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Article

Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil.
Giurgiu, M., Wittstruck, N., Rodriguez-Fos, E., Chamorro González, R., Brückner, L., Krienelke-Szymansky, A., Helmsauer, K., Hartebrodt, A., Euskirchen, P., Koche, R.P., Haase, K., Reinert, K. and Henssen, A.G.
Genome Research 34 (9): 1355-1364. September 2024

Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky, D., Vollger, M.R., Harvey, W.T., Rozanski, A.N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A.D., Stober, C., Korbel, J.O., Paten, B., Marschall, T. and Eichler, E.E.
Genome Research 33 (4): 496-510. April 2023

A high-resolution map of small-scale inversions in the gibbon genome.
Mercuri, L., Palmisano, D., L'Abbate, A., D'Addabbo, P., Montinaro, F., Catacchio, C.R., Hasenfeld, P., Ventura, M., Korbel, J.O., Sanders, A.D., Maggiolini, F.A.M. and Antonacci, F.
Genome Research 32 (10): 1941-1951. October 2022

DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia.
Giacopelli, B., Wang, M., Cleary, A., Wu, Y.Z., Schultz, A.R., Schmutz, M., Blachly, J.S., Eisfeld, A.K., Mundy-Bosse, B., Vosberg, S., Greif, P.A., Claus, R., Bullinger, L., Garzon, R., Coombes, K.R., Bloomfield, C.D., Druker, B.J., Tyner, J.W., Byrd, J.C. and Oakes, C.C.
Genome Research 31 (5): 747-761. May 2021

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution.
Maggiolini, F.A.M., Sanders, A.D., Shew, C.J., Sulovari, A., Mao, Y., Puig, M., Catacchio, C.R., Dellino, M., Palmisano, D., Mercuri, L., Bitonto, M., Porubský, D., Cáceres, M., Eichler, E.E., Ventura, M., Dennis, M.Y., Korbel, J.O. and Antonacci, F.
Genome Research 30 (11): 1680-1693. November 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping.
Ramilowski, J.A., Yip, C.W., Agrawal, S., Chang, J.C., Ciani, Y., Kulakovskiy, I.V., Mendez, M., Ooi, J.L.C., Ouyang, J.F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I.V., Arner, E., Bonetti, A., Bono, H., Borsari, B., Brombacher, F., Cameron, C.J.F., Cannistraci, C.V., Cardenas, R., Cardon, M., Chang, H., Dostie, J., Ducoli, L., Favorov, A., Fort, A., Garrido, D., Gil, N., Gimenez, J., Guler, R., Handoko, L., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, K., Hayatsu, N., Heutink, P., Hirose, T., Imada, E.L., Itoh, M., Kaczkowski, B., Kanhere, A., Kawabata, E., Kawaji, H., Kawashima, T., Kelly, S.T., Kojima, M., Kondo, N., Koseki, H., Kouno, T., Kratz, A., Kurowska-Stolarska, M., Kwon, A.T.J., Leek, J., Lennartsson, A., Lizio, M., López-Redondo, F., Luginbühl, J., Maeda, S., Makeev, V.J., Marchionni, L., Medvedeva, Y.A., Minoda, A., Müller, F., Muñoz-Aguirre, M., Murata, M., Nishiyori, H., Nitta, K.R., Noguchi, S., Noro, Y., Nurtdinov, R., Okazaki, Y., Orlando, V., Paquette, D., Parr, C.J.C., Rackham, O.J.L., Rizzu, P., Sánchez Martinez, D.F., Sandelin, A., Sanjana, P., Semple, C.A.M., Shibayama, Y., Sivaraman, D.M., Suzuki, T., Szumowski, S.C., Tagami, M., Taylor, M.S., Terao, C., Thodberg, M., Thongjuea, S., Tripathi, V., Ulitsky, I., Verardo, R., Vorontsov, I.E., Yamamoto, C., Young, R.S., Baillie, J.K., Forrest, A.R.R., Guigó, R., Hoffman, M.M., Hon, C.C., Kasukawa, T., Kauppinen, S., Kere, J., Lenhard, B., Schneider, C., Suzuki, H., Yagi, K., de Hoon, M.J.L., 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., Hennig, B.P., Wang, J., Zhang, Y., Piazza, I., Pareja Sanchez, Y., Chabbert, C.D., Adjalley, S.H., 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., Costea, P., Coelho, L.P., Kandels-Lewis, S., Willemsen, G., Boomsma, D.I., Segata, N. and Bork, P.
Genome Research 28 (4): 561-568. April 2018

