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Philipp V. Kapranov, Ph.D. - Publications

Affiliations: 
2003 Michigan State University, East Lansing, MI 
Area:
Genetics, Molecular Biology
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100 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Xu D, Tang L, Zhou J, Wang F, Cao H, Huang Y, Kapranov P. Evidence for widespread existence of functional novel and non-canonical human transcripts. Bmc Biology. 21: 271. PMID 38001496 DOI: 10.1186/s12915-023-01753-5  0.328
2023 Xu D, Huang Y, Luo L, Tang L, Lu M, Cao H, Wang F, Diao Y, Lyubchenko L, Kapranov P. Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method. International Journal of Molecular Sciences. 24. PMID 37569439 DOI: 10.3390/ijms241512062  0.301
2023 Wang F, Cao H, Xia Q, Liu Z, Wang M, Gao F, Xu D, Deng B, Diao Y, Kapranov P. Lessons from discovery of true ADAR RNA editing sites in a human cell line. Bmc Biology. 21: 160. PMID 37468903 DOI: 10.1186/s12915-023-01651-w  0.387
2023 Stokes T, Cen HH, Kapranov P, Gallagher IJ, Pitsillides AA, Volmar CH, Kraus WE, Johnson JD, Phillips SM, Wahlestedt C, Timmons JA. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. Advanced Genetics (Hoboken, N.J.). 4: 2200024. PMID 37288167 DOI: 10.1002/ggn2.202200024  0.466
2023 Gao F, Wang F, Cao H, Chen Y, Diao Y, Kapranov P. Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes. International Journal of Molecular Sciences. 24. PMID 36835575 DOI: 10.3390/ijms24044163  0.458
2023 Xu D, Tang L, Kapranov P. Complexities of mammalian transcriptome revealed by targeted RNA enrichment techniques. Trends in Genetics : Tig. PMID 36681580 DOI: 10.1016/j.tig.2022.12.004  0.435
2023 Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, ... ... Kapranov P, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews. Molecular Cell Biology. PMID 36596869 DOI: 10.1038/s41580-022-00566-8  0.454
2022 Cao H, Kapranov P. Methods to Analyze the Non-Coding RNA Interactome-Recent Advances and Challenges. Frontiers in Genetics. 13: 857759. PMID 35368711 DOI: 10.3389/fgene.2022.857759  0.405
2021 Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Chen H, Li D, Chen N, ... ... Kapranov P, et al. Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biology. 22: 233. PMID 34412677 DOI: 10.1186/s13059-021-02444-6  0.371
2021 Cao H, Xu D, Cai Y, Han X, Tang L, Gao F, Qi Y, Cai D, Wang H, Ri M, Antonets D, Vyatkin Y, Chen Y, You X, Wang F, ... ... Kapranov P, et al. Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans. Bmc Biology. 19: 108. PMID 34016118 DOI: 10.1186/s12915-021-01044-x  0.456
2021 Chen Y, Qi F, Gao F, Cao H, Xu D, Salehi-Ashtiani K, Kapranov P. Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nature Chemical Biology. PMID 33753927 DOI: 10.1038/s41589-021-00763-0  0.364
2020 Gao F, Cai Y, Kapranov P, Xu D. Reverse-genetics studies of lncRNAs-what we have learnt and paths forward. Genome Biology. 21: 93. PMID 32290841 DOI: 10.1186/S13059-020-01994-5  0.414
2020 Zheng Y, Kapranov P. Editorial: Recent Progresses of Non-coding RNAs in Biological and Medical Research. Frontiers in Genetics. 11: 187. PMID 32184809 DOI: 10.3389/Fgene.2020.00187  0.387
2020 Xu D, Cai Y, Tang L, Han X, Gao F, Cao H, Qi F, Kapranov P. A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response. Scientific Reports. 10: 1794. PMID 32020014 DOI: 10.1038/S41598-020-58104-5  0.495
2019 Wang C, Song J, Liu W, Yao Y, Kapranov P, Sample KM, Gajendran B, Zacksenhaus E, Hao X, Ben-David Y. FLI1 promotes protein translation via the transcriptional regulation of MKNK1 expression. International Journal of Oncology. PMID 31894299 DOI: 10.3892/Ijo.2019.4943  0.406
