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1

bioWeb3D: an online webGL 3D data visualisation tool

Jean-Baptiste Pettit, John C Marioni

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 546 KB

english, 2013

2

Computational and analytical challenges in single-cell transcriptomics

Stegle, Oliver, Teichmann, Sarah A., Marioni, John C.

Journal:

Nature Reviews Genetics

Year:

2015

Language:

english

File:

PDF, 925 KB

english, 2015

3

Resolving early mesoderm diversification through single-cell expression profiling

Scialdone, Antonio, Tanaka, Yosuke, Jawaid, Wajid, Moignard, Victoria, Wilson, Nicola K., Macaulay, Iain C., Marioni, John C., Göttgens, Berthold

Journal:

Year:

2016

Language:

english

File:

PDF, 12.55 MB

english, 2016

4

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology

Marioni, John C., Arendt, Detlev

Journal:

Annual Review of Cell and Developmental Biology

Year:

2017

Language:

english

File:

PDF, 1.02 MB

english, 2017

5

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

Achim, Kaia, Pettit, Jean-Baptiste, Saraiva, Luis R, Gavriouchkina, Daria, Larsson, Tomas, Arendt, Detlev, Marioni, John C

Journal:

Nature Biotechnology

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

6

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

Haghverdi, Laleh, Lun, Aaron T L, Morgan, Michael D, Marioni, John C

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 3.93 MB

english, 2018

7

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

Stefflova, Klara, Thybert, David, Wilson, Michael D., Streeter, Ian, Aleksic, Jelena, Karagianni, Panagiota, Brazma, Alvis, Adams, David J., Talianidis, Iannis, Marioni, John C., Flicek, Paul, Odom, D

Journal:

Year:

2013

Language:

english

File:

PDF, 875 KB

english, 2013

8

Accounting for technical noise in single-cell RNA-seq experiments

Brennecke, Philip, Anders, Simon, Kim, Jong Kyoung, Kołodziejczyk, Aleksandra A, Zhang, Xiuwei, Proserpio, Valentina, Baying, Bianka, Benes, Vladimir, Teichmann, Sarah A, Marioni, John C, Heisler, Mar

Journal:

Year:

2013

Language:

english

File:

PDF, 609 KB

english, 2013

9

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Buettner, Florian, Natarajan, Kedar N, Casale, F Paolo, Proserpio, Valentina, Scialdone, Antonio, Theis, Fabian J, Teichmann, Sarah A, Marioni, John C, Stegle, Oliver

Journal:

Nature Biotechnology

Year:

2015

Language:

english

File:

PDF, 1.08 MB

english, 2015

10

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

Goolam, Mubeen, Scialdone, Antonio, Graham, Sarah J.L., Macaulay, Iain C., Jedrusik, Agnieszka, Hupalowska, Anna, Voet, Thierry, Marioni, John C., Zernicka-Goetz, Magdalena

Journal:

Year:

2016

Language:

english

File:

PDF, 4.02 MB

english, 2016

11

DNA methylation and the epigenetic clock in relation to physical frailty in older people: the Lothian Birth Cohort 1936

Gale, Catharine R., Marioni, Riccardo E., Harris, Sarah E., Starr, John M., Deary, Ian J.

Journal:

Clinical Epigenetics

Year:

2018

Language:

english

File:

PDF, 845 KB

english, 2018

12

DNA methylation-based measures of accelerated biological ageing and the risk of dementia in the oldest-old: a study of the Lothian Birth Cohort 1921

Sibbett, Ruth A., Altschul, Drew M., Marioni, Riccardo E., Deary, Ian J., Starr, John M., Russ, Tom C.

