Laura L Elo

Laura L Elo

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Laura L Elo

Laura L Elo

Publications by authors named "Laura L Elo"

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Prediction of complication related death after radical cystectomy for bladder cancer with machine learning methodology.

Scand J Urol 2019 Sep 25:1-7. Epub 2019 Sep 25.

Department of Urology, Turku University Hospital and University of Turku , Turku , Finland.

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http://dx.doi.org/10.1080/21681805.2019.1665579DOI Listing
September 2019

Gut microbiota composition is associated with temperament traits in infants.

Brain Behav Immun 2019 Aug 24;80:849-858. Epub 2019 May 24.

The FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical, Medicine, University of Turku, Lemminkäisenkatu 3 a, Teutori Building, 20014 Turun yliopisto, Finland; Department of Child Psychiatry, Turku University Hospital and University of Turku, Kiinamyllynkatu 4-8, 20520 Turku, Finland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08891591193007
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http://dx.doi.org/10.1016/j.bbi.2019.05.035DOI Listing
August 2019

RepViz: a replicate-driven R tool for visualizing genomic regions.

BMC Res Notes 2019 Jul 19;12(1):441. Epub 2019 Jul 19.

Turku Bioscience Centre, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520, Turku, Finland.

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http://dx.doi.org/10.1186/s13104-019-4473-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642542PMC
July 2019

L1TD1 - a prognostic marker for colon cancer.

BMC Cancer 2019 Jul 23;19(1):727. Epub 2019 Jul 23.

Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.

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http://dx.doi.org/10.1186/s12885-019-5952-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6651905PMC
July 2019

A Data Analysis Protocol for Quantitative Data-Independent Acquisition Proteomics.

Methods Mol Biol 2019 ;1871:455-465

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.

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http://dx.doi.org/10.1007/978-1-4939-8814-3_27DOI Listing
June 2019

Hypoxia-inducible factor (HIF)-prolyl hydroxylase 3 (PHD3) maintains high mRNA levels in clear cell renal cell carcinoma.

J Biol Chem 2019 03 7;294(10):3760-3771. Epub 2019 Jan 7.

From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland,

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA118.004902
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http://dx.doi.org/10.1074/jbc.RA118.004902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416423PMC
March 2019

PASI: A novel pathway method to identify delicate group effects.

PLoS One 2018 5;13(7):e0199991. Epub 2018 Jul 5.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199991PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033442PMC
January 2019

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

Brief Bioinform 2018 11;19(6):1344-1355

Biomathematics, Research Director in Bioinformatics and Group Leader in Computational Biomedicine at Turku Centre for Biotechnology, University of Turku, Finland.

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http://dx.doi.org/10.1093/bib/bbx054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291797PMC
November 2018

Intratumoral androgen levels are linked to TMPRSS2-ERG fusion in prostate cancer.

Endocr Relat Cancer 2018 09 17;25(9):807-819. Epub 2018 May 17.

Research Centre for Integrative Physiology and PharmacologyInstitute of Biomedicine, University of Turku, Turku, Finland

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http://dx.doi.org/10.1530/ERC-18-0148DOI Listing
September 2018

Hydroxysteroid (17β) dehydrogenase 13 deficiency triggers hepatic steatosis and inflammation in mice.

FASEB J 2018 06 31;32(6):3434-3447. Epub 2018 Jan 31.

Research Centre for Integrative Physiology and Pharmacology, Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland.

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http://dx.doi.org/10.1096/fj.201700914RDOI Listing
June 2018

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics.

Bioinformatics 2018 02;34(4):693-694

Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btx573DOI Listing
February 2018

Accurate Detection of Differential Expression and Splicing Using Low-Level Features.

Methods Mol Biol 2017 ;1507:141-151

Turku Centre for Biotechnology, Tykistökatu 6, 20520, Turku, Finland.

