2013

Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner
Stricker, S. H., Feber A., Engström P. G., Carén H., Kurian K.M., Takashima Y., Watts C., Way M., Dirks P., Bertone P., et al.
Genes Dev. Mar, Volume 27, Number 6, (2013), p.654–669
SMIM1 underlies the Vel blood group and influences red blood cell traits
Cvejic, A., Haer-Wigman L., Stephens J.C., Kostadima M., Smethurst P.A., Frontini M., van den Akker E., Bertone P., Bielczyk-Maczyńska E., Farrow S., et al.
Nat Genet. May, Volume 45, (2013), p.542–545 doi:
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
Goldman, N., Bertone P., Chen S., Dessimoz C., LeProust E.M., Sipos B., and Birney E.
Nature. Jan, Volume 494, Number 7435, (2013), p.77–80

2012

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome
Albers, C.A., Paul D.S., Schulze H., Freson K., Stephens J.C., Smethurst P.A., Jolley J.D., Cvejic A., Kostadima M., Bertone P., et al.
Nat Genet. Feb, Volume 44, Number 4, (2012), p.435–439
NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment
Reynolds, N., Latos P., Hynes-Allen A., Loos R., Leaford D., O'Shaughnessy A., Mosaku O., Signolet J., Brennecke P., Kalkan T., et al.
Cell Stem Cell. May, Volume 10, Number 5, (2012), p.583–594
Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors
Metzakopian, E., Lin W., Salmon-Divon M., Dvinge H., Andersson E., Ericson J., Perlmann T., Whitsett J.A., Bertone P., and Ang S.L.
Development. Jul, Volume 139, Number 14, (2012), p.2625–2634
Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
Engström, P. G., Tommei D., Stricker S. H., Ender C., Pollard S. M., and Bertone P.
Genome Med. Oct, Volume 4, Number 10, (2012), p.76

2011

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome
Albers, C.A., Cvejic A., Favier R., Bouwmans E. E., Alessi M. C., Bertone P., Jordan G., Kettleborough R. N. W., Kiddle G., Kostadima M., et al.
Nat Genet. Jul, Volume 43, Number 8, (2011), p.735–737
NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression
Reynolds, N., Salmon-Divon M., Dvinge H., Hynes-Allen A., Balasooriya G., Leaford D., Behrens A., Bertone P., and Hendrich B.
EMBO J. Dec, Volume 31, Number 3, (2011), p.593–605

2010

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
Git, A., Dvinge H., Salmon-Divon M., Osborne M., Kutter C., Hadfield J., Bertone P., and Caldas C.
RNA. May, Volume 16, Number 5, (2010), p.991–1006
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci
Salmon-Divon, M., Dvinge H., Tammoja K., and Bertone P.
BMC Bioinformatics. Aug, Volume 11, Number 1, (2010), p.415

2009

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R
Dvinge, H., and Bertone P.
Bioinformatics. Dec, Volume 25, Number 24, (2009), p.3325–3326
Mapping organelle proteins and protein complexes in Drosophila melanogaster
Tan, D. J. L., Dvinge H., Christoforou A., Bertone P., Martinez Arias A., and Lilley K. S.
J Proteome Res. Jun, Volume 8, Number 6, (2009), p.2667–2678

2008

Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells
Kirstetter, P., Schuster M. B., Bereshchenko O., Moore S., Dvinge H., Kurz E., Theilgaard-Mönch K., Mansson R., Pedersen T.A., Pabst T., et al.
Cancer Cell. Apr, Volume 13, Number 4, (2008), p.299–310
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila
Kind, J., Vaquerizas J.M., Gebhardt P., Gentzel M., Luscombe N.M., Bertone P., and Akhtar A.
Cell. May, Volume 133, Number 5, (2008), p.813–828