Journal:

Year:

2020

File:

PDF, 1017 KB

2020

13

Genomic-scale capture and sequencing of endogenous DNA from feces

GEORGE H. PERRY, JOHN C. MARIONI, PÁLL MELSTED, YOAV GILAD

Journal:

Molecular Ecology

Year:

2010

Language:

english

File:

PDF, 7.69 MB

english, 2010

14

Understanding mechanisms underlying human gene expression variation with RNA sequencing

Pickrell, Joseph K., Marioni, John C., Pai, Athma A., Degner, Jacob F., Engelhardt, Barbara E., Nkadori, Everlyne, Veyrieras, Jean-Baptiste, Stephens, Matthew, Gilad, Yoav, Pritchard, Jonathan K.

Journal:

Year:

2010

Language:

english

File:

PDF, 1.12 MB

english, 2010

15

ESR1 gene amplification in breast cancer: a common phenomenon?

Brown, Lindsay A, Hoog, Jeremy, Chin, Suet-Feung, Tao, Yu, Zayed, Abd Alnaser, Chin, Koei, Teschendorff, Andrew E, Quackenbush, John F, Marioni, John C, Leung, Samuel

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 137 KB

english, 2008

16

Feeding Behavior of Two Sympatric Caiman Species, Melanosuchus niger and Caiman crocodilus, in the Brazilian Amazon

Marioni, Boris, Da Silveira, Ronis, Magnusson, William E, Thorbjarnarson, John

Journal:

Journal of Herpetology

Year:

2008

Language:

english

File:

PDF, 143 KB

english, 2008

17

The pitfalls of platform comparison: DNA copy number array technologies assessed

Christina Curtis, Andy G Lynch, Mark J Dunning, Inmaculada Spiteri, John C Marioni, James Hadfield, Suet-Feung Chin, James D Brenton, Simon Tavaré, Carlos Caldas

Journal:

Year:

2009

Language:

english

File:

PDF, 1.46 MB

english, 2009

18

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: a double-blind, randomized, placebo-controlled study

Graham S Hillis, Claire V Pearson, Scott A Harding, Sheena Sutherland, Christopher A Ludlam, John C Marioni, Robin J Prescott, Keith A.A Fox, Andrew D Flapan

Journal:

American Heart Journal

Year:

2004

Language:

english

File:

PDF, 137 KB

english, 2004

19

Conservation and management implications of nest-site selection of the sympatric crocodilians Melanosuchus niger and Caiman crocodilus in Central Amazonia, Brazil

Francisco Villamarín, Boris Marioni, John B. Thorbjarnarson, Bruce W. Nelson, Robinson Botero-Arias, William E. Magnusson

Journal:

Biological Conservation

Year:

2011

Language:

english

File:

PDF, 722 KB

english, 2011

20

O10: An improved algorithm for segmenting array-CGH data

John C. Marioni, Natalie P. Thorne, Jessica C. Pole, Paul A.W. Edwards, Simon Tavaré

Journal:

European Journal of Medical Genetics

Year:

2005

Language:

english

File:

PDF, 46 KB

english, 2005

21

Association of KIBRA and memory

Timothy C. Bates, Jackie F. Price, Sarah E. Harris, Riccardo E. Marioni, F. Gerry R. Fowkes, Marlene C. Stewart, Gordon D. Murray, Lawrence J. Whalley, John M. Starr, Ian J. Deary

Journal:

Neuroscience Letters

Year:

2009

Language:

english

File:

PDF, 131 KB

english, 2009

22

Numbers of Copy-Number Variations and False-Negative Rates Will Be Underestimated If We Do Not Account for the Dependence between Repeated Experiments

Andy G. Lynch, John C. Marioni, Simon Tavaré

Journal:

The American Journal of Human Genetics

Year:

2007

Language:

english

File:

PDF, 64 KB

english, 2007

23

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

Jong Kyoung Kim, John C Marioni

Journal:

Year:

2013

Language:

english

File:

PDF, 467 KB

english, 2013

24

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

Suet F Chin, Andrew E Teschendorff, John C Marioni, Yanzhong Wang…

Journal:

Year:

2007

Language:

english

File:

PDF, 1.47 MB

english, 2007

25

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization

John C Marioni, Natalie P Thorne, Armand Valsesia, Tomas Fitzgerald…

Journal:

Year:

2007

Language:

english

File:

PDF, 10.92 MB

english, 2007

26

Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation

Eckersley-Maslin, Mélanie A., Thybert, David, Bergmann, Jan H., Marioni, John C., Flicek, Paul, Spector, David L.

