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Functional annotation of human long noncoding RNAs via molecular phenotyping.
Ramilowski, J.A. and Yip, C.W. and Agrawal, S. and Chang, J.C. and Ciani, Y. and Kulakovskiy, I.V. and Mendez, M. and Ooi, J.L.C. and Ouyang, J.F. and Parkinson, N. and Petri, A. and Roos, L. and Severin, J. and Yasuzawa, K. and Abugessaisa, I. and Akalin, A. and Antonov, I.V. and Arner, E. and Bonetti, A. and Bono, H. and Borsari, B. and Brombacher, F. and Cameron, C.J.F. and Cannistraci, C.V. and Cardenas, R. and Cardon, M. and Chang, H. and Dostie, J. and Ducoli, L. and Favorov, A. and Fort, A. and Garrido, D. and Gil, N. and Gimenez, J. and Guler, R. and Handoko, L. and Harshbarger, J. and Hasegawa, A. and Hasegawa, Y. and Hashimoto, K. and Hayatsu, N. and Heutink, P. and Hirose, T. and Imada, E.L. and Itoh, M. and Kaczkowski, B. and Kanhere, A. and Kawabata, E. and Kawaji, H. and Kawashima, T. and Kelly, S.T. and Kojima, M. and Kondo, N. and Koseki, H. and Kouno, T. and Kratz, A. and Kurowska-Stolarska, M. and Kwon, A.T.J. and Leek, J. and Lennartsson, A. and Lizio, M. and López-Redondo, F. and Luginbühl, J. and Maeda, S. and Makeev, V.J. and Marchionni, L. and Medvedeva, Y.A. and Minoda, A. and Müller, F. and Muñoz-Aguirre, M. and Murata, M. and Nishiyori, H. and Nitta, K.R. and Noguchi, S. and Noro, Y. and Nurtdinov, R. and Okazaki, Y. and Orlando, V. and Paquette, D. and Parr, C.J.C. and Rackham, O.J.L. and Rizzu, P. and Sánchez Martinez, D.F. and Sandelin, A. and Sanjana, P. and Semple, C.A.M. and Shibayama, Y. and Sivaraman, D.M. and Suzuki, T. and Szumowski, S.C. and Tagami, M. and Taylor, M.S. and Terao, C. and Thodberg, M. and Thongjuea, S. and Tripathi, V. and Ulitsky, I. and Verardo, R. and Vorontsov, I.E. and Yamamoto, C. and Young, R.S. and Baillie, J.K. and Forrest, A.R.R. and Guigó, R. and Hoffman, M.M. and Hon, C.C. and Kasukawa, T. and Kauppinen, S. and Kere, J. and Lenhard, B. and Schneider, C. and Suzuki, H. and Yagi, K. and de Hoon, M.J.L. and Shin, J.W. and Carninci, P.
Genome Research 30 (7): 1060-1072. July 2020

Deep neural networks for interpreting RNA-binding protein target preferences.
Ghanbari, M. and Ohler, U.
Genome Research 30 (2): 214-226. February 2020

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.
Wei, W. and Hennig, B.P. and Wang, J. and Zhang, Y. and Piazza, I. and Pareja Sanchez, Y. and Chabbert, C.D. and Adjalley, S.H. and Steinmetz, L.M. and Pelechano, V.
Genome Research 29 (12): 1974-1984. December 2019

Selective maternal seeding and environment shape the human gut microbiome.
Korpela, K. and Costea, P. and Coelho, L.P. and Kandels-Lewis, S. and Willemsen, G. and Boomsma, D.I. and Segata, N. and Bork, P.
Genome Research 28 (4): 561-568. April 2018

DDX54 regulates transcriptome dynamics during DNA damage response.
Milek, M. and Imami, K. and Mukherjee, N. and De Bortoli, F. and Zinnall, U. and Hazapis, O. and Trahan, C. and Oeffinger, M. and Heyd, F. and Ohler, U. and Selbach, M. and Landthaler, M.
Genome Research 27 (8): 1344-1359. August 2017

