The trackRank technology is a ranking algorithm suite which can identify and rank genomics datasets relative to their significance to a given query gene or genomic location.
Advances in high-throughput technologies have resulted in the growth of massive genomics datasets. The global market for bioinformatics is expected to grow from $16.1 billion in 2020 to $24.1 billion by 2025 with a CAGR of 8.4% from 2020-2025 (BCC Research BIO051F). Currently, there is no effective data mining tool available to analyze and visualize these large data resources. There is a need for a tool that can properly analyze massive genomic data sets and have the power to rank the given data by their characteristics at the query gene or region.
Advancement in high-throughput technologies have resulted in the augmented growth of massive genomics data. Due to its large number, it is effectively impossible to analyze and visualize datasets individually and currently no effective data mining tool exists. This project proposes a new method based on analyzing a broad collection of genome-wide profiling datasets. The proposed method will rank all the datasets by their characteristics at the query gene or region when given a query of related genomic features. The method proposes the implementation of the ranking algorithm suit technology trackRank to rank and identify genomic datasets as they relate to their significance to a given genomic location or query gene. This is to be achieved by converting every data type and locus into a “signal measure” that will be comparable across a large variety of data types. Additionally using the signal researchers will develop appropriate ranking algorithms that can be utilized to a diverse collection of genome-wide profiling datasets. Said algorithms are intended to be implemented into the software mining tool OmiSeqs. The long-term priority of this project is to develop informatics, computational apparatus, and statistics that can be used to further the knowledge of and generate testable hypotheses from existing genomics data.
Early-stage. Website publicly available since 5/15/2013.
High Throughput Screening for identifying effective immuno-modulators.
The global market for drug discovery technologies was $69.8 billion in 2020 and is expected to grow to $110.4 billion by 2025 with a CAGR of 9.6% from 2020-2025. The expected second highest market in the drug discovery market is for high throughput screening (HST). The global HST market in 2020 was $12.8 billion and is expected to reach $20.1 billion by 2025 with a CAGR of 9.4% from 2020-2025 (BCC Research BIO020G). Market expansion is supported by innovation in techniques including high throughput techniques for phenotypic profiling of compounds based on changes in cellular activity.
The lack of HT (High Throughput) screening platforms that replicate the complexity of the immunosuppressive nature of cancer cells has delayed the discovery of such compounds. Researchers at Emory have developed an HTiP (High-Throughput immunomodulator Phenotypic) screening platform with the purpose of facilitating the identification of effective small molecule immune-modulators from a larger chemical compound library. The screening platform provides a vigorous ex-vivo tumor environment which reflects the immune response network by co-culturing cancer cells with PBMCs (human peripheral blood mononuclear cells). These PBMCS contain a mixture of dendritic cells, monocytes, and lymphocytes.
A new class of CXCR4 modulators for metastasis and inflammation.
Multiple myeloma, acute myeloid leukemia, HIV, and rheumatoid arthritis all involve the G-protein receptor CXCR4. Currently, there is only one FDA approved CXCR4 antagonist, AMD3100, but the compound has cardiotoxicity issues related to its ability to block Ca2+ flux. Researchers at Emory University have identified ZINC72372983 as having anti-inflammatory effects and upon further development, a 100-fold improvement in binding affinity. This invention could contribute to the immunotherapy drug market which was $130.3 billion in 2019 and is expected to reach $204.4 billion by 2025 with a CAGR of 7.9% from 2019-2025 (BCC Research PIIM249A).
Researchers screened for compounds that bind in allosteric sites to find compounds that module the receptor without having adverse effects. Through ligand-based screening, docking ADMET, and PAINS filters the researchers found 7 compounds from a ZINC database that were taken forward in vitro assay. In vitro assay revealed 4 of the 7 compounds had binding constants between 100-10 nm via fluorescence in moderate throughput assay. These 4 were then put then put through in vitro functional assay revealing that the compound ZINC72372983 had the best inhibitory efficacy against the chemotaxis between CXCR4 and CXCL12.
Animal testing conducted.
HIV-1 BG505 Env protein (clone name: YRK01, YRK02).
HIV-1 BG505 SOSIP Env trimer.
HIV-1 envelope glycoprotein (Env) is a membrane protein complex involved in receptor recognition and viral fusion with CD4+ T cells that allows the virus to enter cells. Emory researchers have identified two clonally related monoclonal antibodies that were recovered from a BG505 SOSIP immunized rhesus macaque via PCR and cloning of the immunoglobulin heavy and light chain variable domain gene segments from single antigen specific B cells. The monoclonal antibodies potently neutralize the autologous BG505 envelope pseudovirus (a virus that infects susceptible cells, but only replicates once). This can be used as a research tool to generate neutralizing antibodies against HIV.
Publication: Ward and Wilson, Trends in Biochemical Sciences, 2015 Feb;40(2):101-7
Catheter with a removable sleeve designed to remove debris that accumulates on the walls, which may be utilized in drainage catheters, but has broad applications in indwelling tubes.
Percutaneous nephrostomy (PCN) represents one instance of the application of this technology, wherein at least 105,000 cases of PCN placement take place annually. Unfortunately, PCN catheters are prone to biofilm development and urine mineral deposits which can lead to catheter obstruction and subsequent clinical infection. The enclosed technology represents a catheter assembly with a removable sleeve, atop which biofouling (biofilm accumulation, encrustation, etc) occurs. When such biofouling leads to catheter dysfunction, the provider has the option to remove the sleeve and insert an other unused sleeve. This sleeve exchange can take place at regular intervals and obviates the need for catheter exchanges as the removable sleeve, rather than the catheter itself, is removed. This invention will compete in the global catheter market, which is expected to reach $34.489 billion by 2023 from $27.24 billion in 2018 at a CAGR of 4.8% (BCC Research HLC019H). Aging population being a contributing factor to this increase in value.
The enclosed technology represents a catheter assembly with a removable sleeve, atop which biofouling (biofilm accumulation, encrustation, etc.) occurs. When such biofouling leads to catheter dysfunction, the provider has the option to remove the sleeve and insert another unused sleeve. The sleeve covers the inner lumen of the catheter. The catheter assembly includes a (1) tube and (2) a sleeve that can be inserted and removed from within the inner lumen of the tube. At some point along the removable sleeve, the sleeve is geometrically shaped to out-pouch and fit within a mating geometric shape within the catheter tube. The sleeve outpouching will lock into place on insertion and with enough force directed away from the catheter in the long axis of the catheter, it will overcome the locking mechanism to be removed from the catheter lumen. Thereafter, another sleeve can be inserted.
The expression levels of genes PCA3, MRC2 and S100A4 for the prognosis, stratification and prostate cancer monitoring using non-invasive methods.