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USD 100 /hr
Hire Dr. Ryan K.
United States
USD 100 /hr

Computational scientist specializing in biotechnology, bioinformatics, genomics, data distillation and machine learning

Profile Summary
Subject Matter Expertise
Services
Writing Technical Writing
Research Secondary Data Collection
Data & AI Statistical Analysis, Data Visualization
Work Experience

Instructor (Bioinformatics, Genomic sequencing)

University of California San Diego

June 2009 - Present

Principal Scientist

VerdAscend Sciences

April 2009 - Present

Principal Scientist Bioinformatics

TOMA Biosystems

September 2015 - September 2019

Staff Scientist Bioinformatics

QuantaLife Inc

September 2010 - April 2013

Staff Scientist Bioinformatics

Applied Biosystems

October 1999 - January 2009

Computational Chemist

Terrapin / Telik

November 1995 - August 1999

Education

BS Biochemistry

University of California

- Present

PhD (Chemsitry)

University of California, Santa Cruz

October 1989 - June 1995

Certifications
  • Certification details not provided.
Publications
OTHER
Hiddessen, Amy L and Ness, Kevin D and Hindson, Benjamin J and Masquelier, Donald A and Chia, Erin R(2017). System for generating droplets with pressure monitoring.
Koehler, Ryan T and Tzonev, Svilen S(2016). Multiplexed digital assay for variant and normal forms of a gene of interest.
Koehler, Ryan T and Livak, Kenneth J and Stevens, Junko and Francisco, M and Rhodes, Michael and Bellon, Laurent R and You, Xiaoqing and Hunkapiller, Michael W and ZIEGLE, Janet S and Williams, Julie and others(2016). Methods for placing, accepting, and filling orders for products and services.
Regan, John and Cooper, Samantha and So, Austin and Koehler, Ryan and Montesclaros, Luz(2016). Digital assays for mutation detection.
Francisco, M and Koehler, Ryan T and Pouliot, Yannick and Bouhlal, Yosr and So, Austin and Goodsaid, Federico and Irvine, Sean and Trigg, Len and Nadauld, Lincoln(2016). Joint somatic mutation and germline variant identification and scoring from tumor molecular profiling and ct-DNA monitoring of cancer patients by high-throughput sequencing. American Association for Cancer Research
Saxonov, Serge and Tzonev, Svilen S and Lucero, Michael Y and Koehler, Ryan T and Hindson, Benjamin J(2014). Library characterization by digital assay.
Litterst, Claudia and Koehler, Ryan Thane(2013). Digital telomerase assay.
Hindson, Benjamin and So, Austin and Koehler, Ryan and Troup, Camille and Heredia, Nick and Karlin-Neumann, George and Saxonov, Serge and White, Helen(2012). Ultra-sensitive detection of rare mutants by droplet digital PCR with conventional TaqMan assays. American Association for Cancer Research
Koehler, Ryan T and Livak, Kenneth J and Stevens, Junko and Francisco, M and Rhodes, Michael and Bellon, Laurent R and Williams, Julie and Gilbert, Dennis A and Scafe, Charles R and Avi-Itzhak, Hadar I and others(2008). Methods For Placing, Accepting, And Filling Orders For Products and Services.
Koehler, Ryan T and Livak, Kenneth J and Stevens, Junko and Francisco, M and Rhodes, Michael and Bellon, Laurent R and Williams, Julie and Gilbert, Dennis A and Scafe, Charles R and Avi-Itzhak, Hadar I and others(2008). Methods For Placing, Accepting, And Filling Orders For Products and Services.
Koehler, Ryan T and Livak, Kenneth J and Stevens, Junko and Francisco, M and Rhodes, Michael and Bellon, Laurent R and Williams, Julie and Gilbert, Dennis A and Scafe, Charles R and Avi-Itzhak, Hadar I and others(2008). Methods For Placing, Accepting, And Filling Orders For Products and Services.
Koehler, Ryan T and Livak, Kenneth J and Stevens, Junko and Francisco, M and Rhodes, Michael and Bellon, Laurent R and Williams, Julie and Gilbert, Dennis A and Scafe, Charles R and Avi-Itzhak, Hadar I and others(2008). Methods For Placing, Accepting, And Filling Orders For Products and Services.
Lao, Kai Qin and Chen, Caifu and Koehler, Ryan T and Scafe, Charles and Schroth, Gary(2007). Universal-tagged oligonucleotide primers and methods of use.
Lao, Kai Qin and Chen, Caifu and Koehler, Ryan T and Scafe, Charles and Schroth, Gary(2007). Universal-tagged oligonucleotide primers and methods of use.