The mRNA-bound proteome of the early fly embryo.
Wessels, H.H. and Imami, K. and Baltz, A.G. and Kolinski, M. and Beldovskaya, A. and Selbach, M. and Small, S. and Ohler, U. and Landthaler, M.
Genome Research 26 (7): 1000-1009. July 2016

Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice.
Spielmann, M. and Kakar, N. and Tayebi, N. and Leettola, C. and Nürnberg, G. and Sowada, N. and Lupiáñez, D.G. and Harabula, I. and Flöttmann, R. and Horn, D. and Chan, W.L. and Wittler, L. and Yilmaz, R. and Altmüller, J. and Thiele, H. and van Bokhoven, H. and Schwartz, C.E. and Nürnberg, P. and Bowie, J.U. and Ahmad, J. and Kubisch, C. and Mundlos, S. and Borck, G.
Genome Research 26 (2): 183-191. February 2016

Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites.
Grandi, F.C. and Rosser, J.M. and Newkirk, S.J. and Yin, J. and Jiang, X. and Xing, Z. and Whitmore, L. and Bashir, S. and Ivics, Z. and Izsvák, Z. and Ye, P. and Yu, Y.E. and An, W.
Genome Research 25 (8): 1135-1146. August 2015

Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo.
Lim, H.W. and Uhlenhaut, N.H. and Rauch, A. and Weiner, J. and Hübner, S. and Hübner, N. and Won, K.J. and Lazar, M.A. and Tuckermann, J. and Steger, D.J.
Genome Research 25 (6): 836-844. June 2015

Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity.
Stroedicke, M. and Bounab, Y. and Strempel, N. and Klockmeier, K. and Yigit, S. and Friedrich, R.P. and Chaurasia, G. and Li, S. and Hesse, F. and Riechers, S.P. and Russ, J. and Nicoletti, C. and Boeddrich, A. and Wiglenda, T. and Haenig, C. and Schnoegl, S. and Fournier, D. and Graham, R.K. and Hayden, M.R. and Sigrist, S. and Bates, G.P. and Priller, J. and Andrade-Navarro, M.A. and Futschik, M.E. and Wanker, E.E.
Genome Research 25 (5): 701-713. May 2015

Natural variation of histone modification and its impact on gene expression in the rat genome.
Rintisch, C. and Heinig, M. and Bauerfeind, A. and Schafer, S. and Mieth, C. and Patone, G. and Hummel, O. and Chen, W. and Cook, S. and Cuppen, E. and Colomé-Tatché, M. and Johannes, F. and Jansen, R.C. and Neil, H. and Werner, M. and Pravenec, M. and Vingron, M. and Hubner, N.
Genome Research 24 (6): 942-953. June 2014

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
Nepal, C. and Hadzhiev, Y. and Previti, C. and Haberle, V. and Li, N. and Takahashi, H. and Suzuki, A.M.M. and Sheng, Y. and Abdelhamid, R.F. and Anand, S. and Gehrig, J. and Akalin, A. and Kockx, C.E.M. and van der Sloot, A.A.J. and van Ijcken, W.F.J. and Armant, O. and Rastegar, S. and Watson, C. and Strähle, U. and Stupka, E. and Carninci, P. and Lenhard, B. and Müller, F.
Genome Research 23 (11): 1938-1950. November 2013

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
Li, S. and Liberman, L. and Mukherjee, N. and Benfey, P. and Ohler, U.
Genome Research 23 (10): 1730-1739. October 2013

Country-specific antibiotic use practices impact the human gut resistome.
Forslund, K. and Sunagawa, S. and Kultima, J.R. and Mende, D.R. and Arumugam, M. and Typas, A. and Bork, P.
Genome Research 23 (7): 1163-1169. July 2013

