design and create new compounds with anti-bacterial, anti-fungal, anti-cancer, or other bioactive properties. Different from the existing art, where the biological effect of a compound must be determined, this invention allows for compounds to be designed and created with these effects known a priori. For example, this shortcoming, which the current invention overcomes, is part of the existing art being applied to anti-bacterial synthesis—such as mutational biosynthesis, ...
A New Bacterial Metastructure and Methods of Use
Organization: University of California, San Diego (UC San Diego)
UC San Diego researchers have developed a systems approach that iteratively integrates multiple genome-scale measurements on the basis of genetic information flow to identify the organizational elements and map them onto the genome sequence. This bioinformatics technology greatly facilitates solving problems associated with the design of specifically targeted gene changes in bacteria for several industrial applications, including: More efficient fermenters Lower cost biofuels Lower cost biodegradable plastics This new ...
Statistical Comparison Of Rank Lists And Molecular Profiles
Organization: University of California, Los Angeles (UCLA)
Comparing independent high-throughput gene-expression experiments can generate hypotheses about which gene-expression programs are shared between particular biological processes. Current techniques to compare expression profiles typically involve choosing a fixed differential expression threshold to summarize results, potentially reducing sensitivity to small but concordant changes. We have developed a threshold-free algorithm called Rank-rank Hypergeometric Overlap (RRHO). This algorithm steps through two gene lists ranked by the ...
Organization: University of California, Los Angeles (UCLA)
Researchers at UCLA have developed a technique that optimizes and identifies “placebo networks” in the brain using functional magnetic resonance imaging (fMRI), but these methods are applicable in general to many brain-imaging modalities such as EEG and PET.Using Blind Signal Separation (BSS) methods, a brain scan can be decomposed into underlying signal sources that operate in either time or space and brain networks corresponding to the placebo effect(s) can be identified using computational machine learning techniques (sometimes ...
A Systems Biology Approach for Identifying Drug Targets
Organization: University of California, San Diego (UC San Diego)
Scientists at UC San Diego have developed a method to identify drug targets using a systems biology approach. Given a network that regulates a disease, the method can predict the effects of inhibiting a set of genes on the marker genes of the disease. For example, if two marker genes are up-regulated in a disease, the method can identify inhibition of genes that can reduce the expression of the two marker genes to normal levels. Therefore, the invention provides a systematic way to evaluate the effects of inhibiting multiple drug targets for ...
Superior Software for Designing Oligonucleotide Probe Pool: PP-Designer v2.0
Organization: University of California, San Diego (UC San Diego)
UC San Diego researchers have developed a software system, Padlock Probe-Designer (PP-Designer) that automatically constructs customizable primers of padlock and non-padlock DNA or RNA probes to any sequenced, annotated genome. These primers are designed to have higher specificities and affinities to their target sequences. Using PP-Designer v1.0, 90-99 percent target specificity from a pool of ~10,000 padlock probes has been demonstrated; it achieves a level of multiplexing far exceeding any comparable assays with traditional primer pairs. ...
Logical Structure Of Amino Acid Stimulons In Bacteria
Organization: University of California, San Diego (UC San Diego)
UCSD inventors invented a method for solving problems associated with design of amino acid metabolism in bacteria. The types of bacteria that can be designed have these industrial applicationsMore efficient fermentersLower cost biofuelsLower cost biodegradable plasticsThe research leading to this invention is available for review at this web site http://www.nature.com/nchembio/journal/v8/n1/abs/nchembio.710.html Related to case 2010-138
Method For Silico Modeling Of Gene Product Expression And Metabolism
Organization: University of California, San Diego (UC San Diego)
This invention enables new biological discoveries with respect to regulatory processes, in particular for realizing various strain designs or limiting bacterial adaptation to antibiotics. ChIP-seq and other traditionally laborious experimental techniques (gel shift assays) can be done to confirm specific predictions of a regulatory factor that may be affecting strain design rather than using blind approaches to discover interfering regulatory processes. The research this invention is based on can be found at this link. ...
A Method and Software Significantly Improving the Accuracy Of Genome Assemblies: SEQuel
Organization: University of California, San Diego (UC San Diego)
UCSD researchers have recently developed a method and companion software, SEQuel, to correct errors (i.e., insertions, deletions, and substitution errors) in the assembled contigs of NGS data. Fundamental of SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model. SEQuel takes as input an assembled contig, the paired-end reads that align to that contig and the approximate positions where they aligned, and returns a refined contig.
Organization: University of California, San Diego (UC San Diego)
CE-Combinatorial Extension, Algorithms and Computer Programs for Comparing the 3-dimensional Structures of Protein Molecules. Download Site License.
SMAP: Software for Functional Site Characterization and Analysis
Organization: University of California, San Diego (UC San Diego)
SMAP Site License Agreement for 2010.
Organization: University of California, San Diego (UC San Diego)
A fiber tractography method has been developed to enable one to define neural pathways based upon a maximal entropy random walk, which is used to construct the neural pathways from a 3D diffusion tensor field. The computational method, which is straightforward to implement, uses a single computation to assess the global connectivity by computing the entropy of paths.
Novel Method of 3D Image Segmentation
Organization: University of California, San Diego (UC San Diego)
A UCSD researcher has developed a novel and robust method, DP2 (Dual Point Decision Process), for the segmentation of complex and massive electron microscopy imaging datasets, such as the ones generated with SBFSEM. The cost effective and highly scalable DP2 combines automatic image processing with human visual processing by a pool of micro-labor workers (contracted human task workers through the internet). An automatic superpixelization process is implemented to partition a large medical image into multiple manageable segments ...
Computation Of Solvent Structure Thermodynamics To Support Drug Design And Molecular Design
Organization: University of California, San Diego (UC San Diego)
A team of researchers from UC San Diego and City University of New York improved upon the implementation of Inhomogeneous Solvation Theory (IST) by developing a three dimensional grid around the solute of interest, in an approach termed Grid Inhomogeneous Solvation Theory (GIST). The GIST approach enables one to choose or design a second molecule (such as a ligand) which will bind a targeted first molecule (such as a receptor) with high affinity. This technique might not only be useful for computer-aided drug design and predicting molecular ...