Lao, Kai and Chen, Caifu and Koehler, Ryan and Scafe, Charles and Schroth, Gary(2007). Universal-tagged oligonucleotide primers and methods of use.
Scaf, Charles R and Peyret, Nicolas and Francisco, M and Koehler, Ryan T and Spier, Eugene G(2006). Methods for searching polynucleotide probe targets in databases.
Scaf, Charles R and Peyret, Nicolas and Francisco, M and Koehler, Ryan T and Spier, Eugene G(2006). Methods for searching polynucleotide probe targets in databases.
Scaf, Charles R and Peyret, Nicolas and Francisco, M and Koehler, Ryan T and Spier, Eugene G(2006). Methods for searching polynucleotide probe targets in databases.
Scaf, Charles R and Peyret, Nicolas and Francisco, M and Koehler, Ryan T and Spier, Eugene G(2006). Methods for searching polynucleotide probe targets in databases.
Koehler, Ryan T and Zhang, Zheng and Tobler, Andreas R and Short, Sabine and Wenz, Michael and Francisco, M(2006). Design of multiplexed oligionucleotide ligation assays for high throughput insertion-deletion polymorphism genotyping. American Association for Cancer Research
Koehler, Ryan T and Livak, Kenneth J and Stevens, Junko and Vega, Francisco DE and Rhodes, Michael and Bellon, Laurent R(2004). METHOD FOR OPERATING A COMPUTER AND/OR COMPUTER NETWORK TO DISTRIBUTE BIOTECHNOLOGY PRODUCTS.
Rosenblum, Barnett and Holden, David and Lou, Yuandan and Koehler, Ryan and Ramachandra, Srinivasa(2003). Polynucleotide sequence detection assays and analysis.
Rosenblum, Barnett and Holden, David and Lou, Yuandan and Koehler, Ryan and Ramachandra, Srinivasa(2003). Polynucleotide sequence detection assays and analysis.
KOEHLER, Ryan and LIVAK, Kenneth and STEVENS, Junko and Francisco, M and RHODES, Michael and BELLON, Laurent and others(2003). METHOD FOR OPERATING A COMPUTER AND/OR COMPUTER NETWORK TO DISTRIBUTE BIOTECHNOLOGY PRODUCTS.
Koehler, Ryan and Livak, Kenneth and Stevens, Junko and De La Vega, Francisco and Rhodes, Michael and Bellon, Laurent and Ziegle, Janet and Williams, Julie and Madden, Dawn and Gilbert, Dennis and others(2003). Methods for placing, accepting, and filling orders for products and services.
Koehler, Ryan and Livak, Kenneth and Stevens, Junko and De La Vega, Francisco and Rhodes, Michael and Bellon, Laurent and Ziegle, Janet and Williams, Julie and Madden, Dawn and Gilbert, Dennis and others(2003). Methods for placing, accepting, and filling orders for products and services.
Kauvar, Lawrence and Sportsman, Richard and Villar, Hugo and Spevak, Wayne and Kohanski, Ron and Satyam, Apparao and Koehler, Ryan and others(2001). Modulators of insulin receptor activity.
JOURNAL ARTICLE
So, Austin and Vilborg, Anna and Bouhlal, Yosr and Koehler, Ryan and Grimes, Susan and Pouliot, Yannick and Mendoza, Daniel and Goodsaid, Federico and Lucero, Mike and De La Vega, Francisco M and others(2017). A Robust Targeted Sequencing Approach For Low Input And Variable Quality DNA From Clinical Samples. bioRxiv. p. 123117. Cold Spring Harbor Labs Journals
Regan, John F and Kamitaki, Nolan and Legler, Tina and Cooper, Samantha and Klitgord, Niels and Karlin-Neumann, George and Wong, Catherine and Hodges, Shawn and Koehler, Ryan and Tzonev, Svilen and others(2015). A rapid molecular approach for chromosomal phasing. PLoS One. 10. (3). p. e0118270. Public Library of Science
Belgrader, Phillip and Tanner, Stephanie C and Regan, John F and Koehler, Ryan and Hindson, Benjamin J and Brown, Alexandra S(2013). Droplet digital PCR measurement of HER2 copy number alteration in formalin-fixed paraffin-embedded breast carcinoma tissue. Clinical chemistry. 59. (6). p. 991--994. Clinical Chemistry
McDermott, Geoffrey P and Do, Duc and Litterst, Claudia M and Maar, Dianna and Hindson, Christopher M and Steenblock, Erin R and Legler, Tina C and Jouvenot, Yann and Marrs, Samuel H and Bemis, Adam and others(2013). Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR. Analytical chemistry. 85. (23). p. 11619--11627. American Chemical Society
Heredia, Nicholas J and Belgrader, Phillip and Wang, Shenglong and Koehler, Ryan and Regan, Jack and Cosman, Angela M and Saxonov, Serge and Hindson, Benjamin and Tanner, Stephanie C and Brown, Alexandra S and others(2013). Droplet Digitalâ„¢ PCR quantitation of HER2 expression in FFPE breast cancer samples. Methods. 59. (1). p. S20--S23. Academic Press