Predicting cell-type-specific gene expression from regions of open chromatin.
Natarajan, A. and Yardimci, G.G. and Sheffield, N.C. and Crawford, G.E. and Ohler, U.
Genome Research 22 (9): 1711-1722. September 2012

Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques.
Liu, X. and Somel, M. and Tang, L. and Yan, Z. and Jiang, X. and Guo, S. and Yuan, Y.P. and He, L. and Oleksiak, A. and Zhang, Y. and Li, N. and Hu, Y. and Chen, W. and Qiu, Z. and Paeaebo, S. and Khaitovich, P.
Genome Research 22 (4): 611-622. April 2012

Promoter architecture of mouse olfactory receptor genes.
Plessy, C. and Pascarella, G. and Bertin, N. and Akalin, A. and Carrieri, C. and Vassalli, A. and Lazarevic, D. and Severin, J. and Vlachouli, C. and Simone, R. and Faulkner, G.J. and Kawai, J. and Daub, C.O. and Zucchelli, S. and Hayashizaki, Y. and Mombaerts, P. and Lenhard, B. and Gustincich, S. and Carninci, P.
Genome Research 22 (3): 486-497. March 2012

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis.
Breakfield, N.W. and Corcoran, D.L. and Petricka, J.J. and Shen, J. and Sae-Seaw, J. and Rubio-Somoza, I. and Weigel, D. and Ohler, U. and Benfey, P.N.
Genome Research 22 (1): 163-176. January 2012

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Adamidi, C. and Wang, Y. and Gruen, D. and Mastrobuoni, G. and You, X. and Tolle, D. and Dodt, M. and Mackowiak, S.D. and Gogol-Doering, A. and Oenal, P. and Rybak, A. and Ross, E. and Alvarado, A.S. and Kempa, S. and Dieterich, C. and Rajewsky, N. and Chen, W.
Genome Research 21 (7): 1193-1200. July 2011

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain.
Somel, M. and Guo, S. and Fu, N. and Yan, Z. and Hu, H.Y. and Xu, Y. and Yuan, Y. and Ning, Z. and Hu, Y. and Menzel, C. and Hu, H. and Lachmann, M. and Zeng, R. and Chen, W. and Khaitovich, P.
Genome Research 20 (9): 1207-1218. September 2010

Phenotypic annotation of the mouse X chromosome.
Cox, B.J. and Vollmer, M. and Tamplin, O. and Lu, M. and Biechele, S. and Gertsenstein, M. and van Campenhout, C. and Floss, T. and Kuehn, R. and Wurst, W. and Lickert, H. and Rossant, J.
Genome Research 20 (8): 1154-1164. August 2010

The genome sequence of the spontaneously hypertensive rat: analysis and functional significance.
Atanur, S.S. and Birol, I. and Guryev, V. and Hirst, M. and Hummel, O. and Morrissey, C. and Behmoaras, J. and Fernandez-Suarez, X.M. and Johnson, M.D. and McLaren, W.M. and Patone, G. and Petretto, E. and Plessy, C. and Rockland, K.S. and Rockland, C. and Saar, K. and Zhao, Y. and Carninci, P. and Flicek, P. and Kurtz, T. and Cuppen, E. and Pravenec, M. and Huebner, N. and Jones, S.J. and Birney, E. and Aitman, T.J.
Genome Research 20 (6): 791-803. June 2010

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models.
Borchert, N. and Dieterich, C. and Krug, K. and Schuetz, W. and Jung, S. and Nordheim, A. and Sommer, R.J. and Macek, B.
Genome Research 20 (6): 837-486. June 2010

A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains.
Wang, Y. and Liska, F. and Gosele, C. and Sedova, L. and Kren, V. and Krenova, D. and Ivics, Z. and Huebner, N. and Izsvak, Z.
Genome Research 20 (1): 19-27. January 2010

