| Year |
Citation |
Score |
| 2019 |
Stuart HT, Stirparo GG, Lohoff T, Bates LE, Kinoshita M, Lim CY, Sousa EJ, Maskalenka K, Radzisheuskaya A, Malcolm AA, Alves MRP, Lloyd RL, Nestorowa S, Humphreys P, Mansfield W, ... ... Bertone P, et al. Distinct Molecular Trajectories Converge to Induce Naive Pluripotency. Cell Stem Cell. PMID 31422912 DOI: 10.1016/J.Stem.2019.07.009 |
0.3 |
|
| 2018 |
Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W. Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency. Cell Systems. PMID 30414923 DOI: 10.1016/J.Cels.2018.09.003 |
0.377 |
|
| 2018 |
Boroviak T, Stirparo GG, Dietmann S, Hernando-Herraez I, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P. Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development. Development (Cambridge, England). 145. PMID 30413530 DOI: 10.1242/Dev.167833 |
0.401 |
|
| 2018 |
Bornelöv S, Reynolds N, Xenophontos M, Gharbi S, Johnstone E, Floyd R, Ralser M, Signolet J, Loos R, Dietmann S, Bertone P, Hendrich B. The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression. Molecular Cell. 71: 56-72.e4. PMID 30008319 DOI: 10.1016/J.Molcel.2018.06.003 |
0.424 |
|
| 2018 |
Stirparo GG, Boroviak T, Guo G, Nichols J, Smith A, Bertone P. Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast. Development (Cambridge, England). PMID 29361568 DOI: 10.1242/Dev.158501 |
0.385 |
|
| 2017 |
Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Epigenetic resetting of human pluripotency. Development (Cambridge, England). 144: 2748-2763. PMID 28765214 DOI: 10.1242/Dev.146811 |
0.389 |
|
| 2017 |
Bulstrode H, Johnstone E, Marques-Torrejon MA, Ferguson KM, Bressan RB, Blin C, Grant V, Gogolok S, Gangoso E, Gagrica S, Ender C, Fotaki V, Sproul D, Bertone P, Pollard SM. Elevated FOXG1 and SOX2 in glioblastoma enforces neural stem cell identity through transcriptional control of cell cycle and epigenetic regulators. Genes & Development. PMID 28465359 DOI: 10.1101/Gad.293027.116 |
0.344 |
|
| 2016 |
Miller A, Ralser M, Kloet SL, Loos R, Nishinakamura R, Bertone P, Vermeulen M, Hendrich B. Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex. Development (Cambridge, England). PMID 27471257 DOI: 10.1242/Dev.139113 |
0.419 |
|
| 2016 |
Guo G, von Meyenn F, Santos F, Chen Y, Reik W, Bertone P, Smith A, Nichols J. Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass. Stem Cell Reports. PMID 26947977 DOI: 10.1016/J.Stemcr.2016.02.005 |
0.333 |
|
| 2016 |
Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, von Paleske L, Boroviak T, Wörsdörfer P, Essers MA, Kloz U, ... ... Bertone P, et al. Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause. Cell. 164: 668-80. PMID 26871632 DOI: 10.1016/J.Cell.2015.12.033 |
0.315 |
|
| 2015 |
Foti R, Gnan S, Cornacchia D, Dileep V, Bulut-Karslioglu A, Diehl S, Buness A, Klein FA, Huber W, Johnstone E, Loos R, Bertone P, Gilbert DM, Manke T, Jenuwein T, et al. Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program. Molecular Cell. PMID 26725008 DOI: 10.1016/J.Molcel.2015.12.001 |
0.32 |
|
| 2015 |
Carén H, Stricker SH, Bulstrode H, Gagrica S, Johnstone E, Bartlett TE, Feber A, Wilson G, Teschendorff AE, Bertone P, Beck S, Pollard SM. Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest. Stem Cell Reports. PMID 26607953 DOI: 10.1016/J.Stemcr.2015.09.014 |
0.336 |
|
| 2015 |
Boroviak T, Loos R, Lombard P, Okahara J, Behr R, Sasaki E, Nichols J, Smith A, Bertone P. Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis. Developmental Cell. 35: 366-82. PMID 26555056 DOI: 10.1016/J.Devcel.2015.10.011 |