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http://dx.doi.org/10.1007/978-1-4939-6518-2_11DOI Listing
January 2018

Antiandrogens Reduce Intratumoral Androgen Concentrations and Induce Androgen Receptor Expression in Castration-Resistant Prostate Cancer Xenografts.

Am J Pathol 2018 01 7;188(1):216-228. Epub 2017 Nov 7.

Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland; Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, Turku, Finland; Center for Bone and Arthritis Research, The Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029440173053
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http://dx.doi.org/10.1016/j.ajpath.2017.08.036DOI Listing
January 2018

A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.

JCO Clin Cancer Inform 2017 11;1:1-15

Fatemeh Seyednasrollah and Laura L. Elo, Turku Centre for Biotechnology; University of Turku; Åbo Akademi University, Turku, Finland; Devin C. Koestler, University of Kansas Medical Center, Kansas City, KS; Tao Wang, University of Texas Southwestern Medical Center, Dallas, TX; Stephen R. Piccolo, Brigham Young University, Provo; University of Utah, Salt Lake City, Utah, UT; Roberto Vega, Russell Greiner, and Luke Kumar, University of Alberta; Alberta Innovates Centre for Machine Learning, Edmonton, Alberta, Canada; Christiane Fuchs, Helmholtz Zentrum München, Neuherberg; Technische Universität München, Garching, Germany; Eyal Gofer, The Hebrew University, Jerusalem, Israel; Russell D. Wolfinger, SAS Institute, Cary, NC; Kimberly Kanigel Winner and James C. Costello, University of Colorado, Anschutz Medical Campus, Aurora, CO; Chris Bare, Elias Chaibub Neto, Thomas Yu, Thea Norman, and Justin Guinney, Sage Bionetworks, Seattle, WA; Liji Shen and Fang Liz Zhou, Sanofi, Bridgewater, NJ; Kald Abdallah, AstraZeneca, Gaithersburg, MD; Gustavo Stolovitzky, IBM Research, Yorktown Heights; Howard I. Scher, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY; Howard R. Soule, Prostate Cancer Foundation, Santa Monica; Charles J. Ryan, University of California, San Francisco, CA; Christopher J. Sweeney, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA; and Oliver Sartor, Tulane University, New Orleans, LA.

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http://dx.doi.org/10.1200/CCI.17.00018DOI Listing
November 2017

Assessing the utilization of radiotherapy near end of life at a Finnish University Hospital: a retrospective cohort study.

Acta Oncol 2017 Oct 13;56(10):1265-1271. Epub 2017 May 13.

a Department of Oncology and Radiotherapy , Turku University Hospital , Turku , Finland.

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http://dx.doi.org/10.1080/0284186X.2017.1324638DOI Listing
October 2017

End-of-life chemotherapy use at a Finnish university hospital: a retrospective cohort study.

Acta Oncol 2017 Oct 31;56(10):1272-1276. Epub 2017 May 31.

a Department of Oncology and Radiotherapy , Turku University Hospital , Turku , Finland.

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http://dx.doi.org/10.1080/0284186X.2017.1332424DOI Listing
October 2017

HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma.

Cancer Metab 2017 4;5. Epub 2017 Jul 4.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland.

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http://dx.doi.org/10.1186/s40170-017-0167-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496173PMC
July 2017

Enhanced differential expression statistics for data-independent acquisition proteomics.

Sci Rep 2017 07 19;7(1):5869. Epub 2017 Jul 19.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.

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http://dx.doi.org/10.1038/s41598-017-05949-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517573PMC
July 2017

Prediction of Adulthood Obesity Using Genetic and Childhood Clinical Risk Factors in the Cardiovascular Risk in Young Finns Study.