Journal:

Developmental Cell

Year:

2014

Language:

english

File:

PDF, 3.72 MB

english, 2014

27

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Uslu, Veli Vural, Petretich, Massimo, Ruf, Sandra, Langenfeld, Katja, Fonseca, Nuno A, Marioni, John C, Spitz, François

Journal:

Nature Genetics

Year:

2014

Language:

english

File:

PDF, 1.07 MB

english, 2014

28

Veterinary Medicine Today What Is Your Neurologic Diagnosis?

Marioni, Katia, Hathcock, John T., Simpson, Stephen T.

Journal:

Journal of the American Veterinary Medical Association

Year:

2001

Language:

english

File:

PDF, 371 KB

english, 2001

29

Corrigendum: Accounting for technical noise in single-cell RNA-seq experiments

Brennecke, Philip, Anders, Simon, Kim, Jong Kyoung, Kołodziejczyk, Aleksandra A, Zhang, Xiuwei, Proserpio, Valentina, Baying, Bianka, Benes, Vladimir, Teichmann, Sarah A, Marioni, John C, Heisler, Mar

Journal:

Year:

2014

Language:

english

File:

PDF, 95 KB

english, 2014

30

Single Cell Genomics meeting in Stockholm: from single cells to cell types

Scialdone, Antonio, Achim, Kaia, Marioni, John C

Journal:

Year:

2014

Language:

english

File:

PDF, 99 KB

english, 2014

31

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

Pai, Athma A., Bell, Jordana T., Marioni, John C., Pritchard, Jonathan K., Gilad, Yoav, Gibson, Greg

Journal:

Year:

2011

Language:

english

File:

PDF, 1.08 MB

english, 2011

32

The Technology and Biology of Single-Cell RNA Sequencing

Kolodziejczyk, Aleksandra A., Kim, Jong Kyoung, Svensson, Valentine, Marioni, John C., Teichmann, Sarah A.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.05 MB

english, 2015

33

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

Pettit, Jean-Baptiste, Tomer, Raju, Achim, Kaia, Richardson, Sylvia, Azizi, Lamiae, Marioni, John, Morris, Quaid

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.50 MB

english, 2014

34

Functional Comparison of Innate Immune Signaling Pathways in Primates

Barreiro, Luis B., Marioni, John C., Blekhman, Ran, Stephens, Matthew, Gilad, Yoav, Gibson, Greg

Journal:

Year:

2010

Language:

english

File:

PDF, 1.75 MB

english, 2010

35

Computational assignment of cell-cycle stage from single-cell transcriptome data

Scialdone, Antonio, Natarajan, Kedar N., Saraiva, Luis R., Proserpio, Valentina, Teichmann, Sarah A., Stegle, Oliver, Marioni, John C., Buettner, Florian

Journal:

Year:

2015

Language:

english

File:

PDF, 2.65 MB

english, 2015

36

Testing the mean matrix in high-dimensional transposable data

Touloumis, Anestis, Tavaré, Simon, Marioni, John C.

Journal:

Year:

2015

Language:

english

File:

PDF, 197 KB

english, 2015

37

Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation

Peat, Julian R., Dean, Wendy, Clark, Stephen J., Krueger, Felix, Smallwood, Sébastien A., Ficz, Gabriella, Kim, Jong Kyoung, Marioni, John C., Hore, Timothy A., Reik, Wolf

Journal:

Year:

2014

Language:

english

File:

PDF, 1.57 MB

english, 2014

38

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

Schmitt, Bianca M., Rudolph, Konrad L.M., Karagianni, Panagiota, Fonseca, Nuno A., White, Robert J., Talianidis, Iannis, Odom, Duncan T., Marioni, John C., Kutter, Claudia