0.394 |
|
| 2014 |
Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, ... Bertone P, et al. Transcriptional diversity during lineage commitment of human blood progenitors. Science (New York, N.Y.). 345: 1251033. PMID 25258084 DOI: 10.1126/Science.1251033 |
0.409 |
|
| 2014 |
Takashima Y, Guo G, Loos R, Nichols J, Ficz G, Krueger F, Oxley D, Santos F, Clarke J, Mansfield W, Reik W, Bertone P, Smith A. Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell. 158: 1254-69. PMID 25215486 DOI: 10.1016/J.Cell.2014.08.029 |
0.34 |
|
| 2014 |
Christophorou MA, Castelo-Branco G, Halley-Stott RP, Oliveira CS, Loos R, Radzisheuskaya A, Mowen KA, Bertone P, Silva JC, Zernicka-Goetz M, Nielsen ML, Gurdon JB, Kouzarides T. Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature. 507: 104-8. PMID 24463520 DOI: 10.1038/Nature12942 |
0.394 |
|
| 2013 |
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods. 10: 1177-84. PMID 24185837 DOI: 10.1038/Nmeth.2714 |
0.371 |
|
| 2013 |
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods. 10: 1185-91. PMID 24185836 DOI: 10.1038/Nmeth.2722 |
0.349 |
|
| 2013 |
Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T. The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells. Genome Biology. 14: R98. PMID 24044525 DOI: 10.1186/Gb-2013-14-9-R98 |
0.396 |
|
| 2013 |
Martello G, Bertone P, Smith A. Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor. The Embo Journal. 32: 2561-74. PMID 23942233 DOI: 10.1038/Emboj.2013.177 |
0.349 |
|
| 2013 |
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, et al. SMIM1 underlies the Vel blood group and influences red blood cell traits. Nature Genetics. 45: 542-5. PMID 23563608 DOI: 10.1038/Ng.2603 |
0.32 |
|
| 2013 |
Stricker SH, Feber A, Engström PG, Carén H, Kurian KM, Takashima Y, Watts C, Way M, Dirks P, Bertone P, Smith A, Beck S, Pollard SM. Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner. Genes & Development. 27: 654-69. PMID 23512659 DOI: 10.1101/Gad.212662.112 |
0.344 |
|
| 2012 |
Engström PG, Tommei D, Stricker SH, Ender C, Pollard SM, Bertone P. Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome Medicine. 4: 76. PMID 23046790 DOI: 10.1186/Gm377 |
0.366 |
|
| 2012 |
Metzakopian E, Lin W, Salmon-Divon M, Dvinge H, Andersson E, Ericson J, Perlmann T, Whitsett JA, Bertone P, Ang SL. Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors. Development (Cambridge, England). 139: 2625-34. PMID 22696295 DOI: 10.1242/Dev.081034 |
0.756 |
|
| 2012 |
Reynolds N, Latos P, Hynes-Allen A, Loos R, Leaford D, O'Shaughnessy A, Mosaku O, Signolet J, Brennecke P, Kalkan T, Costello I, Humphreys P, Mansfield W, Nakagawa K, Strouboulis J, ... Bertone P, et al. NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment. Cell Stem Cell. 10: 583-94. PMID 22560079 DOI: 10.1016/J.Stem.2012.02.020 |
0.378 |
|
| 2012 |
Reynolds N, Salmon-Divon M, Dvinge H, Hynes-Allen A, Balasooriya G, Leaford D, Behrens A, Bertone P, Hendrich B. NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression. The Embo Journal. 31: 593-605. PMID 22139358 DOI: 10.1038/Emboj.2011.431 |
0.734 |
|
| 2010 |
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P. PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. Bmc Bioinformatics. 11: 415. PMID 20691053 DOI: 10.1186/1471-2105-11-415 |
0.769 |
|
| 2010 |
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. Rna (New York, N.Y.). 16: 991-1006. PMID 20360395 DOI: 10.1261/Rna.1947110 |
0.702 |
|
| 2009 |
Dvinge H, Bertone P. HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R. Bioinformatics (Oxford, England). 25: 3325-6. PMID 19808880 DOI: 10.1093/Bioinformatics/Btp578 |
