Scientific Publications

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. Searle
Database  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 E
Hum 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 CE
Fertil 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 Consortium
Nat 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 TJ
Genome 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 Consortium
PLOS 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 A
Eur 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 SM
Nucleic 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 P
Nucleic 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 E
Nucleic 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 Lichter
Journal 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 Angel
Oncogene  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 E
Nucleic 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 Lichter
BMC 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 Angel
Oncogene  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 Lichter
International 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 Lichter
Cancer Research  2004  64(9):3103-11   [Abstract
AutoPrime: Selecting Primers for Expressed Sequences
Gunnar Wrobel, Felix Kokocinski, Peter Lichter
Genome 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 Hahn
BioSpektrum 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 Lichter
BioInformatics  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 Lichter
LabInvest  2002  82, 47-60   [Abstract]  [Full text