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Omics Pipe: A Computational Framework for Reproducible Multi-Omics Data Analysis [article]

Kathleen M Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan Carland, Salvatore Loguercio, Andrew I. Su
2014 bioRxiv   pre-print
Omics Pipe (https://bitbucket.org/sulab/omics_pipe) is a computational platform that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas. Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis.
doi:10.1101/008383 fatcat:ocgnupmjtngvbifilon6gl6psi

The C1q domain containing proteins: Where do they come from and what do they do?

Tristan M. Carland, Lena Gerwick
2010 Developmental and Comparative Immunology  
Carland), lgerwick@ucsd.edu (L.  ...  The cbln1 gene is also expressed in the adrenal Protein modeling of three gC1q homologs from the bacterium B. cereus Q1 (white), the mussel M. edulis (pink), and the vertebrate H. sapiens (blue).  ... 
doi:10.1016/j.dci.2010.02.014 pmid:20214925 fatcat:kuy26ms7krhjfns264gdpvqvtm

Differential expression and intrachromosomal evolution of the sghC1q genes in zebrafish (Danio rerio)

Tristan M. Carland, Jeffrey B. Locke, Victor Nizet, Lena Gerwick
2012 Developmental and Comparative Immunology  
Acknowledgements This publication was prepared by Tristan M.  ...  Carland This work was also supported by the University of California at San Diego Academic Senate and the Scripps Institution of Oceanography Graduate Department.  ...  ., 2009) and hybrid striped bass (Morone saxatilis x M. chrysops) (Pasnik and Smith, 2006) among others.  ... 
doi:10.1016/j.dci.2011.05.013 pmid:21683091 fatcat:mshmhntsvfbjderpph43ps6ste

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

Kathleen M. Fisch, Tobias Meißner, Louis Gioia, Jean-Christophe Ducom, Tristan M. Carland, Salvatore Loguercio, Andrew I. Su
2015 Computer applications in the biosciences : CABIOS  
Motivation: Omics Pipe (http://sulab.scripps.edu/omicspipe) is a computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation
more » ... cing analysis. The goal of Omics Pipe is to democratize next-generation sequencing analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results. Results: Using Omics Pipe, we analyzed 100 TCGA breast invasive carcinoma paired tumor-normal datasets based on the latest UCSC hg19 RefSeq annotation. Omics Pipe automatically downloaded and processed the desired TCGA samples on a high throughput compute cluster to produce a results report for each sample. We aggregated the individual sample results and compared them to the analysis in the original publications. This comparison revealed high overlap between the analyses, as well as novel findings due to the use of updated annotations and methods. Availability and implementation: Source code for Omics Pipe is freely available on the web (https://bitbucket.org/sulab/omics_pipe). Omics Pipe is distributed as a standalone Python package for installation (https://pypi.python.org/pypi/omics_pipe) and as an Amazon Machine Image in Amazon Web Services Elastic Compute Cloud that contains all necessary third-party software dependencies and databases (https://pythonhosted.org/omics_pipe/AWS_installation.html).
doi:10.1093/bioinformatics/btv061 pmid:25637560 pmcid:PMC4443682 fatcat:3gwz4pvy7reaflqx2ojcxzlcqq

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

Kristopher A. Standish, Tristan M. Carland, Glenn K. Lockwood, Wayne Pfeiffer, Mahidhar Tatineni, C Chris Huang, Sarah Lamberth, Yauheniya Cherkas, Carrie Brodmerkel, Ed Jaeger, Lance Smith, Gunaretnam Rajagopal (+2 others)
2015 BMC Bioinformatics  
Motivation: Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads associated with NGS technologies requires care and sophistication in order to draw compelling inferences about phenotypic consequences of variation in human genomes. It has been shown that different approaches to variant calling from NGS data can lead to different conclusions.
more » ... ng appropriate accuracy and quality in variant calling can come at a computational cost. Results: We describe our experience implementing and evaluating a group-based approach to calling variants on large numbers of whole human genomes. We explore the influence of many factors that may impact the accuracy and efficiency of group-based variant calling, including group size, the biogeographical backgrounds of the individuals who have been sequenced, and the computing environment used. We make efficient use of the Gordon supercomputer cluster at the San Diego Supercomputer Center by incorporating job-packing and parallelization considerations into our workflow while calling variants on 437 whole human genomes generated as part of large association study. Conclusions: We ultimately find that our workflow resulted in high-quality variant calls in a computationally efficient manner. We argue that studies like ours should motivate further investigations combining hardware-oriented advances in computing systems with algorithmic developments to tackle emerging 'big data' problems in biomedical research brought on by the expansion of NGS technologies.
doi:10.1186/s12859-015-0736-4 pmid:26395405 pmcid:PMC4580299 fatcat:q4otwefczjg2tfi7su2holnstu