0.699 |
|
| 2009 |
Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. Mapping organelle proteins and protein complexes in Drosophila melanogaster. Journal of Proteome Research. 8: 2667-78. PMID 19317464 DOI: 10.1021/Pr800866N |
0.711 |
|
| 2008 |
Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell. 133: 813-28. PMID 18510926 DOI: 10.1016/J.Cell.2008.04.036 |
0.448 |
|
| 2008 |
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, et al. Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells. Cancer Cell. 13: 299-310. PMID 18394553 DOI: 10.1016/J.Ccr.2008.02.008 |
0.692 |
|
| 2007 |
Sayward FG, Yang J, Nelson FK, Euskirchen G, Urban AE, Bertone P, Rinn J, Weissman S, Gerstein M, Snyder M, Miller PL. Design issues in implementing a portable Sample Tracking and Analysis Research Support (STARS) system for PCR based microarray research 2006 Ieee Conference On Information Sciences and Systems, Ciss 2006 - Proceedings. 1578-1598. DOI: 10.1109/CISS.2006.286390 |
0.451 |
|
| 2006 |
Seshasayee AS, Bertone P, Fraser GM, Luscombe NM. Transcriptional regulatory networks in bacteria: from input signals to output responses. Current Opinion in Microbiology. 9: 511-9. PMID 16942903 DOI: 10.1016/J.Mib.2006.08.007 |
0.338 |
|
| 2006 |
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. Target hub proteins serve as master regulators of development in yeast. Genes & Development. 20: 435-48. PMID 16449570 DOI: 10.1101/Gad.1389306 |
0.526 |
|
| 2006 |
Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. Design optimization methods for genomic DNA tiling arrays. Genome Research. 16: 271-81. PMID 16365382 DOI: 10.1101/Gr.4452906 |
0.496 |
|
| 2005 |
Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M. Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes & Development. 19: 2953-68. PMID 16319195 DOI: 10.1101/Gad.1371305 |
0.728 |
|
| 2005 |
Bertone P, Snyder M. Advances in functional protein microarray technology. The Febs Journal. 272: 5400-11. PMID 16262682 DOI: 10.1111/J.1742-4658.2005.04970.X |
0.48 |
|
| 2005 |
Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends in Genetics : Tig. 21: 466-75. PMID 15979196 DOI: 10.1016/J.Tig.2005.06.007 |
0.539 |
|
| 2005 |
Bertone P, Snyder M. Prospects and challenges in proteomics. Plant Physiology. 138: 560-2. PMID 15955915 DOI: 10.1104/Pp.104.900154 |
0.488 |
|
| 2005 |
Bertone P, Gerstein M, Snyder M. Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 13: 259-74. PMID 15868420 DOI: 10.1007/S10577-005-2165-0 |
0.581 |
|
| 2005 |
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Research. 15: 674-80. PMID 15867429 DOI: 10.1101/Gr.3335705 |
0.689 |
|
| 2005 |
Rozowsky J, Bertone P, Royce T, Weissman S, Snyder M, Gerstein M. Analysis of genomic tiling microarrays for transcript mapping and the identification of transcription factor binding sites Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3594: 28-29. |
0.312 |
|
| 2004 |
Berman P, Bertone P, Dasgupta B, Gerstein M, Kao MY, Snyder M. Fast optimal genome tiling with applications to microarray design and homology search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 766-85. PMID 15579244 DOI: 10.1089/Cmb.2004.11.766 |
0.437 |
|
| 2004 |
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science (New York, N.Y.). 306: 2242-6. PMID 15539566 DOI: 10.1126/Science.1103388 |
0.749 |
|
| 2004 |
Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Molecular and Cellular Biology. 24: 3804-14. PMID 15082775 DOI: 10.1128/Mcb.24.9.3804-3814.2004 |