Circ Cardiovasc Genet 2017 Jun;10(3)

From the Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Finland (F.S., J.M., L.L.E.); Department of Mathematics and Statistics (F.S.), Research Centre of Applied and Preventive Cardiovascular Medicine (N.P., O.T.R.), and Department of Medicine (M.J., J.V.), University of Turku, Finland; Division of Medicine (M.J., J.V.) and Clinical Physiology and Nuclear Medicine (O.T.R.), Turku University Hospital, Finland; Department of Pediatrics (N.H.-K.) and School of Medicine (T.L.), University of Tampere, Finland; Tampere University Hospital, Finland (N.H.-K.); Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland (T.L.); Tulane University Health Sciences Center, New Orleans, LA (T.K., L.B.); and Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens (C.L.).

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http://dx.doi.org/10.1161/CIRCGENETICS.116.001554DOI Listing
June 2017

ROTS: An R package for reproducibility-optimized statistical testing.

PLoS Comput Biol 2017 05 25;13(5):e1005562. Epub 2017 May 25.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.

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http://dx.doi.org/10.1371/journal.pcbi.1005562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470739PMC
May 2017

Erratum to: A survey of best practices for RNA-seq data analysis.

Genome Biol 2016 Aug 26;17(1):181. Epub 2016 Aug 26.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA.

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http://dx.doi.org/10.1186/s13059-016-1047-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000515PMC
August 2016

Brief Isoflurane Anesthesia Produces Prominent Phosphoproteomic Changes in the Adult Mouse Hippocampus.

ACS Chem Neurosci 2016 06 28;7(6):749-56. Epub 2016 Apr 28.

Turku Centre for Biotechnology, University of Turku , FI-20014 Turku, Finland.

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http://dx.doi.org/10.1021/acschemneuro.6b00002DOI Listing
June 2016

Empirical comparison of structure-based pathway methods.

Brief Bioinform 2016 Mar 21;17(2):336-45. Epub 2015 Jul 21.

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http://dx.doi.org/10.1093/bib/bbv049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793894PMC
March 2016

Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse.

J Proteomics 2016 Feb 9;133:66-75. Epub 2015 Dec 9.

Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland; Turku Center for Disease Modeling, University of Turku, Turku, Finland. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2015.12.009DOI Listing
February 2016

ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer.

Nucleic Acids Res 2016 Jan 11;44(1):e1. Epub 2015 Aug 11.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FI-20520, Finland Department of Mathematics and Statistics, University of Turku, Turku, FI-20014, Finland

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http://dx.doi.org/10.1093/nar/gkv806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705679PMC
January 2016

A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.

PLoS One 2014 26;9(12):e115964. Epub 2014 Dec 26.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland; Department of Mathematics and Statistics, University of Turku, Turku, Finland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115964PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277429PMC
November 2015

Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins.

J Proteome Res 2015 Nov 29;14(11):4564-70. Epub 2015 Sep 29.

Van't Hoff Institute for Molecular Sciences, University of Amsterdam , 1090 GD Amsterdam , The Netherlands.

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http://dx.doi.org/10.1021/acs.jproteome.5b00363DOI Listing
November 2015

Optimization of Statistical Methods Impact on Quantitative Proteomics Data.

J Proteome Res 2015 Oct 8;14(10):4118-26. Epub 2015 Sep 8.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University , Tykistökatu 6, FI-20520 Turku, Finland.

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http://dx.doi.org/10.1021/acs.jproteome.5b00183DOI Listing
October 2015

Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia.

Proteomics 2014 Nov 15;14(21-22):2443-53. Epub 2014 Oct 15.

Department of Mathematics and Statistics, University of Turku, Turku, Finland; Turku Centre for Biotechnology, Turku, Finland.

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http://dx.doi.org/10.1002/pmic.201300460DOI Listing
November 2014

Analysis of time-resolved gene expression measurements across individuals.

PLoS One 2013 9;8(12):e82340. Epub 2013 Dec 9.

Systems Biology Lab, Department of Genomes and Genetics, Institut Pasteur, Paris, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082340PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3857324PMC
October 2014

Innate immune activity is detected prior to seroconversion in children with HLA-conferred type 1 diabetes susceptibility.