2019 Cao H, Salazar-García L, Gao F, Wahlestedt T, Wu CL, Han X, Cai Y, Xu D, Wang F, Tang L, Ricciardi N, Cai D, Wang H, Chin MPS, Timmons JA, ... ... Kapranov P, et al. Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. Nature Communications. 10: 5799. PMID 31862872 DOI: 10.1038/S41467-019-13602-7  0.427
2019 Mouawad R, Prasad J, Thorley D, Himadewi P, Kadiyala D, Wilson N, Kapranov P, Arnosti DN. Diversification of retinoblastoma protein function associated with cis and trans adaptations. Molecular Biology and Evolution. PMID 31418797 DOI: 10.1093/Molbev/Msz187  0.433
2018 Diao Y, Rahman MF, Vyatkin Y, Azatyan A, St Laurent G, Kapranov P, Zaphiropoulos PG. Identification of novel GLI1 target genes and regulatory circuits in human cancer cells. Molecular Oncology. PMID 30098229 DOI: 10.1002/1878-0261.12366  0.453
2018 Cao H, Wahlestedt C, Kapranov P. Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls. Trends in Genetics : Tig. PMID 30017313 DOI: 10.1016/J.Tig.2018.06.002  0.46
2016 Laurent GS, Vyatkin Y, Antonets D, Ri M, Qi Y, Saik O, Shtokalo D, de Hoon MJ, Kawaji H, Itoh M, Lassmann T, Arner E, Forrest AR, Nicolas E, ... ... Kapranov P, et al. Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. Nucleic Acids Research. PMID 27001520 DOI: 10.1093/Nar/Gkw162  0.542
2015 Pastori C, Kapranov P, Penas C, Peschansky V, Volmar CH, Sarkaria JN, Bregy A, Komotar R, St Laurent G, Ayad NG, Wahlestedt C. The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation. Proceedings of the National Academy of Sciences of the United States of America. 112: 8326-31. PMID 26111795 DOI: 10.1073/Pnas.1424220112  0.453
2015 St Laurent G, Wahlestedt C, Kapranov P. The Landscape of long noncoding RNA classification. Trends in Genetics : Tig. 31: 239-51. PMID 25869999 DOI: 10.1016/J.Tig.2015.03.007  0.461
2015 Lazorthes S, Vallot C, Briois S, Aguirrebengoa M, Thuret JY, St Laurent G, Rougeulle C, Kapranov P, Mann C, Trouche D, Nicolas E. A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus. Nature Communications. 6: 5971. PMID 25601475 DOI: 10.1038/Ncomms6971  0.48
2014 Wang Q, Dong B, Firrman J, Roberts S, Moore AR, Cao W, Diao Y, Kapranov P, Xu R, Xiao W. Efficient production of dual recombinant adeno-associated viral vectors for factor VIII delivery. Human Gene Therapy Methods. 25: 261-8. PMID 25093498 DOI: 10.1089/Hgtb.2014.093  0.309
2014 Laurent GS, Vyatkin Y, Kapranov P. Dark matter RNA illuminates the puzzle of genome-wide association studies Bmc Medicine. 12: 97-97. PMID 24924000 DOI: 10.1186/1741-7015-12-97  0.519
2014 Villegas VE, Rahman MF, Fernandez-Barrena MG, Diao Y, Liapi E, Sonkoly E, StÃ¥hle M, Pivarcsi A, Annaratone L, Sapino A, Ramírez Clavijo S, Bürglin TR, Shimokawa T, Ramachandran S, Kapranov P, et al. Identification of novel non-coding RNA-based negative feedback regulating the expression of the oncogenic transcription factor GLI1. Molecular Oncology. 8: 912-26. PMID 24726458 DOI: 10.1016/J.Molonc.2014.03.009  0.527
2014 Mitra SA, Mitra AP, Buckley JD, May WA, Kapranov P, Arceci RJ, Triche TJ. Abstract A43: Therapeutic importance of a long noncoding RNA in Ewing sarcoma Cancer Research. 74. DOI: 10.1158/1538-7445.Pedcan-A43  0.539
2014 Mitra AP, Mitra SA, Buckley JD, Kapranov P, Anderson JR, Skapek SX, Hawkins DS, Triche TJ. Abstract A16: Discovery and validation of novel prognostic genomic signatures in rhabdomyosarcoma Cancer Research. 74. DOI: 10.1158/1538-7445.Pedcan-A16  0.376
2014 Pastori C, Penas C, Kapranov P, Laurent GS, Zhang M, Ayad N, Wahlestedt C. Abstract LB-114: The long noncoding RNA HOTAIR promotes glioblastoma cell proliferation Cancer Research. 74. DOI: 10.1158/1538-7445.Am2014-Lb-114  0.52
