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2-D Polymer-Based Device for Serial X-Ray Crystallography

Researchers at the University of California, Davis have developed a single-use chip for the identification of protein crystals using X-ray based instruments.

Composition and Methods of a Nuclease Chain Reaction for Nucleic Acid Detection

This invention leverages the nuclease activity of CRISPR proteins for the direct, sensitive detection of specific nucleic acid sequences. This all-in-one detection modality includes an internal Nuclease Chain Reaction (NCR), which possesses an amplifying, feed-forward loop to generate an exponential signal upon detection of a target nucleic acid.Cas13 or Cas12 enzymes can be programmed with a guide RNA that recognizes a desired target sequence, activating a non-specific RNase or DNase activity. This can be used to release a detectable label. On its own, this approach is inherently limited in sensitivity and current methods require an amplification of genetic material before CRISPR-base detection. 

Compression of Genetic Information in Multiple Reading Frames

Techniques such as genome editing, gene therapy, and CRISPR-based gene expression require robust methods of delivering genetic information. The effectiveness of delivery depends on the amount of DNA or RNA that can be delivered.  In some cases there is a strict upper-limit on the amount of DNA or RNA that can be delivered.  For example, AAV vectors for mammalian gene delivery are limited to genetic cargos of < 5 kb.  In general, and irrespective of the delivery vector, larger DNA constructs are delivered less efficiently and so it is advantageous to use smaller constructs where possible. It is therefore advantageous to compress constructs. Methods of compression that do not require removal of genetic elements (“lossless compression”) are very desirable since size requirements can be met without compromising functionality.     In order to reduce the number of bases (DNA or RNA) required to encode larger constructs, UC Berkeley researchers have developed a method for compressing genetic information.   The method can be applied to two elements which be encoded in the same or different reading and can also be applied to a single genetic elements. 

Cellular Potassium Imaging Using A Ratiometric Fluorescent Sensor

The inventors developed a ratiometric fluorescent small molecule probe for potassium ion detection composed of a duo-fluorophore system (KR-1). UV-vis detector and fluorometer measurement support ratiometric response of the probe towards potassium ion concentration. The probe was further applied to cellular potassium level detection using confocal microscope imaging technique. KR-1 enables simple determination of potassium levels in various cancer or non-cancer cell lines.

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.

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.

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.

DNA Methylation Biomarker of Aging for Human Ex Vivo and In Vivo Studies

A UCLA researcher in the Department of Human Genetic and Biostatistics has developed a DNA methylation biomarker for detecting aging in humans.

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.

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