of Dr. Felix Kokocinski
The Ensembl gene annotation system
Bronwen L. Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri, Felix Kokocinski, Fergal J. Martin, Daniel N. Murphy, Rishi Nag, Magali Ruffier, Michael Schuster, Y. Amy Tang, Jan-Hinnerk Vogel, Simon White, Amonida Zadissa, Paul Flicek, Stephen M. J. SearleDatabase 2016 2016: baw093 [Abstract] [Full text]
Distribution patterns of segmental aneuploidies in human blastocysts identified by next-generation sequencing
Vera-Rodríguez M, Michel CE, Mercader A, Bladon AJ, Rodrigo L, Kokocinski F, Mateu E, Al-Asmar N, Blesa D, Simón C, Rubio C.Fertil. Steril. 2016 105(4):1047-1055.e2 [Abstract]
Altered levels of mitochondrial DNA are associated with female age, aneuploidy, and provide an independent measure of embryonic implantation potential.
Fragouli E, Spath K, Alfarawati S, Kaper F, Craig A, Michel CE, Kokocinski F, Cohen J, Munne S, Wells D.PLoS Genetics 2015 11(6):e1005241 [Abstract] [Full text]
Application of next-generation sequencing technology for comprehensive aneuploidy screening of blastocysts in clinical preimplantation genetic screening cycles
Fiorentino F, Bono S, Biricik A, Nuccitelli A, Cotroneo E, Cottone G, Kokocinski F, Michel CE, Minasi MG, Greco EHum Reprod. 2014 [Abstract]
Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos
Fiorentino F, Biricik A, Bono S, Spizzichino L, Cotroneo E, Cottone G, Kokocinski F, Michel CEFertil Steril 2014 101(5):1375-82 [Abstract]
Assessment of transcript reconstruction methods for RNA-seq
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P; RGASP ConsortiumNat Methods 2013 10(12):1177-84 [Abstract] [Full text]
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigo R, Hubbard TJGenome Res. 2012 22(9):1760-74. [Abstract] [Full text]
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigo R, Reymond A.Genome Res. 2012 22(9):1698-710 [Abstract] [Full text]
Landscape of transcription in human cells
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al.Nature 2012 489(7414):101-8 [Abstract] [Full text]
An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.Nature 2012 489(7414):57-74 [Abstract] [Full text]
A Users Guide to the Encyclopedia of DNA Elements (ENCODE)
The ENCODE Project ConsortiumPLOS Biologie 2011 [Abstract] [Full text]
The GENCODE exome: sequencing the complete human exome
Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ, Palotie AEur J Hum Genet 2011 [Abstract] [Full text]
AnnoTrack--a tracking system for genome annotation.
Kokocinski F, Harrow J, Hubbard T.BMC Genomics 2010 11:538 [Abstract] [Full text]
Ensembl's 10th year
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SMNucleic Acids Research 2010 38(Database issue):D557-62 [Abstract] [Full text]
The genome sequence of taurine cattle: a window to ruminant biology and evolution
Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, et al.Science 2009 324(5926):522-8 [Abstract] [Full text]
Ensembl 2009
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek PNucleic Acids Res. (Database issue) 2009 D690-7 [Abstract] [Full text]
Ensembl 2008
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.Nucleic Acids Res. (Database issue) 2008 [Abstract] [Full text]
Ensembl 2007
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney ENucleic Acids Res. (Database issue) 2007 35: D610-7 [Abstract] [Full text]
The DNA sequence and biological annotation of human chromosome 1
S. G. Gregory, K. F. Barlow, K. E. McLay, R. Kaul, D. Swarbreck, A. Dunham, C. E. Scott, K. L. Howe, K. Woodfine, C. C. A. Spencer, M. C. Jones, C. Gillson, S. Searle, Y. Zhou, F. Kokocinski, et al.Nature 2006 441, 315-321 [Abstract] [Full text]
Ensembl 2006