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets.
Hausser, J. and Landthaler, M. and Jaskiewicz, L. and Gaidatzis, D. and Zavolan, M.
Genome Research 19 (11): 2009-2020. November 2009

mGene: Accurate SVM-based gene finding with an application to nematode genomes.
Schweikert, G. and Zien, A. and Zeller, G. and Behr, J. and Dieterich, C. and Ong, C.S. and Philips, P. and De Bona, F. and Hartmann, L. and Bohlen, A. and Krueger, N. and Sonnenburg, S. and Raetsch, G.
Genome Research 19 (11): 2133-2143. November 2009

A transcription factor affinity-based code for mammalian transcription initiation.
Megraw, M. and Pereira, F. and Jensen, S.T. and Ohler, U. and Hatzigeorgiou, A.G.
Genome Research 19 (4): 644-656. April 2009

Mapping translocation breakpoints by next-generation sequencing.
Chen, W. and Kalscheuer, V. and Tzschach, A. and Menzel, C. and Ullmann, R. and Schulz, M.H. and Erdogan, F. and Li, N. and Kijas, Z. and Arkesteijn, G. and Pajares, I.L. and Goetz-Sothmann, M. and Heinrich, U. and Rost, I. and Dufke, A. and Grasshoff, U. and Glaeser, B. and Vingron, M. and Ropers, H.H.
Genome Research 18 (7): 1143-1149. July 2008

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.
Kikuta, H. and Laplante, M. and Navratilova, P. and Komisarczuk, A.Z. and Engstroem, P.G. and Fredman, D. and Akalin, A. and Caccamo, M. and Sealy, I. and Howe, K. and Ghislain, J. and Pezeron, G. and Mourrain, P. and Ellingsen, S. and Oates, A.C. and Thisse, C. and Thisse, B. and Foucher, I. and Adolf, B. and Geling, A. and Lenhard, B. and Becker, T.S.
Genome Research 17 (5): 545-555. May 2007

Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos, M. and von Mering, C. and Jensen, L.J. and Bork, P.
Genome Research 16 : 374-382. 31 January 2006

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Bourque, G. and Zdobnov, E.M. and Bork, P. and Pevzner, P.A. and Tesler, G.
Genome Research 15 : 98-110. 1 January 2005

Complex genomic rearrangements lead to novel primate gene function.
Ciccarelli, F.D. and von Mering, C. and Suyama, M. and Harrington, E.D. and Izaurralde, E. and Bork, P.
Genome Research 15 (3): 343-351. 1 January 2005

Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.
Krzywinski, M. and Wallis, J. and Goesele, C. and Bosdet, I. and Chiu, R. and Graves, T. and Hummel, O. and Layman, D. and Mathewson, C. and Wye, N. and Zhu, B. and Albracht, D. and Asano, J. and Barber, S. and Brown-John, M. and Chan, S. and Chand, S. and Cloutier, A. and Davito, J. and Fjell, C. and Gaige, T. and Ganten, D. and Girn, N. and Guggenheimer, K. and Himmelbauer, H. and Kreitler, T. and Leach, S. and Lee, D. and Lehrach, H. and Mayo, M. and Mead, K. and Olson, T. and Pandoh, P. and Prabhu, A.L. and Shin, H. and Taenzer, S. and Thompson, J. and Tsai, M. and Walker, J. and Yang, G. and Sekhon, M. and Hillier, L. and Zimdahl, H. and Marziali, A. and Osoegawa, K. and Zhao, S. and Siddiqui, A. and de Jong, P.J. and Warren, W. and Mardis, E. and McPherson, J.D. and Wilson, R. and Huebner, N. and Jones, S. and Marra, M. and Schein, J.
Genome Research 14 (4): 766-779. April 2004

A genome-wide survey of human pseudogenes.
Torrents, D. and Suyama, M. and Zdobnov, E. and Bork, P.
Genome Research 13 : 2559-2567. 1 December 2003

Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes.
Burgtorf, C. and Kepper, P. and Hoehe, M. and Schmitt, C. and Reinhardt, R. and Lehrach, H. and Sauer, S.
Genome Research 13 (12): 2717-2724. December 2003