Hindson, Benjamin J and Ness, Kevin D and Masquelier, Donald A and Belgrader, Phillip and Heredia, Nicholas J and Makarewicz, Anthony J and Bright, Isaac J and Lucero, Michael Y and Hiddessen, Amy L and Legler, Tina C and others(2011). High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Analytical chemistry. 83. (22). p. 8604--8610. American Chemical Society
Koehler, Ryan and Issac, Hadar and Cloonan, Nicole and Grimmond, Sean M(2010). The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics. 27. (2). p. 272--274. Oxford University Press
Tobler, Andreas R and Short, Sabine and Andersen, Mark R and Paner, Teodoro M and Briggs, Jason C and Lambert, Stephen M and Wu, Priscilla P and Wang, Yiwen and Spoonde, Alexander Y and Koehler, Ryan T and others(2005). The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. Journal of biomolecular techniques: JBT. 16. (4). p. 398. The Association of Biomolecular Resource Facilities
Francisco, M and Isaac, Hadar and Collins, Andrew and Scafe, Charles R and Halld{\'o}rsson, Bjarni V and Su, Xiaoping and Lippert, Ross A and Wang, Yu and Laig-Webster, Marion and Koehler, Ryan T and others(2005). The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome research. 15. (4). p. 454--462. Cold Spring Harbor Lab
Koehler, Ryan T and Peyret, Nicolas(2005). Effects of DNA secondary structure on oligonucleotide probe binding efficiency. Computational biology and chemistry. 29. (6). p. 393--397. Elsevier
Koehler, Ryan T and Peyret, Nicolas(2005). Thermodynamic properties of DNA sequences: characteristic values for the human genome. Bioinformatics. 21. (16). p. 3333--3339. Oxford University Press
Villar, Hugo O and Koehler, Ryan T(2000). Amino acid preferences of small, naturally occurring polypeptides. Biopolymers. 53. (3). p. 226--232. Wiley Online Library
Villar, Hugo O and Koehler, Ryan T(2000). Comments on the design of chemical libraries for screening. Molecular diversity. 5. (1). p. 13--24. Springer Netherlands
Koehler, Ryan T and Villar, Hugo O(2000). Design of screening libraries biased for pharmaceutical discovery. Journal of Computational Chemistry. 21. (13). p. 1145--1152. Wiley Online Library
Koehler, Ryan T and Villar, Hugo O(2000). Statistical relationships among docking scores for different protein binding sites. Journal of computer-aided molecular design. 14. (1). p. 23--37. Springer Netherlands
Dixon, Steven L and Koehler, Ryan T(1999). The hidden component of size in two-dimensional fragment descriptors: side effects on sampling in bioactive libraries. Journal of medicinal chemistry. 42. (15). p. 2887--2900. American Chemical Society
Koehler, Ryan T and Dixon, Steven L and Villar, Hugo O(1999). LASSOO: A generalized directed diversity approach to the design and enrichment of chemical libraries. Journal of medicinal chemistry. 42. (22). p. 4695--4704. ACS Publications
Koehler, Ryan T and Villar, Hugo O and Bauer, Karin E and Higgins, Deborah L(1997). Ligand-based protein alignment and isozyme specificity of glutathione S-transferase inhibitors. Proteins: Structure, Function, and Bioinformatics. 28. (2). p. 202--216. Wiley Online Library
Koehler, Ryan Thane(1997). Methodologies to evaluate, visualize, and characterize molecules and molecular populations designed with the INVENTON computer program.
Hindson, Benjamin J and Ness, Kevin D and Masquelier, Donald A and Belgrader, Phillip and Heredia, Nicholas J and Makarewicz, Anthony J and Bright, Isaac J and Lucero, Michael Y and Hiddessen, Amy L and Legler, Tina C and othersAnalytical chemistry Volume: 83 ISSN: 1520-6882 ISO Abbreviation: Anal. Chem. Publication Date: 2011 Nov. Detail:.
Istrail, Michael W Hunkapiller and Spier, Eugene G and Gilbert, Dennis A and Stevens, Junko F and Leinen, Kyle M and Olson, Sheri J and Guegler, Karl J and You, Xiaoqing and Xu, Lily H and Su, Heinz G and othersThe linkage disequilibrium maps of three human chromosomes. Citeseer
CONFERENCE PAPER