2014 Mitra SA, Mitra AP, Buckley JD, May WA, Kapranov P, Arceci RJ, Triche TJ. Abstract 4973: Long non-coding RNA promotes metastatic behavior in Ewing sarcoma Cancer Research. 74: 4973-4973. DOI: 10.1158/1538-7445.Am2014-4973  0.511
2014 Mitra AP, Mitra SA, Buckley JD, Kapranov P, Anderson JR, Skapek SX, Hawkins DS, Triche TJ. Abstract 4730: Identification of novel prognostic signatures in rhabdomyosarcoma by whole transcriptome expression profiling: A discovery and validation study Cancer Research. 74: 4730-4730. DOI: 10.1158/1538-7445.Am2014-4730  0.386
2014 Pastori C, Kapranov P, Penas C, Laurent GS, Ayad N, Wahlestedt C. EG-10 * LONG NON-CODING RNAs IN GLIOBLASTOMA Neuro-Oncology. 16: v77-v77. DOI: 10.1093/Neuonc/Nou254.10  0.498
2013 Mao J, Xi X, Kapranov P, Dong B, Firrman J, Xu R, Xiao W. In vitro and In vivo Model Systems for Hemophilia A Gene Therapy. Journal of Genetic Syndromes & Gene Therapy. PMID 25401041 DOI: 10.4172/2157-7412.S1-014  0.312
2013 Savva YA, Jepson JE, Chang YJ, Whitaker R, Jones BC, St Laurent G, Tackett MR, Kapranov P, Jiang N, Du G, Helfand SL, Reenan RA. RNA editing regulates transposon-mediated heterochromatic gene silencing. Nature Communications. 4: 2745. PMID 24201902 DOI: 10.1038/Ncomms3745  0.497
2013 St Laurent G, Tackett MR, Nechkin S, Shtokalo D, Antonets D, Savva YA, Maloney R, Kapranov P, Lawrence CE, Reenan RA. Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila. Nature Structural & Molecular Biology. 20: 1333-9. PMID 24077224 DOI: 10.1038/Nsmb.2675  0.522
2013 St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P. VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biology. 14: R73. PMID 23876380 DOI: 10.1186/Gb-2013-14-7-R73  0.487
2013 Dong B, Moore AR, Dai J, Roberts S, Chu K, Kapranov P, Moss B, Xiao W. A concept of eliminating nonhomologous recombination for scalable and safe AAV vector generation for human gene therapy. Nucleic Acids Research. 41: 6609-17. PMID 23677609 DOI: 10.1093/Nar/Gkt404  0.328
2013 St Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P. On the importance of small changes in RNA expression. Methods (San Diego, Calif.). 63: 18-24. PMID 23563143 DOI: 10.1016/J.Ymeth.2013.03.027  0.514
2013 Mitra SA, Mitra AP, Buckley JD, May WA, Kapranov P, Arceci RA, Triche TJ. Abstract PR04: Genomic and epigenomic interactions of an Ewing sarcoma-specific long noncoding RNA Cancer Research. 73. DOI: 10.1158/1538-7445.Cec13-Pr04  0.536
2013 Mitra SA, Mitra AP, Buckley JD, May WA, Kapranov P, Arceci RJ, Triche TJ. Abstract 1823: Influence of a long non-coding RNA on epigenetic, genetic and phenotypic changes in Ewing sarcoma. Cancer Research. 73: 1823-1823. DOI: 10.1158/1538-7445.Am2013-1823  0.533
2013 Mitra AP, Mitra SA, Buckley JD, Kapranov P, Anderson JR, Skapek SX, Hawkins DS, Triche TJ. Abstract 17: Prognostic value of coding and non-coding genomic meta-features in rhabdomyosarcoma. Cancer Research. 73: 17-17. DOI: 10.1158/1538-7445.Am2013-17  0.411
2012 St Laurent G, Shtokalo D, Tackett MR, Yang Z, Eremina T, Wahlestedt C, Urcuqui-Inchima S, Seilheimer B, McCaffrey TA, Kapranov P. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. Bmc Genomics. 13: 504. PMID 23006825 DOI: 10.1186/1471-2164-13-504  0.505
2012 Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, Tice R, Tochigi M, Moréra S, Nazarians A, Belsham D, ... ... Kapranov P, et al. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nature Structural & Molecular Biology. 19: 1037-43. PMID 22961382 DOI: 10.1038/Nsmb.2372  0.387
2012 Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, ... ... Kapranov P, et al. Landscape of transcription in human cells. Nature. 489: 101-8. PMID 22955620 DOI: 10.1038/Nature11233  0.534
