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1

De novo assembly and genotyping of variants using colored de Bruijn graphs

Iqbal, Zamin, Caccamo, Mario, Turner, Isaac, Flicek, Paul, McVean, Gil

Journal:

Nature Genetics

Year:

2012

Language:

english

File:

PDF, 764 KB

english, 2012

2

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

Down, Thomas A, Rakyan, Vardhman K, Turner, Daniel J, Flicek, Paul, Li, Heng, Kulesha, Eugene, Gräf, Stefan, Johnson, Nathan, Herrero, Javier, Tomazou, Eleni M

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 984 KB

english, 2008

3

Sense from sequence reads: methods for alignment and assembly

Flicek, Paul, Birney, Ewan

Journal:

Year:

2009

Language:

english

File:

PDF, 663 KB

english, 2009

4

Sense from sequence reads: methods for alignment and assembly

Flicek, Paul, Birney, Ewan

Journal:

Year:

2010

Language:

english

File:

PDF, 100 KB

english, 2010

5

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

6

EGASP: the human ENCODE Genome Annotation Assessment Project

Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond…

Journal:

Year:

2006

Language:

english

File:

PDF, 2.61 MB

english, 2006

7

Functional annotation of noncoding sequence variants

Ritchie, Graham R S, Dunham, Ian, Zeggini, Eleftheria, Flicek, Paul

Journal:

Year:

2014

Language:

english

File:

PDF, 352 KB

english, 2014

8

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

Mateo, Juan L., van den Berg, Debbie L.C., Haeussler, Maximilian, Drechsel, Daniela, Gaber, Zachary B., Castro, Diogo S., Robson, Paul, Crawford, Gregory E., Flicek, Paul, Ettwiller, Laurence, Wittbro

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 11.80 MB

english, 2015

9

Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks

Raisaro, Jean Louis, Tramèr, Florian, Ji, Zhanglong, Bu, Diyue, Zhao, Yongan, Carey, Knox, Lloyd, David, Sofia, Heidi, Baker, Dixie, Flicek, Paul, Shringarpure, Suyash, Bustamante, Carlos, Wang, Shuan

Journal:

Journal of the American Medical Informatics Association

Year:

2017

Language:

english

File:

PDF, 374 KB

english, 2017

10

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

Kentepozidou, Elissavet, Aitken, Sarah J., Feig, Christine, Stefflova, Klara, Ibarra-Soria, Ximena, Odom, Duncan T., Roller, Maša, Flicek, Paul

Journal:

Year:

2020

Language:

english

File:

PDF, 2.25 MB

english, 2020

11

Guidelines for the Safe Use of Radioactive Materials During Localization and Resection of the Sentinel Lymph Node

Thomas J. Miner, Craig D. Shriver, Paul R. Flicek, Frederick C. Miner, David P. Jaques, Mary E. Maniscalco-Theberge, David N. Krag

Journal:

Annals of Surgical Oncology

Year:

1999

Language:

english

File:

PDF, 65 KB

english, 1999

12

Journal club

Journal:

Year:

2010

Language:

english

File:

PDF, 488 KB

english, 2010

13

SNP and haplotype mapping for genetic analysis in the rat

Saar, Kathrin, Beck, Alfred, Bihoreau, Marie-Thérèse, Birney, Ewan, Brocklebank, Denise, Chen, Yuan, Cuppen, Edwin, Demonchy, Stephanie, Dopazo, Joaquin, Flicek, Paul

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 332 KB

english, 2008

14

TranscriptSNPView: a genome-wide catalog of mouse coding variation

Cunningham, Fiona, Rios, Daniel, Griffiths, Mark, Smith, James, Ning, Zemin, Cox, Tony, Flicek, Paul, Marin-Garcin, Pablo, Herrero, Javier, Rogers, Jane

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 81 KB

english, 2006

15

Population genomics of human gene expression

Stranger, Barbara E, Nica, Alexandra C, Forrest, Matthew S, Dimas, Antigone, Bird, Christine P, Beazley, Claude, Ingle, Catherine E, Dunning, Mark, Flicek, Paul, Koller, Daphne

Journal:

Nature Genetics

Year:

2007

Language:

english

File:

PDF, 359 KB

english, 2007

16

Maps for the world of genomic medicine: The 2011 CSHL Personal Genomes meeting

Xiangqun Zheng-Bradley, Paul Flicek

Journal:

Year:

2012

Language:

english

File:

PDF, 129 KB

english, 2012

17

A database and API for variation, dense genotyping and resequencing data

Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1012 KB

english, 2010

18

eHive: An Artificial Intelligence workflow system for genomic analysis

Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 4.39 MB

english, 2010

19

Gene finding in the chicken genome

Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline M Bye, Francisco Camara, Paul Flicek, Elizabeth J Huckle, Genis Parra, David D Shteynberg, Carine Wyss, Jane Rogers, Stylianos E Antonaraki

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 448 KB

english, 2005

20

Optimising oligonucleotide array design for ChIP-on-chip

Fiona Nielsen, Stefan Graef, Xinmin Zhang, Stefan Kurtz, Sergei Denissov, Roland Green, Ewan Birney, Paul Flicek, Martijn Huynen, Henk Stunnenberg

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 134 KB

english, 2007

21

nGASP – the nematode genome annotation assessment project

Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, the nGASP Consortium, Lincoln D Stein

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.81 MB

english, 2008

22

Consistent annotation of gene expression arrays

Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek

Journal:

Year:

2010

Language:

english

File:

PDF, 1.35 MB

english, 2010

23

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets

Sebastian Oeder, Joerg Mages, Paul Flicek, Roland Lang

Journal:

Year:

2007

Language:

english

File:

PDF, 4.10 MB

english, 2007

24

An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma

Andrew C Nelson, Nischalan Pillay, Stephen Henderson, Nadège Presneau, Roberto Tirabosco, Dina Halai, Fitim Berisha, Paul Flicek, Derek L Stemple, Claudio D Stern, Fiona C Wardle, Adrienne M Flanagan

Journal:

The Journal of Pathology

Year:

2012

Language:

english

File:

PDF, 6.88 MB

english, 2012

25

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

Dominic Schmidt, Petra C. Schwalie, Michael D. Wilson, Benoit Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom

Journal:

Year:

2012

Language:

english

File:

PDF, 1.90 MB

english, 2012

26

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

Dominic Schmidt, Petra C. Schwalie, Michael D. Wilson, Benoit Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom

Journal:

Year:

2012

Language:

english

File:

PDF, 213 KB

english, 2012

27

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

Daan Peric-Hupkes, Wouter Meuleman, Ludo Pagie, Sophia W.M. Bruggeman, Irina Solovei, Wim Brugman, Stefan Gräf, Paul Flicek, Ron M. Kerkhoven, Maarten van Lohuizen, Marcel Reinders, Lodewyk Wessels, B

Journal:

Year:

2010

Language:

english

File:

PDF, 1.54 MB

english, 2010

28

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

Ann-Marie Mallon, Vivek Iyer, David Melvin, Hugh Morgan, Helen Parkinson, Steve D. M. Brown, Paul Flicek, William C. Skarnes

Journal:

Mammalian Genome

Year:

2012

Language:

english

File:

PDF, 955 KB

english, 2012

29

18-P003 A gene regulatory network for mesoderm directed by zebrafish No tail

Rosie Morley, Kim Lachani, Damian Keefe, Andrew Nelson, Michael Gilchrist, Paul Flicek, Jim Smith, Fiona Wardle

Journal:

Mechanisms of Development

Year:

2009

Language:

english

File:

PDF, 95 KB

english, 2009

30

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero

Journal:

Year:

2011

Language:

english

File:

PDF, 847 KB

english, 2011

31

The need for speed

Journal:

Year:

2009

Language:

english

File:

PDF, 59 KB

english, 2009

32

Gene prediction: compare and CONTRAST

Journal:

Year:

2007

Language:

english

File:

PDF, 101 KB

english, 2007

33

Using several pair-wise informant sequences forde novoprediction of alternatively spliced transcripts

Paul Flicek, Michael R Brent

Journal:

Year:

2006

Language:

english

File:

PDF, 144 KB

english, 2006

34

Locus Reference Genomic sequences: an improved basis for describing human DNA variants

Raymond Dalgleish, Paul Flicek, Fiona Cunningham, Alex Astashyn…

Journal:

Genome Medicine

Year:

2010

Language:

english

File:

PDF, 166 KB

english, 2010

35

Evolutionary biology: The handiwork of tinkering

Journal:

Year:

2013

Language:

english

File:

PDF, 218 KB

english, 2013

36

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

Villar, Diego, Flicek, Paul, Odom, Duncan T.