Diabetes 2014 Jul 18;63(7):2402-14. Epub 2014 Feb 18.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FinlandThe Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Helsinki, Finland

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http://dx.doi.org/10.2337/db13-1775DOI Listing
July 2014

Optimizing detection of transcription factor-binding sites in ChIP-seq experiments.

Methods Mol Biol 2013 ;1038:181-91

CSC-IT Center for Science Ltd, Espoo, Finland.

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http://dx.doi.org/10.1007/978-1-62703-514-9_11DOI Listing
February 2014

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

Nucleic Acids Res 2013 May 5;41(10):e110. Epub 2013 Apr 5.

Department of Veterinary Bioscience, University of Helsinki, Agnes Sjöbergin katu 2, PO Box 66, FI-00014 University of Helsinki, Finland.

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http://dx.doi.org/10.1093/nar/gkt229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664815PMC
May 2013

Optimized detection of transcription factor-binding sites in ChIP-seq experiments.

Nucleic Acids Res 2012 Jan 18;40(1):e1. Epub 2011 Oct 18.

Department of Mathematics, University of Turku, FI-20014 Turku, Finland.

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http://dx.doi.org/10.1093/nar/gkr839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245948PMC
January 2012

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays.

IEEE/ACM Trans Comput Biol Bioinform 2011 Jan-Mar;8(1):217-25

Helsinki Institute for Information Technology, Department of Information and Computer Science, Aalto University School of Science and Technology, PO Box 15400, FI-00076 Aalto, Finland.

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http://ieeexplore.ieee.org/document/4906986/
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http://dx.doi.org/10.1109/TCBB.2009.38DOI Listing
February 2011

Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling.

J Autoimmun 2010 Aug 30;35(1):70-6. Epub 2010 Mar 30.

Turku Centre for Biotechnology, University of Turku and Abo Akademi University, FI-20521 Turku, Finland.

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http://dx.doi.org/10.1016/j.jaut.2010.03.001DOI Listing
August 2010

Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies.

Genome Biol 2009 16;10(7):R77. Epub 2009 Jul 16.

Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, FI-20521, Finland.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2009-10-7-r77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728531PMC
January 2010

Resampling reveals sample-level differential expression in clinical genome-wide studies.

OMICS 2009 Oct;13(5):381-96

Biomathematics Research Group, Department of Mathematics, University of Turku, Turku, Finland.

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http://dx.doi.org/10.1089/omi.2009.0027DOI Listing
October 2009

Reproducibility-optimized test statistic for ranking genes in microarray studies.

IEEE/ACM Trans Comput Biol Bioinform 2008 Jul-Sep;5(3):423-31

Department of Mathematics, University of Turku, Turku, Finland.

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http://dx.doi.org/10.1109/tcbb.2007.1078DOI Listing
September 2008

Predicting quantitative genetic interactions by means of sequential matrix approximation.

PLoS One 2008 Sep 26;3(9):e3284. Epub 2008 Sep 26.

Biomathematics Research Group, Department of Mathematics, University of Turku, Turku, Finland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003284PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538561PMC
September 2008

Missing value imputation improves clustering and interpretation of gene expression microarray data.

BMC Bioinformatics 2008 Apr 18;9:202. Epub 2008 Apr 18.

Department of Information Technology and TUCS, University of Turku, FI-20014 Turku, Finland.

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http://dx.doi.org/10.1186/1471-2105-9-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386492PMC
April 2008

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process.

Bioinformatics 2007 Aug 6;23(16):2096-103. Epub 2007 Jun 6.

Department of Mathematics, FI-20014 University of Turku, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btm309DOI Listing
August 2007

Integrating probe-level expression changes across generations of Affymetrix arrays.

Nucleic Acids Res 2005 Dec 14;33(22):e193. Epub 2005 Dec 14.

Department of Mathematics, FIN-20014, University of Turku, Finland.

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http://dx.doi.org/10.1093/nar/gni193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1316121PMC
December 2005