Vilborg, A and Bouhlal, Y and Koehler, R and Mendoza, D and Goodsaid, F and Pouliot, Y and De La Vega, F and Lucero, M and Ji, HP and So, A(2016). TOMA OS-Seq: A Novel Capture-Based Library Preparation Platform with Minimal PCR-Dependency for Detecting Clinically Relevant Mutations Using NGS. JOURNAL OF MOLECULAR DIAGNOSTICS. 18. (6). p. 1027--1027.
Tanner, SC and Monico, J and Belgrader, P and Regan, J and Koehler, R and Brown, AS(2012). Droplet Digital PCR (TM): Comparison of a Novel Method of HER2 Testing to Immunohistochemistry and Fluorescence In Situ Hybridization. LABORATORY INVESTIGATION. 92. p. 70A--70A.
White, Helen and So, A and Koehler, R and Troup, C and Heredia, N and Hindson, C and McDermott, G and Karlin-Neumann, G and Saxonov, S and Skinner, A and others(2012). Ultra-sensitive detection of somatic mutations by droplet digital PCR with conventional TaqMan assays. JOURNAL OF MEDICAL GENETICS. 49. p. S55--S55.
Hennig, G and Acht, T and Euting, H and von Salis, A and Koehler, R and Windbergs, C and Bohmann, K(2008). Analytical Evaluation of a Manually and Fully Automated Nucleic Acid Isolation Technology for RNA from Formalin-Fixed Paraffin-Embedded Tissue Sections. JOURNAL OF MOLECULAR DIAGNOSTICS. 10. (6). p. 614--614.
Hyland, FCL and Ziegle, J and Day, J and Scafe, C and Koehler, R and Peyret, N and Larry, C and Rhodes, M and Woodage, T and You, X and others(2005). A cluster-based SNP linkage mapping set based on genetic distances and on haplotype heterozygosity. GENETIC EPIDEMIOLOGY. 29. (3). p. 257--257.
Day, JP and Koehler, RT and Peyret, N and Scafe, C and Lippert, R and Rhodes, M and Ziegle, J and Hayashibara, KC and Chen, C and Wenz, M and others(2003). A multiplexed ultra-high throughput genotyping platform based on the oligonucleotide ligation assay: Design pipeline, conversion rate, and genotyping accuracy. AMERICAN JOURNAL OF HUMAN GENETICS. 73. (5). p. 441--441.
Koehler, Ryan and Peyret, Nicolas(2002). A Theoretical Survey of DNA Oligomers Thermodynamic Properties. APS Meeting Abstracts.
Rhodes, MD and Dailey, D and Dong, P and Gilbert, DA and Scafe, C and Wang, Y and Laig-Webster, M and Su, X and Koehler, R and Avi-Itzhak, H and others(2002). A validated set of SNIPS for linkage mapping studies. AMERICAN JOURNAL OF HUMAN GENETICS. 71. (4). p. 442--442.
Gilbert, D and Scafe, C and Wang, Y and Laig-Webster, M and Su, X and Koehler, R and Avi-Izthak, H and Ziegle, J and Wogan, L and Spier, E and others(2002). A whole-genome linkage disequilibrium SNP map and validated assay resource. AMERICAN JOURNAL OF HUMAN GENETICS. 71. (4). p. 404--404.
Wenz, MH and Bach, A and Day, J and de la Vega, F and Friedlander, E and Hayashibara, K and Holden, D and Johnson, S and Koehler, R and Leong, L and others(2002). Accurate SNP genotypes determined using a multiplex ligation/PCR based assay (OLA/PCR) in combination with a universal DNA microarray. EUROPEAN JOURNAL OF HUMAN GENETICS. 10. p. 299--299.
Koehler, Ryan T and Peyret, Nicolas(2002). Distributions of free energy, melting temperature, and hybridization propensity for genomic DNA oligomers. Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society. p. 337.
Koehler, RT and Dixon, SL and Villar, HO(1999). Simple method to simultaneously increase diversity and favorably enrich the content of chemical libraries. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 218. p. U353--U354.
Koehler, RT and Villar, HO(1999). Simulating affinity fingerprints: Statistical relationships among docking scores for different protein-binding sites. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 218. p. U493--U493.
Wipke, WT and Koehler, R(1995). Characterizing molecular diversity of molecular populations. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 209. p. 2--COMP.
WIPKE, WT and PITMAN, MC and KOEHLER, RT(1994). DE-NOVO DESIGN WITHIN THE HIV PROTEASE ACTIVE-SITE-APPLICATIONS OF THE INVENTION SYSTEM. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 208. p. 155--COMP.
WIPKE, WT and PITMAN, M and KOEHLER, R and KAPPLER, M(1993). EXPLORATION OF DESIGNING MOLECULES AUTOMATICALLY. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 205. p. 20--COMP.
WIPKE, WT and PITMAN, MC and KOEHLER, RT and KISLIN, BS and ANDERSON, GD(1991). INVENTON-A SYSTEM TO INVENT CHEMICAL STRUCTURES. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. 202. p. 16--CINF.