Journal:

Genome Research

Year:

2014

Language:

english

File:

PDF, 1.29 MB

english, 2014

39

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength

Wickramasinghe, Vihandha O., Gonzàlez-Porta, Mar, Perera, David, Bartolozzi, Arthur R., Sibley, Christopher R., Hallegger, Martina, Ule, Jernej, Marioni, John C., Venkitaraman, Ashok R.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.94 MB

english, 2015

40

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

Kolodziejczyk, Aleksandra A., Kim, Jong Kyoung, Tsang, Jason C.H., Ilicic, Tomislav, Henriksson, Johan, Natarajan, Kedar N., Tuck, Alex C., Gao, Xuefei, Bühler, Marc, Liu, Pentao, Marioni, John C., Te

Journal:

Year:

2015

Language:

english

File:

PDF, 5.62 MB

english, 2015

41

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

Kim, Jong Kyoung, Kolodziejczyk, Aleksandra A., Illicic, Tomislav, Teichmann, Sarah A., Marioni, John C.

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 644 KB

english, 2015

42

Feeding Behavior of Two Sympatric Caiman Species, Melanosuchus niger and Caiman crocodilus, in the Brazilian Amazon

Boris Marioni, Ronis Da Silveira, William E. Magnusson and John Thorbjarnarson

Journal:

Journal of Herpetology

Year:

2008

Language:

english

File:

PDF, 956 KB

english, 2008

43

Longitudinal telomere length shortening and cognitive and physical decline in later life: The Lothian Birth Cohorts 1936 and 1921

Harris, Sarah E., Marioni, Riccardo E., Martin-Ruiz, Carmen, Pattie, Alison, Gow, Alan J., Cox, Simon R., Corley, Janie, von Zglinicki, Thomas, Starr, John M., Deary, Ian J.

Journal:

Mechanisms of Ageing and Development

Year:

2016

Language:

english

File:

PDF, 796 KB

english, 2016

44

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts

L. Lun, Aaron T., Bach, Karsten, Marioni, John C.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.45 MB

english, 2016

45

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

Vallejos, Catalina A., Richardson, Sylvia, Marioni, John C.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.16 MB

english, 2016

46

Classification of low quality cells from single-cell RNA-seq data

Ilicic, Tomislav, Kim, Jong Kyoung, Kolodziejczyk, Aleksandra A., Bagger, Frederik Otzen, McCarthy, Davis James, Marioni, John C., Teichmann, Sarah A.

Journal:

Year:

2016

Language:

english

File:

PDF, 4.01 MB

english, 2016

47

HDTD: analyzing multi-tissue gene expression data

Touloumis, Anestis, Marioni, John C., Tavaré, Simon

Journal:

Year:

2016

Language:

english

File:

PDF, 90 KB

english, 2016

48

Reverse Causation in the Association Between C-Reactive Protein and Fibrinogen Levels and Cognitive Abilities in an Aging Sample

Luciano, Michelle, Marioni, Riccardo E., Gow, Alan J., Starr, John M., Deary, Ian J.

Journal:

Psychosomatic Medicine

Year:

2009

Language:

english

File:

PDF, 219 KB

english, 2009

49

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Howe, Kerstin, Schiffer, Philipp H., Zielinski, Julia, Wiehe, Thomas, Laird, Gavin K., Marioni, John C., Soylemez, Onuralp, Kondrashov, Fyodor, Leptin, Maria

Journal:

Year:

2016

Language:

english

File:

PDF, 1.39 MB

english, 2016

50

Caiman hunting in Central Amazonia, Brazil

Mendonça, Washington Carlos Da Silva, Marioni, Boris, Thorbjarnarson, John B., Magnusson, William E., Da Silveira, Ronis

Journal:

Journal of Wildlife Management

Year:

2016

Language:

english

File:

PDF, 336 KB

english, 2016

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