2006

Design optimization methods for genomic DNA tiling arrays
Bertone, P., Trifonov V., Rozowsky J. S., Schubert F., Emanuelsson O., Karro J., Kao M. Y., Snyder M., and Gerstein M.
Genome Res. Feb, Volume 16, Number 2, (2006), p.271–281
Target hub proteins serve as master regulators of development in yeast
Borneman, A. R., Leigh-Bell J. A., Yu H., Bertone P., Gerstein M., and Snyder M.
Genes Dev. Feb, Volume 20, Number 4, (2006), p.435–448

2005

Advances in functional protein microarray technology
Bertone, P., and Snyder M.
FEBS J. Nov, Volume 272, Number 21, (2005), p.5400–5411
Global changes in STAT target selection and transcription regulation upon interferon treatments
Hartman, S. E., Bertone P., Nath A. K., Royce T.E., Gerstein M., Weissman S., and Snyder M.
Genes Dev. Dec, Volume 19, Number 24, (2005), p.2953–2968
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery
Bertone, P., Gerstein M., and Snyder M.
Chromosome Res. Apr, Volume 13, Number 3, (2005), p.259–274
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
Gilad, Y., Rifkin S. A., Bertone P., Gerstein M., and White K. P.
Genome Res. May, Volume 15, Number 5, (2005), p.674–680
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
Royce, T.E., Rozowsky J. S., Bertone P., Samanta M., Stolc V., Weissman S., Snyder M., and Gerstein M.
Trends Genet. Aug, Volume 21, Number 8, (2005), p.466–475

2004

Fast optimal genome tiling with applications to microarray design and homology search
Berman, P., Bertone P., Dasgupta B., Gerstein M., Kao M. Y., and Snyder M.
J Comput Biol. Dec, Volume 11, Number 4, (2004), p.766–785
Global identification of human transcribed sequences with genome tiling arrays
Bertone, P., Stolc V., Royce T.E., Rozowsky J. S., Urban A. E., Zhu X., Rinn J. L., Tongprasit W., Samanta M., Weissman S., et al.
Science. Dec, Volume 306, Number 5705, (2004), p.2242–2246
CREB binds to multiple loci on human chromosome 22
Euskirchen, G., Royce T.E., Bertone P., Martone R., Rinn J. L., Nelson F. K., Sayward F., Luscombe N.M., Miller P., Gerstein M., et al.
Mol Cell Biol. May, Volume 24, Number 9, (2004), p.3804–3814
The ENCODE (ENCyclopedia Of DNA Elements) Project
Feingold, E.A., Good P.J., Guyer M.S., Kamholz S., Liefer L., Wetterstrand K., and et al. Collins F. S.
Science. Oct, Volume 306, Number 5696, (2004), p.636–640

2003

ExpressYourself: A modular platform for processing and visualizing microarray data
Luscombe, N.M., Royce T.E., Bertone P., Echols N., Horak C. E., Chang J. T., Snyder M., and Gerstein M.
Nucleic Acids Res. Jul, Volume 31, Number 13, (2003), p.3477–3482
Identification of novel functional elements in the human genome
Lian, Z., Euskirchen G., Rinn J., Martone R., Bertone P., Hartman S., Royce T., Nelson K., Sayward F., Luscombe N., et al.
Cold Spring Harbor Symposia on Quantitative Biology. Volume 68, Number 1, (2003), p.317–322
Distribution of NF-kappaB-binding sites across human chromosome 22
Martone, R., Euskirchen G., Bertone P., Hartman S., Royce T.E., Luscombe N.M., Rinn J. L., Nelson F. K., Miller P., Gerstein M., et al.
Proc Nat Acad Sci USA. Oct, Volume 100, Number 21, (2003), p.12247–12252
Computational Methods and Bioinformatic Tools
Kumar, A., Cheung K. H., Marenco L., Tosches N., Masiar P., Liu Y., Bertone P., Miller P., and Snyder M.
Analysing Gene Expression – a Handbook of Methods: Possibilities and Pitfalls. (2003), Weinhein, p.769–904
Identification of pseudogenes in the Drosophila melanogaster genome
Harrison, P. M., Milburn D., Zhang Z., Bertone P., and Gerstein M.
Nucleic Acids Res. Feb, Volume 31, Number 3, (2003), p.1033–1037
Fast optimal genome tiling with applications to microarray design and homology search
Berman, P., Bertone P., Dasgupta B., Gerstein M., Kao M. Y., and Snyder M.
Number DIMACS 2003-05, (2003),
The transcriptional activity of human chromosome 22
Rinn, J. L., Euskirchen G., Bertone P., Martone R., Luscombe N.M., Hartman S., Harrison P. M., Nelson F. K., Miller P., Gerstein M., et al.
Genes Dev. Feb, Volume 17, Number 4, (2003), p.529–540
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, C. S., Lan N., Echols N., Douglas S. M., Milburn D., Bertone P., Xiao R., Ma L. C., Zheng D., Wunderlich Z., et al.
Nucleic Acids Res. Jun, Volume 31, Number 11, (2003), p.2833–2838

