About

SoCal Bioinformatics Inc provdes data mining and machine learning solutions for developing proteomic biomarkers for predictive diagnostics.

Jeff Jones Ph.D. CEO

Jeff Jones Ph.D. co-founded SoCal Bioinformatics Inc. to fill a need protemic data mining and biomarker discovery. He has been successful in data mining large plasma based LCMS datasets for viable biomarkers, including a study culminating in the launch of a colorectal cancer diagnostic CLIA LDT.

Affiliations
Member American Society for Mass Spectrometry
Advisory Board The Alliance for Safe Biologic Medicines link



Ryan Benz Ph.D. CDS

Ryan Benz Ph.D. co-founded SoCal Bioinformatics Inc. to bring his background in computational sciences, bioinformatics, machine learning and data visualizaiton to fill the obvious need in proteomics. He has been successful in applying advanced algorithms to discoverying plasma based cancer biomarkers, including a set specific to a colorectal cancer diagnostic CLIA LDT.

Affiliations
Member American Society for Mass Spectrometry
Member American Chemical Society
Organizer OC R Users Group Organizer link





Publications

A plasma-based protein marker panel for colorectal cancer detection identified by multiplex targeted mass spectrometry
J Jones, BE Wilcox, RW Benz, N Babbar, G Boragine, T Burrell, et.al
Clinical colorectal cancer 15 (2), 186-194. e13 2016

Discovery and Validation of Plasma-Protein Biomarker Panels for the Detection of Colorectal Cancer and Advanced Adenoma in a Danish Collection of Samples from Patients Referred for Diagnostic Colonoscopy
JE Blume, M Wilhelmsen, RW Benz, N Brunner, IJ Christensen, LJ Croner, J Jones, et.al
The Journal of Applied Laboratory Medicine: An AACC Publication, jalm-2016

The Discovery and Validation of Blood Plasma Protein-Based Classifier Panels for Colorectal Cancer and Advanced Adenoma using a Combined Mass Spectrometry-and ELISA-based Workflow in Studies Including 1,605 Patient Samples
BE Wilcox, RW Benz, LJ Croner, R Dillon, JJ Jones, A Kao, J You, et.al
Abstract Accepted for Oral Presentation May 24, 2016 at Digestive Disease Week 2016

Data-Driven High-Throughput Prediction of the 3-D Structures of Small Molecules: Review and Progress
A Androcico, A Randall, RW Benz, P Baldi
J Chemical Information and Modeling, 51 (4), 760-776, 2011.

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors
TC Whisenant, DT Ho, RW Benz, JS Rogers, RM Kaake, EA Gordon, L Huang, P Baldi, L Bardwell
PLOS Computational Biology, 6 (8), e1000908, 2010.

A targeted proteomic analysis of the ubiquitin-like modifier nedd8 and associated proteins
J Jones, K Wu, Y Yang, C Guerrero, N Nillegoda, ZQ Pan, L Huang
Journal of proteome research 7 (3), 1274 2008

BLASTing Small Molecules – Statistics and Extreme Statistics of Chemical Similarity Scores
P Baldi, RW Benz
Bioinformatics, 24 (13), i357-i365, 2008.

Discovery of Power-Laws in Chemical Space
RW Benz, SJ Swamidass, P Baldi
J Chemical Information and Modeling, 48 (6), 1138-1151, 2008.

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval
P Baldi, RW Benz, DS Hirschberg, SJ Swamidass
J Chemical Information and Modeling, 47 (6), 2098-2109, 2007.

Characterizing the phospholipid profiles in mammalian tissues by MALDI FTMS
J Jones, S Borgmann, CL Wilkins, RM O'Brien
Analytical chemistry 78 (9), 3062-3071 2006

Investigation of Finite System-Size Effects in Molecular Dynamics Simulations of Lipid Bilayers
F Castro-Romàn, RW Benz, SH White, DJ Tobias
J Physical Chemistry B, 110 (47), 24157-24164, 2006.

Diffraction-Based Density Restraints for Membrane and Membrane-Peptide Molecular Dynamics Simulation
RW Benz, H Nanda, F Castro-Romàn, SH White, DJ Tobias
Biophysical Journal, 91, 3617-3629, 2006.

MALDI-FTMS of Whole-Cell bacteria
J Jones, MJ Stump, CL Wilkins
Identification of Microorganisms by Mass Spectrometry 169, 279 2005

Ionic liquid matrix-induced metastable decay of peptides and oligonucleotides and stabilization of phospholipids in MALDI FTMS analyses
J Jones, SMAB Batoy, CL Wilkins, R Liyanage, JO Lay
Journal of the American Society for Mass Spectrometry 16 (12), 2000-2008 2005

A comprehensive and comparative analysis for MALDI FTMS lipid and phospholipid profiles from biological samples
J Jones, SMAB Batoy, CL Wilkins
Computational biology and chemistry 29 (4), 294-302 2005

Strategies and data analysis techniques for lipid and phospholipid chemistry elucidation by intact cell MALDI-FTMS
J Jones, MJ Stump, RC Fleming, JO Lay Jr, CL Wilkins
Journal of the American Society for Mass Spectrometry 15 (11), 1665-1674 2004

Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach
RW Benz, F Castro-Romàn, DJ Tobias, SH White
Biophysical Journal, 88, 805-817, 2005.

Investigation of MALDI-TOF and FT-MS Techniques for Analysis of Escherichia coli Whole Cells
J Jones, MJ Stump, RC Fleming, JO Lay, CL Wilkins
Analytical chemistry 75 (6), 1340-1347 2003

Patents

Protein biomarker panels for detecting colorectal cancer and advanced adenoma
J Blume, J Jones, R Benz, A Kao, L Croner, R Dillon, J You, B Wilcox, et.al
US Patent App. 15/094,767

Method for evaluation of presence of or risk of colon tumors J Blume, R Benz, L Croner, R Dillon, AZ Randall, J Jones, H Skor, et.al
US Patent App. 14/526,181 | US Patent App. 14/526,282 | US Patent App. 14/094,594