0.783 |
|
| 2003 |
Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, et al. Identification of novel functional elements in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 68: 317-22. PMID 15338632 DOI: 10.1101/Sqb.2003.68.317 |
0.734 |
|
| 2003 |
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proceedings of the National Academy of Sciences of the United States of America. 100: 12247-52. PMID 14527995 DOI: 10.1073/Pnas.2135255100 |
0.749 |
|
| 2003 |
Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Research. 31: 3477-82. PMID 12824348 DOI: 10.1093/Nar/Gkg628 |
0.7 |
|
| 2003 |
Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. The transcriptional activity of human Chromosome 22. Genes & Development. 17: 529-40. PMID 12600945 DOI: 10.1101/Gad.1055203 |
0.758 |
|
| 2003 |
Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M. Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Research. 31: 1033-7. PMID 12560500 DOI: 10.1093/Nar/Gkg169 |
0.463 |
|
| 2003 |
Zhu H, Bilgin M, Ptacek J, Hall D, Casamayor A, Bertone P, Lopez N, Lan N, Jansen R, Bidlingmaier S, Devgan G, Miller P, Gerstein M, Snyder M. Workshop I – Global Analysis of Protein Activities Using Protein Chips Biophysical Journal. 84: 3488. DOI: 10.1016/S0006-3495(03)70069-1 |
0.733 |
|
| 2002 |
Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes & Development. 16: 3017-33. PMID 12464632 DOI: 10.1101/Gad.1039602 |
0.703 |
|
| 2002 |
Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M. GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Research. 30: 4574-82. PMID 12384605 DOI: 10.1093/Nar/Gkf555 |
0.377 |
|
| 2002 |
Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M. SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes. Pharmacogenomics. 3: 393-402. PMID 12052146 DOI: 10.1517/14622416.3.3.393 |
0.339 |
|
| 2002 |
Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M. Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Research. 30: 2515-23. PMID 12034841 DOI: 10.1093/Nar/30.11.2515 |
0.402 |
|
| 2002 |
Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison P, Zhang Z, Gerstein M. Structural genomics: a new era for pharmaceutical research. Genome Biology. 3: REPORTS4004. PMID 11864367 DOI: 10.1186/Gb-2002-3-2-Reports4004 |
0.301 |
|
| 2002 |
Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Research. 12: 272-80. PMID 11827946 DOI: 10.1101/Gr.207102 |
0.45 |
|
| 2002 |
Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. An integrated approach for finding overlooked genes in yeast. Nature Biotechnology. 20: 58-63. PMID 11753363 DOI: 10.1038/Nbt0102-58 |
0.549 |
|
| 2001 |
Bertone P, Gerstein M. Integrative data mining: the new direction in bioinformatics. Ieee Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society. 20: 33-40. PMID 11494767 DOI: 10.1109/51.940042 |
0.398 |
|
| 2001 |
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. Global analysis of protein activities using proteome chips. Science (New York, N.Y.). 293: 2101-5. PMID 11474067 DOI: 10.1126/science.1062191 |
0.721 |
|
| 2001 |
Bertone P, Kluger Y, Lan N, Zheng D, Christendat D, Yee A, Edwards AM, Arrowsmith CH, Montelione GT, Gerstein M. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Research. 29: 2884-98. PMID 11433035 DOI: 10.1093/Nar/29.13.2884 |
0.334 |
|
| 2000 |
Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M. Analysis of yeast protein kinases using protein chips. Nature Genetics. 26: 283-9. PMID 11062466 DOI: 10.1038/81576 |
0.471 |
|
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