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Identification Of Pan-Cancer Small Cell Neuroendocrine Phenotypes And Vulnerabilities

UCLA researchers in the Department of Molecular and Medical Pharmacology have developed a classifier for the identification and treatment of small cell neuroendocrine cancers and small-round-blue cell tumors not previously identified.

4D-seq: Single Cell RNA-sequencing with in situ Spatiotemporal Information

To develop a novel imaging-based single cell RNA-sequencing (scRNA-Seq) platform that allows capturing of spatiotemporal information and cellular behavior of the sequenced cells within tissue.

DARTS: Deep Learning Augmented RNA-seq Analysis of Transcript Splicing

Researchers led by Yi Xing have developed a novel deep learning algorithm to detect alternative splicing patterns in RNA-seq data

A New Human-Monitor Interface For Interpreting Clinical Images

UCLA researchers in the Department of Radiological Sciences have invented a novel interactive tool that can rapidly focus and zoom on a large number of images using eye tracking technology.

Dicom/Pacs Compression Techniques

Researchers led by Xiao Hu from the Department of Surgery at UCLA have created a novel and convenient way to compress and query medical images from a PACS system.

3D Population Maps for Noninvasively Identifying Phenotypes and Pathologies in Individual Patients

UCLA researchers in the Department of Radiological Sciences have developed a novel computation system that uses large imaging datasets to aid in clinical diagnosis and prognosis.

Surfaceome Profiling Of Advanced Prostate Cancer To Identify Target Antigens For Immune-Based Therapy

Dr. Witte and colleagues at UCLA have developed a novel approach to identify surface biomarkers and targetable antigens in prostate cancer by combining multiple omics analyses across different cell lines.

Development Of A Method For Endocrine Network Discovery Uncovers Peptide Therapeutic Targets

UCLA researchers in the Division of Cardiology at the Geffen School of Medicine have developed a bioinformatics methodology to identify and functionally annotate novel endocrine pathways.

High Throughput Digital Cell Quantification Of Immune Cell Subsets Via Epigenetic Markers

UCLA researchers in the Department of Molecular, Cell, and Developmental Biology have developed a novel high-throughput method for the quantification of immune cell subtype.

Joint Pharmacophoric Space through Geometric Features

Pharmacophore analysis through examination of Joint Pharmacophore Space of chemical compounds, targets, and chemical/biological properties.

Global Training Of Neural Networks For Phenomic Classification

UCLA researchers in the Department of Electrical Engineering have developed a high-throughput, label-free cell classification method based on time-stretch quantitative phase imaging.

Sieve Container For Contactless Media Exchange For Cell Growth

Media that contains nutrients and growth factors is necessary to grow all types of cells, a process that is widely used in many fields of research. Such media should be routinely changed either to different media or a fresh batch of the same media. This change currently involves either using a pipette to transfer cells from their current dish of media to a new dish, or aspirating the media out of the dish and replacing it with new media. Both methods have inherent risks to stressing and damaging the cells. Researchers at UCI have developed a unique dish for growing cells that allows for safer aspiration of the old media, which reduces stress and damage to the cells.

UCSF Chimera: Molecular Modeling Software for Visualization and Analysis of Molecular Structures

This invention consists of software that facilitates modeling and interactive visualization of molecular structures and related data.

Integrative Approach for the Analysis and Visualization of Static or Dynamic Omic Data, Including Genomic, Proteomic, Gene Expression, and Metabolic Data

The technology is a method for analysis and mapping of a broad range of omic data.It features maps and visualizes interactions between omic data, such as how the circadian metabolome, transcriptome, and proteome operate in concert.With this technology, users can use non-public and public data, per tissue/organ data and data across multiple conditions.

Alignment-Free Rapid Sequence Census Quantification (Kallisto)

Sequence census experiments utilize next-generation sequence data to estimate the relative abundance of target sequences.  Since the samples are often short DNA fragments, they must first be assigned to the correct transcripts and genes that produced them, and this alignment or mapping step currently takes up the majority of computing power and time in most expression analyses. To avoid this costly process, UC Berkeley researchers have developed a software program (kallisto) for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads based on pseudo-alignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudo-alignment of reads preserves the key information needed for quantification. 