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Graf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.Nucleic Acids Res. (Database issue) 2006 34:D556-61 [Abstract] [Full text]
Genomic and Protein Expression Profiling Identifies CDK6 As Novel Independent Prognostic Marker in Medulloblastoma
Frank Mendrzyk, Bernhard Radlwimmer, Stefan Joos, Felix Kokocinski, Axel Benner, Daniel E. Stange, Kai Neben, Heike Fiegler, Nigel P. Carter, Guido Reifenberger, Andrej Korshunov, and Peter LichterJournal of Clinical Oncology 2005 23(34):8853-62
Identification of novel tumour-associated genes differentially expressed in the process of squamous cell cancer development
Lars Hummerich, Regina Muller, Jochen Hess, Felix Kokocinski, Meinhaad Hahn, Gerhard Furstenberger, Cornelia Mauch, Peter Lichter, Peter AngelOncogene 2005 25(1):111-21 [Abstract]
Ensembl 2005
Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinski F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney ENucleic Acids Research 2005 33:D447-53 [Abstract] [Full text]
FACT - a framework for the functional interpretation of high-throughput experiments
Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt and Peter LichterBMC Bioinformatics 2005 6(1):161 [Abstract | Zusammenfassung] [Full text]
Identification of novel AP-1 target genes in fibroblasts regulated during cutaneous wound healing
Lore Florin, Lars Hummerich, Bernd T. Dittrich, Felix Kokocinski, Gunnar Wrobel, Sabine Gack, Marina Schorpp-Kistner, Sabine Werner, Meinhard Hahn, Peter Lichter, Axel Szabowski, Peter AngelOncogene 2004 23(42):7005-17 [Abstract]
Microarray-based gene expression profiling of benign, atypical and anaplastic meningiomas identifies novel genes associated with meningioma progression
Gunnar Wrobel, Peter Roerig, Felix Kokocinski, Kai Neben, Meinhard Hahn, Guido Reifenberger, Peter LichterInternational Journal of Cancer 2004 114(2):249-56 [Abstract]
Distinct gene expression patterns associated with FLT3- and NRAS-activating mutations in acute myeloid leukemia with normal karyotype
Neben K, Schnittger S, Brors B, Tews B, Kokocinski F, Haferlach T, Müller J, Hahn M, Hiddemann W, Eils R, Lichter P, Schoch C.Oncogene 2004 24(9):1580-8 [Abstract]
Microarray-Based Screening for Molecular Markers in Medulloblastoma Revealed STK15 as Independent Predictor for Survival
Kai Neben, Andrey Korshunov, Axel Benner, Gunnar Wrobel, Meinhard Hahn, Felix Kokocinski, Andrey Golanov, Stefan Joos, Peter LichterCancer Research 2004 64(9):3103-11 [Abstract]
AutoPrime: Selecting Primers for Expressed Sequences
Gunnar Wrobel, Felix Kokocinski, Peter LichterGenome Research 2004 5:P11 [Abstract] [Full text]
Gene expression patterns in acute myeloid leukemia correlate with centrosome aberrations and numerical chromosome changes.
Neben K, Schnittger S, Brors B, Tews B, Kokocinski F, Haferlach T, Müller J, Hahn M, Hiddemann W, Eils R, Lichter P, Schoch C.Oncogene 2004 23(13):2379-84 [Abstract]
Anwendungen der DNA-Chiptechnologie in der Krebsforschung.
Bjoern Fritz, Felix Kokocinski, Joerg Schlingemann und Meinhard HahnBioSpektrum Special 2003 1, 78-83 [Abstract | Zusammenfassung] [Full text]
QuickLims: Facilitating the data management for DNA-microarray production.
Felix Kokocinski , Gunnar Wrobel, Meinhard Hahn, Peter LichterBioInformatics 2003 19 (2), 283-284 [Abstract | Zusammenfassung] [Full text]
Automated screening for genomic imbalances using matrix-based comparative genomic hybridization (matrix-CGH).
Swen Wessendorf, Bjoern Fritz, Gunnar Wrobel, Michelle Nessling, Stefan Lampel, Daniel Goettel, Manfred Kuepper, Stefan Joos, Ton Hopman, Felix Kokocinski, Hartmut Doehner, Martin Bentz, Carsten Schwaenen, and Peter LichterLabInvest 2002 82, 47-60 [Abstract] [Full text]