Functionality of system components: conservation of protein function in protein feature space.
Jensen, L.J. and Ussery, D.W. and Brunak, S.
Genome Research 13 : 2444-2449. November 2003

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.
Yang, E. and van Nimwegen, E. and Zavolan, M. and Rajewsky, N. and Schroeder, M. and Magnasco, M. and Darnell, J.E.
Genome Research 13 (8): 1863-1872. August 2003

Genome function and nuclear architecture: from gene expression to nanoscience.
O'Brien, T.P. and Bult, C.J. and Cremer, C. and Grunze, M. and Knowles, B.B. and Langowski, J. and McNally, J. and Pederson, T. and Politz, J.C. and Pombo, A. and Schmahl, G. and Spatz, J.P. and van Driel, R.
Genome Research 13 (6A): 1029-1041. June 2003

Predicting protein cellular localization using a domain projection method.
Mott, R. and Schultz, J. and Bork, P. and Ponting, C.P.
Genome Research 12 (8): 1168-1174. August 2002

The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons.
Rajewsky, N. and Socci, N.D. and Zapotocky, M. and Siggia, E.D.
Genome Research 12 (2): 298-308. February 2002

Systematic identification of novel protein domain families associated with nuclear functions.
Doerks, T. and Copley, R.R. and Schultz, J. and Ponting, C.P. and Bork, P.
Genome Research 12 (1): 47-56. 1 January 2002

Genomes in flux: The evolution of archaeal and proteobacterial gene content.
Snel, B. and Bork, P. and Huynen, M.A.
Genome Research 12 (1): 17-25. 1 January 2002

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.
Ponting, C.P. and Mott, R. and Bork, P. and Copley, R.R.
Genome Research 11 : 1996-2008. 1 December 2001

A dominant modifier of transgene methylation is mapped by QTL analysis to mouse chromosome 13.
Valenza-Schaerly, P. and Pickard, B. and Walter, J. and Jung, M. and Pourcel, L. and Reik, W. and Gauguier, D. and Vergnaud, G. and Pourcel, C.
Genome Research 11 (3): 382-388. 1 January 2001

Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences.
Huynen, M. and Snel, B. and Lathe, W. and Bork, P.
Genome Research 10 (8): 1204-1210. 1 August 2000

Promoter prediction on a genomic scale-the Adh experience.
Ohler, U.
Genome Research 10 (4): 539-542. April 2000

Genome annotation assessment in Drosophila melanogaster.
Reese, M.G. and Hartzell, G. and Harris, N.L. and Ohler, U. and Abril, J.F. and Lewis, S.E.
Genome Research 10 (4): 483-501. April 2000

Panel of microsatellite markers for whole-genome scans and radiation hybrid mapping and a mouse family tree.
Schalkwyk, L.C. and Jung, M. and Daser, A. and Weiher, M. and Walter, J. and Hummelbauer, H. and Lehrach, H.
Genome Research 9 : 878-887. 1 September 1999

A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.
Steen, R.G. and Kwitek-Black, A.E. and Glenn, C. and Gullings-Handley, J. and Van Etten, W. and Atkinson, O.S. and Appel, D. and Twigger, S. and Muir, M. and Mull, T. and Granados, M. and Kissebah, M. and Russo, K. and Crane, R. and Popp, M. and Peden, M. and Matise, T. and Brown, D.M. and Lu, J. and Kingsmore, S. and Tonellato, P.J. and Rozen, S. and Slonim, D. and Young, P. and Knoblauch, M. and Provoost, A. and Ganten, D. and Colman, S.D. and Rothberg, J. and Lander, E.S. and Jacob, H.J.
Genome Research 9 : 1-8. 1 January 1999


Powers and pitfalls in sequence analysis: The 70% hurdle.
Bork, P.
Genome Research 10 (4): 398-400. 1 April 2000

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