Platform for Large-Scale Determination of Biomolecular Turnover Rate

Dr. Peipei Ping and colleagues at UCLA have developed a novel, high-throughput method to evaluate the metabolic kinetics of proteins, lipids, nucleic acid and other biomolecules in vivo, including model systems and human. This technology has the potential to identify novel biomarkers for disease prevention, diagnosis, prognosis and determine treatment strategies.  

DNA Sequence Assembly Software (Design Evolver)

DNA sequence assembly software is used for designing the construction of longer DNA molecules from fragments of shorter DNA molecules. Current methods of sequence assembly are expensive, slow and prone to failure. Investigators at UC Berkeley have developed a sequence assembly tool, Design Evolver, which is cheaper, faster, easier to implement and less prone to failure than alternate tools. The software works in conjunction with the j5 DNA assembly tool developed and licensed by the Joint BioEnergy Institute (JBEI). Design Evolver’s algorithm can further optimize designs that have been processed by j5.

Inclined Single Plane Imaging Microscope Box (iSPIM Box)

Researchers at University of California, Irvine, have responded to the worldwide growing demand for fast 3D microscopy in bioimaging, by creating iSPIM Box (Inclined Single Plane Imaging Microscope Box), an adapter for commercial body microscopes, which can be used to achieve high spatial and temporal resolution in live cell imaging with only simple sample preparation in common culture dishes.

High-sensitivity Angular Interferometer

Researchers at the University of California, Berkeley have developed an invention that consists of an angular interferometer able to measure angle variations of a coherent, collimated light source with an accuracy below 30 nrad. The optical setup is compact and consists of a few simple optical components. The novelty of this innovation lies in the use of a simple, cost-effect technique to amplify the sensitivity of the instrument. The disclosed invention is in principle capable of being integrated into more compact, high-sensitivity commercial instruments for a fraction of the cost of current, state-of-the-art instruments (currently exceeding $30,000).   Commercial devices used to measure the angular deviation of a single beam include autocollimators and interferometers. The highest resolution offered by a commercial system is 25 nrad. The disclosed angular interferometer is able to measure relative angle variations (of a sample beam relative to a reference beam) below 30 nrad, though the resolution is known to currently be limited by the specific details of the current application and can therefore be further reduced with minor, inexpensive improvements.

CE Software

Brief description not available

A Method and Software Significantly Improving the Accuracy Of Genome Assemblies: SEQuel

Assemblies of next generation sequencing (NGS) data, while accurate, still contain a substantial number of errors that need to be corrected after the assembly process. Earlier assembly algorithms developed for Sanger sequencing follow an "overlap - layout - consensus" paradigm, where consensus refers to fixing errors in the contigs. Since this paradigm faces difficulties in short read assembly, most NGS assemblers employ a de Bruijn graph approach that effectively deals with large amounts of data. However, most NGS assemblers neglect the consensus step, i.e., there exists no postprocessing of the contigs in Velvet and many other popular assemblers. Relying on high and uniform coverage, NGS assembly algorithms push the burden of producing high quality assemblies onto the construction of the de Bruijn graph. Our work demonstrates that NGS assemblers can benefit from the use of a consensus step. There are currently no tools that aim to accomplish this same goal.

Gene Knockout And Replacement In Stem Cells

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.

Peripheral Biomarkers For The Assessment Of Autism

Researchers in the Department of Neurology and the Autism Center in the Semel Institute at UCLA have identified genetic factors which are associated with autism.

Converting Genomic Protein Sequences into Music

Brief description not available

Genome-Scale Kinetic Models

Historically, genome-scale analysis has used bottom-up reconstruction of available, biochemical information (from high-throughput datasets and public archives) to provide a snapshot of biochemical relationships in a network. While this approach has been extremely useful, it is an obvious simplification of real, dynamic systems, which continually change in response to perturbations.

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