2012 Kapranov P, Laurent GS. Genomic "dark matter": implications for understanding human disease mechanisms, diagnostics, and cures. Frontiers in Genetics. 3: 95-95. PMID 22661986 DOI: 10.3389/Fgene.2012.00095  0.335
2012 Laurent GS, Savva YA, Kapranov P. Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape Frontiers in Genetics. 3: 57-57. PMID 22539933 DOI: 10.3389/Fgene.2012.00057  0.465
2012 Kapranov P, Laurent GS. Dark Matter RNA: Existence, Function, and Controversy Frontiers in Genetics. 3: 60-60. PMID 22536205 DOI: 10.3389/Fgene.2012.00060  0.479
2012 Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/Journal.Pone.0028213  0.498
2012 Kapranov P, Ozsolak F, Milos PM. Profiling of short RNAs using Helicos single-molecule sequencing. Methods of Molecular Biology. 822: 219-232. PMID 22144202 DOI: 10.1007/978-1-61779-427-8_15  0.402
2012 Kapranov P, Chen L, Dederich D, Dong B, He J, Steinmann KE, Moore AR, Thompson JF, Milos PM, Xiao W. Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing. Human Gene Therapy. 23: 46-55. PMID 21875357 DOI: 10.1089/Hum.2011.160  0.371
2012 Thompson JF, Reifenberger JG, Giladi E, Kerouac K, Gill J, Hansen E, Kahvejian A, Kapranov P, Knope T, Lipson D, Steinmann KE, Milos PM. Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations. Genome Research. 22: 340-5. PMID 21765009 DOI: 10.1101/Gr.122192.111  0.38
2012 Mitra AP, Buckley JD, Mitra SA, Davicioni E, Anderson JR, Kapranov P, Skapek SX, Hawkins DS, Triche TJ. Abstract 5581: A non-coding RNA panel is prognostically superior to standard pathologic criteria and coding transcripts in rhabdomyosarcoma Cancer Research. 72: 5581-5581. DOI: 10.1158/1538-7445.Am2012-5581  0.45
2012 Mitra SA, Wai DH, Buckley J, Kapranov P, Arceci RJ, Triche TJ. Abstract 1441: Role of a long non-coding RNA in oncogenesis of Ewing sarcoma Cancer Research. 72: 1441-1441. DOI: 10.1158/1538-7445.Am2012-1441  0.532
2011 Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KA, et al. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research. 21: 1705-19. PMID 21803858 DOI: 10.1101/Gr.122747.111  0.315
2011 Raz T, Kapranov P, Lipson D, Letovsky S, Milos PM, Thompson JF. Protocol Dependence of Sequencing-Based Gene Expression Measurements Plos One. 6. PMID 21573114 DOI: 10.1371/Journal.Pone.0019287  0.5
2011 Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 473: 394-7. PMID 21552279 DOI: 10.1038/Nature10102  0.441
2011 Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Research. 21: 301-14. PMID 21177962 DOI: 10.1101/Gr.112961.110  0.367
2011 Bajaj SV, Wai DH, Buckley JD, Kapranov P, Lawlor ER, Triche TJ. Abstract 1182: A large non-coding RNA that is characteristic of Ewing sarcoma family of tumors Cancer Research. 71: 1182-1182. DOI: 10.1158/1538-7445.Am2011-1182  0.501
2011 Kapranov P, Laurent GS, Raz T, Ozsolak F, Reynolds CP, Sorensen PH, Reaman G, Milos PM, Arceci RJ, Thompson JF, Triche TJ. Abstract 1177: The majority of total nuclear-encoded non-ribosomal RNA in human normal and tumor cells is “dark matter” unannotated RNA Cancer Research. 71: 1177-1177. DOI: 10.1158/1538-7445.Am2011-1177  0.541
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Kapranov P, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.498
2010 Kapranov P, St Laurent G, Raz T, Ozsolak F, Reynolds CP, Sorensen PH, Reaman G, Milos P, Arceci RJ, Thompson JF, Triche TJ. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. Bmc Biology. 8: 149. PMID 21176148 DOI: 10.1186/1741-7007-8-149  0.546
2010 Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 143: 1018-29. PMID 21145465 DOI: 10.1016/J.Cell.2010.11.020  0.526
2010 Kapranov P, Ozsolak F, Kim SW, Foissac S, Lipson D, Hart C, Roels S, Borel C, Antonarakis SE, Monaghan AP, John B, Milos PM. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature. 466: 642-6. PMID 20671709 DOI: 10.1038/Nature09190  0.525