2002

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Horak, C. E., Luscombe N.M., Qian J., Bertone P., Piccirrillo S., Gerstein M., and Snyder M.
Genes Dev. Dec, Volume 16, Number 23, (2002), p.3017–3033
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing
Lin, J., Qian J., Greenbaum D., Bertone P., Das R., Echols N., Senes A., Stenger B., and Gerstein M.
Nucleic Acids Res. Oct, Volume 30, Number 20, (2002), p.4574–4582
Structural genomics: a new era for pharmaceutical research
Liu, Y., Luscombe N.M., Alexandrov V., Bertone P., Harrison P., Zhang Z., and Gerstein M.
Genome Biol. Jan, Volume 3, Number 2, (2002), p.4004.1–4004.3
An integrated approach for finding overlooked genes in yeast
Kumar, A., Harrison P. M., Cheung K. H., Lan N., Echols N., Bertone P., Miller P., Gerstein M. B., and Snyder M.
Nat Biotechnol. Jan, Volume 20, Number 1, (2002), p.58–63
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22
Harrison, P. M., Hegyi H., Balasubramanian S., Luscombe N.M., Bertone P., Echols N., Johnson T., and Gerstein M.
Genome Res. Feb, Volume 12, Number 2, (2002), p.272–280
SNPs on human chromosomes 21 and 22-analysis in terms of protein features and pseudogenes
Balasubramanian, S., Harrison P., Hegyi H., Bertone P., Luscombe N., Echols N., McGarvey P., Zhang Z. L., and Gerstein M.
Pharmacogenomics. May, Volume 3, Number 3, (2002), p.393–402
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes
Echols, N., Harrison P., Balasubramanian S., Luscombe N.M., Bertone P., Zhang Z., and Gerstein M.
Nucleic Acids Res. Jun, Volume 30, Number 11, (2002), p.2515–2523
Fast optimal genome tiling with applications to microarray design and homology search
Berman, P., Bertone P., Dasgupta B., Gerstein M., Kao M. Y., and Snyder M.
Algorithms in Bioinformatics: Second International Workshop. Sep, Volume 2452, (2002), p.419–433

2001

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics
Bertone, P., Kluger Y., Lan N., Zheng D., Christendat D., Yee A., Edwards A. M., Arrowsmith C. H., Montelione G. T., and Gerstein M.
Nucleic Acids Res. Jul, Volume 29, Number 13, (2001), p.2884–2898
Integrative data mining: the new direction in bioinformatics
Bertone, P., and Gerstein M.
IEEE Eng Med Biol. Jul-Aug, Volume 20, Number 4, (2001), p.33–40
Global analysis of protein activities using proteome chips
Zhu, H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S., Houfek T., et al.
Science. Sep, Volume 293, Number 5537, (2001), p.2101–2105

2000

Analysis of yeast protein kinases using protein chips
Zhu, H., Klemic J.F., Chang S., Bertone P., Casamayor A., Klemic K. G., Smith D., Gerstein M., Reed M. A., and Snyder M.
Nat Genet. Nov, Volume 26, Number 3, (2000), p.283–290