Bertone Group Publications
Reynolds N, Salmon-Divon M, Dvinge H, Hynes-Allen A, Balasooriya G, Leaford D, Behrens A, Bertone P, Hendrich B. (2011)
NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression.
EMBO J. 31:593–605
Albers CA, Cvejic A, Favier R, Bouwmans EE, Alessi MC, Bertone P, Jordan G, Kettleborough RN, Kiddle G, Kostadima M, Read RJ, Sipos B, Sivapalaratnam S, Smethurst PA, Stephens J, Voss K, Nurden A, Rendon A, Nurden P, Ouwehand WH. (2011)
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome.
Nat Genet. 43: 735–737.
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P. (2010)
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
BMC Bioinformatics 11: 415.
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C. (2010)
Systematic comparison of microarray profiling, real-time PCR and next-generation sequencing technologies for measuring differential microRNA expression.
RNA 16: 991–1006.
Dvinge H, Bertone P. (2009)
HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
Bioinformatics 25: 3325–3326.
Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. (2009)
Mapping organelle proteins and protein complexes in Drosophila melanogaster.
J Proteome Res. 8: 2667–2678.
Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A. (2008)
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
Cell 133: 813–828.
Kirstetter P, Schuster MB, Bereshchenko O, Moore S, Dvinge H, Kurz E, Theilgaard-Mönch K, Månsson R, Pedersen TA, Pabst T, Schrock E, Porse BT, Jacobsen SE, Bertone P, Tenen DG, Nerlov C. (2008)
Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells.
Cancer Cell 13: 299–310.
Seshasayee AS, Bertone P, Fraser GM, Luscombe NM. (2006)
Transcriptional regulatory networks in bacteria: from input signals to output responses.
Curr Opin Microbiol. 9: 511–519.
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. (2006)
Target hub proteins serve as master regulators of development in yeast.
Genes Dev. 20: 435–448.
Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. (2006)
Design optimization methods for genomic DNA tiling arrays.
Genome Res. 16: 271–281.
Hartman SE, Bertone P, Nath A, Royce TE, Gerstein M, Weissman S, Snyder M. (2005)
Global changes in STAT target selection and transcription regulation upon interferon treatments.
Genes Dev. 19: 2953–2968.
Bertone P, Snyder M. (2005)
Advances in functional protein microarray technology.
FEBS J. 272: 5400–5411.
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. (2005)
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.
Genome Res. 15: 674–680.
Bertone P, Snyder M. (2005)
Prospects and challenges in proteomics.
Plant Physiol. 138: 560–562.
Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. (2005)
Issues in the analysis of oligonucleotide tiling microarrays.
Trends Genet. 21: 466–475.
Bertone P, Gerstein M, Snyder M. (2005)
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.
Chromosome Res. 13: 259–274.
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. (2004)
Global identification of human transcribed sequences with genome tiling arrays.
Science 306: 2242–2246.
Berman P, Bertone P, DasGupta B, Gerstein M, Kao MY, Snyder M. (2004)
Fast optimal genome tiling with applications to microarray design and homology search.
J Comput Biol. 11: 766–785.
Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS et al. (2004)
The ENCODE (ENCyclopedia Of DNA Elements) project.
Science 306: 636–640.
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. (2004)
CREB binds to many loci on human chromosome 22.
Mol Cell Biol. 24: 3804–3814.
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. (2003)
Distribution of NF-κB binding sites across human chromosome 22.
Proc Nat Acad Sci USA. 100: 12247–12252.
Zheng L, Euskirchen G, Rinn JL, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Gerstein M, Weissman S, Snyder M. (2003)
Identification of novel functional elements in the human genome.
Cold Spring Harb Symp Quant Biol. 68: 317–322.
Bertone P. (2003)
Protein microarrays for high-throughput interaction screening.
In Genetic and Proteomic Applications in Toxicity Testing (MJ Cunningham, Ed.). Totowa, NJ: Humana Press. ISBN 0896039471.
Luscombe NM, Royce T, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. (2003)
ExpressYourself: a modular platform for processing and visualizing microarray data.
Nucleic Acids Res. 31: 3477–3482.
Goh CS, Lan N, Echols N, Douglas S, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M. (2003)
SPINE 2: a system for collaborative structural proteomics within a federated database framework.
Nucleic Acids Res. 31: 2833–2838.
Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. (2003)
The transcriptional activity of human chromosome 22.
Genes Dev. 17: 529–540.
Harrison PM, Zhang Z, Milburn D, Bertone P, Gerstein M. (2003)
Identification of pseudogenes in the Drosophila melanogaster genome.
Nucleic Acids Res. 31: 1033–1037.
Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M. (2002)
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Genes Dev. 16: 3017–3033.
Berman P, Bertone P, DasGupta B, Gerstein M, Kao MY, Snyder M. (2002)
Fast optimal genome tiling with applications to microarray design and homology search.
In Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics (R Guigó and D Gusfield, Eds.) Lecture Notes in Computer Science 2452: 419–433. Heidelberg: Springer. ISBN 3-540-44211-1.
Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. (2002)
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
Nucleic Acids Res. 30: 4574–4582.
Kumar A, Cheung KH, Marenco L, Tosches N, Masiar P, Liu Y, Bertone P, Miller P, Snyder M. (2002)
Computational methods and bioinformatic tools.
In Analysing Gene Expression – A Handbook of Methods: Possibilities and Pitfalls (S Lorkowski and P Cullen, Eds.). Weinhein: Wiley-VCH Verlag GmbH. ISBN 3-527-30488-6.
Balasubramanian S, Harrison PM, Bertone P, Echols N, Luscombe N, Zhang Z, Gerstein M. (2002)
SNPs on human chromosomes 21 and 22 – analysis in terms of protein features and pseudogenes.
Pharmacogenomics 3: 393–402.
Echols N, Harrison PM, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M. (2002)
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Nucleic Acids Res. 30: 2515–2523.
Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M. (2002)
Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22.
Genome Res. 12: 272–280.
Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. (2002)
An integrated approach for finding overlooked genes in yeast.
Nat Biotechnol. 20: 58–63.
Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison P, Zhang Z, Gerstein M. (2002)
Structural genomics: A new era for pharmaceutical research.
Genome Biol. 3: 4004.1–4004.3.
Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M. (2001)
Global analysis of protein activities using proteome chips.
Science 293: 2101–2105.
Bertone P, Gerstein M. (2001)
Integrative data mining: the new direction in bioinformatics.
IEEE Eng Med Biol. 20: 33–40.
Bertone P, Kluger Y, Lan N, Zheng D, Christendat D, Yee A, Edwards AM, Arrowsmith CH, Montelione GT, Gerstein M. (2001)
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
Nucleic Acids Res. 29: 2884–2898.
Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M. (2000)
Analysis of yeast protein kinases using protein chips.
Nat Genet. 26: 283–289.
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