2010 Yang A, Zhu Z, Kettenbach A, Kapranov P, McKeon F, Gingeras TR, Struhl K. Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo. Plos One. 5: e11572. PMID 20644729 DOI: 10.1371/Journal.Pone.0011572  0.333
2010 Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D, Hornig N, Orlando V, Bell I, Gao H, Dumais J, ... Kapranov P, et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods. 7: 528-34. PMID 20543846 DOI: 10.1038/Nmeth.1470  0.517
2010 Wai DH, Wu D, Wing MR, Arceci RJ, Reynolds CP, Sorensen PH, Reamon GH, Milos PM, Lawlor ER, Buckley JD, Kapranov P, Triche TJ. Abstract 4087: Large intergenic noncoding RNAs associated with Ewing sarcoma family of tumors Cancer Research. 70: 4087-4087. DOI: 10.1158/1538-7445.Am10-4087  0.524
2009 Ramani AK, Nelson AC, Kapranov P, Bell I, Gingeras TR, Fraser AG. High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology. 10: R101. PMID 19778439 DOI: 10.1186/Gb-2009-10-9-R101  0.377
2009 Makrythanasis P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, Drenkow J, Rossier C, Ariani F, Capra V, Excoffier L, Renieri A, Gingeras TR, Antonarakis SE. Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Human Mutation. 30: E866-79. PMID 19562714 DOI: 10.1002/Humu.21073  0.403
2009 Kapranov P. Studying chromosome-wide transcriptional networks: new insights into disease? Genome Medicine. 1: 50-50. PMID 19480644 DOI: 10.1186/Gm50  0.549
2009 Kapranov P. From transcription start site to cell biology. Genome Biology. 10: 217-217. PMID 19435485 DOI: 10.1186/Gb-2009-10-4-217  0.456
2009 Fejes-Toth K, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ, Kapranov P, Foissac S, Willingham AT, Duttagupta R, Dumais E, Gingeras TR. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs Nature. 457: 1028-1032. PMID 19169241 DOI: 10.1038/Nature07759  0.513
2009 Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood. 113: 2526-34. PMID 19144990 DOI: 10.1182/Blood-2008-06-162164  0.46
2008 Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods. 5: 629-35. PMID 18500348 DOI: 10.1038/Nmeth.1216  0.402
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, ... Kapranov P, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  0.343
2008 Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Research. 18: 380-92. PMID 18230803 DOI: 10.1101/Gr.6880908  0.462
2007 Ghosh S, Hirsch HA, Sekinger EA, Kapranov P, Struhl K, Gingeras TR. Differential analysis for high density tiling microarray data. Bmc Bioinformatics. 8: 359. PMID 17892592 DOI: 10.1186/1471-2105-8-359  0.494
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Kapranov P, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.488
2007 Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, ... ... Kapranov P, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Research. 17: 852-64. PMID 17568003 DOI: 10.1101/Gr.5650707  0.496
2007 Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research. 17: 839-51. PMID 17568002 DOI: 10.1101/Gr.5586307  0.501
2007 Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research. 17: 746-59. PMID 17567994 DOI: 10.1101/Gr.5660607  0.535
2007 Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (New York, N.Y.). 316: 1484-8. PMID 17510325 DOI: 10.1126/Science.1138341  0.52
2007 Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nature Reviews. Genetics. 8: 413-23. PMID 17486121 DOI: 10.1038/Nrg2083  0.461
2006 Willingham AT, Dike S, Cheng J, Manak JR, Bell I, Cheung E, Drenkow J, Dumais E, Duttagupta R, Ganesh M, Ghosh S, Helt G, Nix D, Piccolboni A, Sementchenko V, ... ... Kapranov P, et al. Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harbor Symposia On Quantitative Biology. 71: 101-10. PMID 17480199 DOI: 10.1101/Sqb.2006.71.068  0.515
