Biomarker Technologies Inc.

Rohnert Park, CA, United States

Biomarker Technologies Inc.

Rohnert Park, CA, United States
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Wang Y.,Stanford University | Wang Y.,Royal Dutch Shell | Peters K.E.,Stanford University | Peters K.E.,Schlumberger | And 4 more authors.
AAPG Bulletin | Year: 2014

Forty-one crude oil samples from the North Slope of Alaska have variable diamondoid and biomarker concentrations, indicating different extents of oil cracking. Some of the samples are mixtures of high- and low-maturity components containing high concentrations of both diamondoids and biomarkers. Compound-specific isotope analysis of diamondoids (CSIAD) shows that the Shublik Formation accounts for the higher maturity component in several mixed oil samples, whereas biomarkers, especially those providing information on the age of the source rock, show either a Cretaceous Hue-gamma ray zone (GRZ) or Triassic Shublik source for the lower maturity component. Oil samples in this study mainly correlate to six source rocks based on their biomarker characteristics and CSIAD. Chemometrics of selected source-related biomarker and isotope ratios helps to classify the oil samples into different genetic families. The source rocks include carbonate and shale organofacies of the Triassic Shublik Formation, Jurassic Kingak Shale, Lower Cretaceous Pebble shale, Lower Cretaceous Hue-GRZ, and Cenozoic Canning Formation. Oil presumed to originate from a seventh source rock interval, the Carboniferous-Permian Lisburne Group, was not clearly differentiated from well-established Shublik oil by any geochemical age-related parameter or CSIAD, which suggests that the Lisburne is not an effective source rock for any of the studied oil samples. Four oil samples collected from wells located north of the Barrow arch show unique biomarker characteristics, but age-related biomarker parameters indicate likely Triassic source rock organofacies that is not represented by any of the samples from south of the arch. The source rock for these four oil samples appears to be a clay-rich equivalent of the calcareous Shublik Formation that occurs to the north of the Barrow arch. Copyright © 2014. The American Association of Petroleum Geologists. All rights reserved.

Peters K.E.,Schlumberger | Peters K.E.,Stanford University | Moldowan J.M.,Biomarker Technologies Inc. | LaCroce M.V.,Pennsylvania State University | Kubicki J.D.,Pennsylvania State University
Organic Geochemistry | Year: 2014

Gas chromatography-mass spectrometry-mass spectrometry (GC-MS-MS) reveals four C28 13β,17α(H)-diasterane (diaergostane) peaks in petroleum from clay-rich source rocks, although only two diasterane peaks are commonly observed for each of the C26, C27, and C29 diasteranes. Co-injection of two laboratory synthesized diaergostane standards having 5β(CH3),13β(H),14β(CH3),17α(H)-20S,24R and -20R,24R stereochemistry allowed assignment of the elution order for the four diaergostane peaks as follows: 20S,24R; 20S,24S; 20R,24S; 20R,24R. Partial least-squares regression analysis of 11 quantum chemical descriptors (e.g., molar volume, polarizability, torsion angles and surface area) determined by molecular modeling of the C27-C30 diasteranes, can be used to construct a model that validates the relative GC retention times of the stereoisomers of these compounds. Similar calculated Gibbs free energies for the lowest-energy conformers of the modeled C28 20S,24R versus 20S,24S and 20R,24S versus 20R,24R diasteranes explain why they occur in similar abundance. © 2014 Elsevier Ltd.

Chichester C.,Swiss Institute of Bioinformatics | Gaudet P.,Swiss Institute of Bioinformatics | Karch O.,Biomarker Technologies Inc. | Groth P.,VU University Amsterdam | And 6 more authors.
Journal of Web Semantics | Year: 2014

Understanding how genetic differences between individuals impact the regulation, expression, and ultimately function of proteins is an important step toward realizing the promise of personal medicine. There are several technical barriers hindering the transition of biological knowledge into the applications relevant to precision medicine. One important challenge for data integration is that new biological sequences (proteins, DNA) have multiple issues related to interoperability potentially creating a quagmire in the published data, especially when different data sources do not appear to be in agreement. Thus, there is an urgent need for systems and methodologies to facilitate the integration of information in a uniform manner to allow seamless querying of multiple data types which can illuminate, for example, the relationships between protein modifications and causative genomic variants. Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information about human proteins. We have applied the nanopublication model to demonstrate querying over several named graphs, including the provenance information associated with the curated scientific assertions from neXtProt. We show by way of use cases using sequence variations, post-translational modifications (PTMs) and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach for expanding biological insight. © 2014 Elsevier B.V.

Moldowan J.M.,Stanford University | Moldowan J.M.,Biomarker Technologies Inc. | Dahl J.,Stanford University | Zinniker D.,Stanford University | And 2 more authors.
Journal of Petroleum Science and Engineering | Year: 2015

In many regional geochemical studies of prolific basins, thermally-altered fluids generated from deep, post-mature sources mixed with normally-mature black oil from mature sources have gone unrecognized, uncharacterized, and the extent to which those mixtures have occurred has been underestimated. Quantitative diamondoid analysis (QDA) is discussed as a method to reveal such mixtures and examples from the San Joaquin Basin, California, USA, and the offshore Santos Basin, Brazil, are used to illustrate this application. While QDA reveals mixed-source oils, other techniques are necessary to correlate the mature component of the oil to its source, an identification which is necessary for correct input of effective sources into basin models. One of these methods is quantitative extended diamondoid analysis (QEDA). It consists of comparing relative concentrations of large diamondoid isomers and homologs in oils and condensates. Correlations using QEDA are much like biomarkers correlations. However, due to the stability of diamondoids, QEDA can be done on fluids of very high thermal maturity. Compound specific isotope analysis of diamondoids (CSIA-D), the determination of the carbon isotopic signature of a variety of individual diamondoid species, is another novel and complementary method to tie high-maturity fluids back to their source. QEDA and CSIA-D are, in fact, universally applicable to all source-correlation problems. Example correlations using QEDA and CSIA-D from Eastern Venezuela, West Africa (Ghana), Brazil margin, West Siberia and the Williston Basin are discussed. © 2014 Elsevier B.V.

Chichester C.,Swiss Institute of Bioinformatics | Karch O.,Biomarker Technologies Inc. | Gaudet P.,Swiss Institute of Bioinformatics | Lane L.,Swiss Institute of Bioinformatics | And 2 more authors.
Semantic Web | Year: 2015

neXtProt provides a comprehensive knowledgebase on human proteins complemented by an extensive cross incorporation of annotations from many databases. With the diversity of published data, provenance information becomes critical to providing reliable and trustworthy services to scientists, thus the tracking of provenance in open, decentralized systems is especially important. Since the nanopublication system addresses many of these challenges, we have developed the neXtProt Linked Data by serializing in RDF/XML annotations specific to neXtProt and started employing the nanopublication model to give appropriate attribution to all data. Specifically, a use case demonstrates the handling of post-translational modification (PTM) data modeled as nanopublications to illustrate how the different levels of provenance and data quality thresholds can be captured in this model. © IOS Press and the authors

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