p53-Dependent DNA damage response sensitive to editing-defective tRNA synthetase in zebrafish

Youngzee Song, Yi Shi, Tristan M. Carland, Shanshan Lian, Tomoyuki Sasaki, Nicholas J. Schork, Steven R. Head, Shuji Kishi, Paul Schimmel
2016 Proceedings of the National Academy of Sciences of the United States of America  
(Scale bar, 250 μm.) (C) Enlarged pictures of γ-H2AX staining in the nuclei of different samples of zebrafish. (Scale bar, 40 μm.) (D) Quantification of γ-H2AX staining.  ...  (Scale bar, 500 μm.) (C) Quantification of AO staining. Bars represent mean ± SEM.  ...  (Scale bar, 500 μm.) (C) Quantification of AO staining. Bars represent mean ± SEM.  ... 
doi:10.1073/pnas.1608139113 pmid:27402763 pmcid:PMC4968768 fatcat:tqk5m6vldnabzkxfh3u3uv4od4

Activity of novel lipid glycine transporter inhibitors on synaptic signalling in the dorsal horn of the spinal cord

Bryony L Winters, Tristan Rawling, Robert J Vandenberg, Macdonald J Christie, Rebecca F Bhola, Wendy L Imlach
2018 British Journal of Pharmacology  
IC50 data shows inhibition of 30 µM glycine transport by GlyT2 and GlyT1, expressed in Xenopus laevis oocytes from a) Mostyn et al, 2017 and b) Carland et al., 2013.  ...  Oocyte studies show similar GlyT2 IC50 values for the four compounds tested, which range from 0.32 to 0.81 M (Mostyn et al., 2017; Carland et al., 2013; Wiles et al., 2006) .  ... 
doi:10.1111/bph.14189 pmid:29500820 fatcat:zcvlkw337nbufaievwpm5cuquy

Identification of an allosteric binding site on the human glycine transporter, GlyT2, for bioactive lipid analgesics

Shannon N Mostyn, Katie A Wilson, Alexandra Schumann-Gillett, Zachary J Frangos, Susan Shimmon, Tristan Rawling, Renae M Ryan, Megan L O'Mara, Robert J Vandenberg
2019 eLife  
We are grateful for preliminary experimentation and discussions with Amelia Edington, Jane Carland, Robyn Mansfield, Lachlan Munro, Chris Sirote, Emily Crisafulli, Michael Thomas, Diba Sheipouri, and Casey  ...  The simple point charge model was used to describe the water molecules and 0.15 M of Na + and Clions were added. The overall charge of each system was neutral.  ...  We have demonstrated that chimeric GlyT2 transporters containing EL4 from GlyT1 are insensitive to inhibition by NAGly and OLCarn (Carland et al., 2013; Edington et al., 2009) .  ... 
doi:10.7554/elife.47150 pmid:31621581 pmcid:PMC6797481 fatcat:6h3czrkqsrcbrclwway4vltjim

Page 694 of National Union Catalog Vol. 10, Issue [page]

National Union Catalog  
OkU-M NUC68-103667 Savage, George, 1909- L’Art du verre. Texte francais de Jeanine Carlander. Pete Hachette, 11968 ?, lus, (part col.) 22 cm.  ...  Y NUC68-21456 Sauvage, Tristan, pseud. see Schwarz, Arturo, 1924- Sauv: Description F gay d'un dialecte Wolof: le parler de | Dyolot.  ... 

OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing [article]

Tobias Meißner, Kathleen M. Fisch, Louis Gioia, Andrew I. Su
2014 bioRxiv   pre-print
The authors thank Brian Leyland-Jones, Nicholas Schork, Casey Williams, Brandon Young, Tristan Carland and Ali Torkamani for comments and assistance.  ...  ., Campone, M., Bachelot, T. & Jerusalem, G. mTOR inhibitors in advanced breast cancer: ready for prime time? Cancer treatment reviews 39, 742-52 (2013).  ... 
doi:10.1101/008748 fatcat:tfpzipfqingcthgmrmhvc4lf2q

Streptococcus iniae M-Like Protein Contributes to Virulence in Fish and Is a Target for Live Attenuated Vaccine Development

Jeffrey B. Locke, Ramy K. Aziz, Mike R. Vicknair, Victor Nizet, John T. Buchanan, Niyaz Ahmed
2008 PLoS ONE  
Conclusions/Significance: Analysis of M-like protein and C5a peptidase through allelic replacement revealed that M-like protein plays a significant role in S. iniae virulence, and the Mga-like locus, which  ...  The M-like protein mutant created in this research holds promise as live-attenuated vaccine.  ...  Lena Gerwick for providing use of zebrafish challenge facilities, Tristan Carland for assistance with the zebrafish challenges, Carlo Milani for help with the vaccine studies, Dr.  ... 
doi:10.1371/journal.pone.0002824 pmid:18665241 pmcid:PMC2483786 fatcat:lap26skxtva4bbkpebknmnaxze

The 9th European Conference on Marine Natural Products

RuAngelie Edrada-Ebel, Marcel Jaspars
2015 Marine Drugs  
The structural elucidation of 1 was established by NMR spectroscopic and mass spectrometric analysis TOF MS ( ): m/z 259.1009 (C12H19O4S).  ...  Houssen 2,4 , Rainer Ebel 2 , Marcel Jaspars 2 and Luis M Botana 1 We are currently using methods including genome "mining" and co cultivation of our 15 marine Actinomycete species to uncover novel metabolites  ...  Andrén 4 , M. Strand 5,6 and U.  ... 
doi:10.3390/md13127059 pmid:26633429 pmcid:PMC4698589 fatcat:bvnucbwvw5gtpi7cnsixefuyl4

Determinants of entrepreneurial intention and firm performance - evidence from three meta-analyses [article]

Michael König, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität, Christopher Schlägel
2018
Contrary to this, several researchers assume the personality of an entrepreneur as an important impact factor on performance (Carland, Hoy, & Carland, 1988; Rauch & Frese, 2007a; Rauch, 2014) , with a  ...  , Hoy, & Carland, 1988; Rauch & Frese 2007b; Rauch, 2014) .  ...  While some researchers have proposed the entrepreneur and his or her personality as being an important factor to performance (Carland, Hoy, & Carland, 1988; Rauch & Frese, 2007a; Rauch, 2014) , the usefulness  ... 
doi:10.25673/4499 fatcat:7ly3abli3jaz7pkfm3mplxzyou

National Women's Studies Association First National Conference [article]

National Women's Studies Association
1979
M.  ...  Bald, Politics, University of California, Santa Cruz Participants Noriko M.  ... 
doi:10.13016/m2v698f9c fatcat:q6frb3cbgna5dowhhqp2g5n2ju

FOLIA HISTORIAE ARTIUM POLSKA AKADEMIA UMIEJĘTNOŚCI KOMISJA HISTORII SZTUKI KRAKÓW 2017 15 Seria Nowa Seria Pierwsza (tomy I-XXX) wydawana była przez Polską Akademię Nauk-Oddział w Krakowie

Komitet Redakcyjny, David Crowley, Thomas Kaufmann, Marcin Fabiański, Uniwersytet Jagielloński, Kraków, Adam Małkiewicz, Michaela Marek, Sergiusz Michalski, Eberhard Karls, Jan Ostrowski, Uniwersytet Jagielloński (+16 others)
unpublished
Carlander, Svenska bibliotek och ex-libris, s. 21 (jak w przyp. 21). .  ...  M.  ...  the relationship of his own times with the Baroque, declared that both epochs were dominated by similar affects, which can be summarised by the lyrics of Isolde's aria from Richard Wagner's music drama Tristan  ... 
fatcat:ryvigpn63zgn7dsqg67rexgbkq