2006 Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. Novel transcribed regions in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 71: 111-6. PMID 17381286 DOI: 10.1101/Sqb.2006.71.054  0.414
2006 Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Molecular Cell. 24: 593-602. PMID 17188034 DOI: 10.1016/J.Molcel.2006.10.018  0.39
2006 Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, Long J, Cheng J, Bell I, Ghosh S, Piccolboni A, Gingeras TR. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genetics. 38: 1151-8. PMID 16951679 DOI: 10.1038/Ng1875  0.503
2006 Schumacher A, Kapranov P, Kaminsky Z, Flanagan JM, Assadzadeh A, Yau P, Virtanen C, Winegarden NA, Cheng J, Gingeras TR, Petronis A. Microarray-based DNA methylation profiling: technology and applications Nucleic Acids Research. 34: 528-542. PMID 16428248 DOI: 10.1093/Nar/Gkj461  0.324
2005 Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S, Gingeras TR. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research. 15: 987-97. PMID 15998911 DOI: 10.1101/Gr.3455305  0.412
2005 Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America. 102: 6419-24. PMID 15845769 DOI: 10.1073/Pnas.0405088102  0.326
2005 Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (New York, N.Y.). 308: 1149-54. PMID 15790807 DOI: 10.1126/Science.1108625  0.518
2004 Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, ... ... Kapranov P, et al. The ENCODE (ENCyclopedia of DNA Elements) Project Science. 306: 636-640. PMID 15499007 DOI: 10.1126/Science.1105136  0.382
2004 Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research. 14: 331-42. PMID 14993201 DOI: 10.1101/Gr.2094104  0.57
2004 Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, et al. Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs Cell. 116: 499-509. PMID 14980218 DOI: 10.1016/S0092-8674(04)00127-8  0.526
2003 Kapranov P, Sementchenko VI, Gingeras TR. Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Briefings in Functional Genomics & Proteomics. 2: 47-56. PMID 15239943 DOI: 10.1093/Bfgp/2.1.47  0.532
2002 Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. Large-scale transcriptional activity in chromosomes 21 and 22. Science (New York, N.Y.). 296: 916-9. PMID 11988577 DOI: 10.1126/Science.1068597  0.442
2001 Kapranov P, Routt SM, Bankaitis VA, de Bruijn FJ, Szczyglowski K. Nodule-specific regulation of phosphatidylinositol transfer protein expression in Lotus japonicus. The Plant Cell. 13: 1369-82. PMID 11402166 DOI: 10.1105/Tpc.010059  0.434
1999 Kapranov P, Jensen TJ, Poulsen C, Bruijn FJd, Szczyglowski K. A Protein Phosphatase 2C Gene, Ljnpp2C1, From Lotus Japonicus Induced During Root Nodule Development Proceedings of the National Academy of Sciences of the United States of America. 96: 1738-1743. PMID 9990094 DOI: 10.1073/Pnas.96.4.1738  0.372
1998 Szczyglowski K, Kapranov P, Hamburger D, Bruijn FJD. The Lotus japonicus LjNOD70 nodulin gene encodes a protein with similarities to transporters. Plant Molecular Biology. 37: 651-661. PMID 9687069 DOI: 10.1023/A:1006043428636  0.38
1997 Szczyglowski K, Hamburger D, Kapranov P, Bruijn FJd. Construction of a Lotus japonicus Late Nodulin Expressed Sequence Tag Library and Identification of Novel Nodule-Specific Genes Plant Physiology. 114: 1335-1346. PMID 9276951 DOI: 10.1104/Pp.114.4.1335  0.428
1997 Kapranov P, Bruijn FJd, Szczyglowski K. Novel, highly expressed late nodulin gene (LjNOD16) from Lotus japonicus. Plant Physiology. 113: 1081-1090. PMID 9112769 DOI: 10.1104/Pp.113.4.1081  0.413
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