Journal:

Nature Reviews Genetics

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

37

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

38

CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System

Schauer, Tamás, Schwalie, Petra C., Handley, Ava, Margulies, Carla E., Flicek, Paul, Ladurner, Andreas G.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.94 MB

english, 2013

39

The 1000 Genomes Project: data management and community access

Clarke, Laura, Zheng-Bradley, Xiangqun, Smith, Richard, Kulesha, Eugene, Xiao, Chunlin, Toneva, Iliana, Vaughan, Brendan, Preuss, Don, Leinonen, Rasko, Shumway, Martin, Sherry, Stephen, Flicek, Paul

Journal:

Year:

2012

Language:

english

File:

PDF, 882 KB

english, 2012

40

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

Wong, Emily S., Thybert, David, Schmitt, Bianca M., Stefflova, Klara, Odom, Duncan T., Flicek, Paul

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 1.38 MB

english, 2015

41

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

Ing-Simmons, Elizabeth, Seitan, Vlad C., Faure, Andre J., Flicek, Paul, Carroll, Thomas, Dekker, Job, Fisher, Amanda G., Lenhard, Boris, Merkenschlager, Matthias

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 9.30 MB

english, 2015

42

Avianbase: a community resource for bird genomics

Eöry, Lél, Gilbert, M, Li, Cai, Li, Bo, Archibald, Alan, Aken, Bronwen L, Zhang, Guojie, Jarvis, Erich, Flicek, Paul, Burt, David W

Journal:

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

43

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression

Nelson, Andrew C, Cutty, Stephen J, Niini, Marie, Stemple, Derek L, Flicek, Paul, Houart, Corinne, Bruce, Ashley, Wardle, Fiona C

Journal:

Year:

2014

Language:

english

File:

PDF, 3.74 MB

english, 2014

44

Computational approaches to interpreting genomic sequence variation

Ritchie, Graham RS, Flicek, Paul

Journal:

Genome Medicine

Year:

2014

Language:

english

File:

PDF, 996 KB

english, 2014

45

The Ensembl Regulatory Build

Zerbino, Daniel R, Wilder, Steven P, Johnson, Nathan, Juettemann, Thomas, Flicek, Paul R

Journal:

Year:

2015

Language:

english

File:

PDF, 1.31 MB

english, 2015

46

Epigenome data release: a participant-centered approach to privacy protection

Dyke, Stephanie O. M., Cheung, Warren A., Joly, Yann, Ammerpohl, Ole, Lutsik, Pavlo, Rothstein, Mark A., Caron, Maxime, Busche, Stephan, Bourque, Guillaume, Rönnblom, Lars, Flicek, Paul, Beck, Stephan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

47

LaGomiCs - Lagomorph Genomics Consortium: an international collaborative effort for sequencing the genomes of an entire mammalian order

Fontanesi, Luca, Di Palma, Federica, Flicek, Paul, Smith, Andrew T, Thulin, Carl-Gustaf, Alves, Paulo C.

Journal:

Journal of Heredity

Year:

2016

Language:

english

File:

PDF, 937 KB

english, 2016

48

ncRNA orthologies in the vertebrate lineage

Pignatelli, Miguel, Vilella, Albert J., Muffato, Matthieu, Gordon, Leo, White, Simon, Flicek, Paul, Herrero, Javier

Journal:

Year:

2016

Language:

english

File:

PDF, 2.00 MB

english, 2016

49

Divergence in gene expression within and between two closely related flycatcher species

Uebbing, Severin, Künstner, Axel, Mäkinen, Hannu, Backström, Niclas, Bolivar, Paulina, Burri, Reto, Dutoit, Ludovic, Mugal, Carina F., Nater, Alexander, Aken, Bronwen, Flicek, Paul, Martin, Fergal J.,

Journal:

Molecular Ecology

Year:

2016

Language:

english

File:

PDF, 804 KB

english, 2016

50

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

Clarke, Laura, Fairley, Susan, Zheng-Bradley, Xiangqun, Streeter, Ian, Perry, Emily, Lowy, Ernesto, Tassé, Anne-Marie, Flicek, Paul

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.00 MB

english, 2016