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

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments.
Robson, M.I., de Las Heras, J.I., Czapiewski, R., Sivakumar, A., Kerr, A.R.W. and Schirmer, E.C.
Genome Research 27 (7): 1126-1138. July 2017

Direct chromosome-length haplotyping by single-cell sequencing.
Porubský, D., Sanders, A.D., van Wietmarschen, N., Falconer, E., Hills, M., Spierings, D.C.J., Bevova, M.R., Guryev, V. and Lansdorp, P.M.
Genome Research 26 (11): 1565-1574. November 2016

Characterizing polymorphic inversions in human genomes by single-cell sequencing.
Sanders, A.D., Hills, M., Porubský, D., Guryev, V., Falconer, E. and Lansdorp, P.M.
Genome Research 26 (11): 1575-1587. November 2016

The mRNA-bound proteome of the early fly embryo.
Wessels, H.H., Imami, K., Baltz, A.G., Kolinski, M., Beldovskaya, A., Selbach, M., Small, S., 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., Kakar, N., Tayebi, N., Leettola, C., Nürnberg, G., Sowada, N., Lupiáñez, D.G., Harabula, I., Flöttmann, R., Horn, D., Chan, W.L., Wittler, L., Yilmaz, R., Altmüller, J., Thiele, H., van Bokhoven, H., Schwartz, C.E., Nürnberg, P., Bowie, J.U., Ahmad, J., Kubisch, C., 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., Rosser, J.M., Newkirk, S.J., Yin, J., Jiang, X., Xing, Z., Whitmore, L., Bashir, S., Ivics, Z., Izsvák, Z., Ye, P., 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., Uhlenhaut, N.H., Rauch, A., Weiner, J., Hübner, S., Hübner, N., Won, K.J., Lazar, M.A., 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., Bounab, Y., Strempel, N., Klockmeier, K., Yigit, S., Friedrich, R.P., Chaurasia, G., Li, S., Hesse, F., Riechers, S.P., Russ, J., Nicoletti, C., Boeddrich, A., Wiglenda, T., Haenig, C., Schnoegl, S., Fournier, D., Graham, R.K., Hayden, M.R., Sigrist, S., Bates, G.P., Priller, J., Andrade-Navarro, M.A., Futschik, M.E. and Wanker, E.E.
Genome Research 25 (5): 701-713. May 2015

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.
Agirre, X., Castellano, G., Pascual, M., Heath, S., Kulis, M., Segura, V., Bergmann, A., Esteve, A., Merkel, A., Raineri, E., Agueda, L., Blanc, J., Richardson, D., Clarke, L., Datta, A., Russiñol, N., Queirós, A.C., Beekman, R., Rodríguez-Madoz, J.R., San José-Enériz, E., Fang, F., Gutiérrez, N.C., García-Verdugo, J.M., Robson, M.I., Schirmer, E.C., Guruceaga, E., Martens, J.H.A., Gut, M., Calasanz, M.J., Flicek, P., Siebert, R., Campo, E., Miguel, J.F.S., Melnick, A., Stunnenberg, H.G., Gut, I.G., Prosper, F. and Martín-Subero, J.I.
Genome Research 25 (4): 478-487. April 2015

BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies.
Borck, G., Hög, F., Dentici, M.L., Tan, P.L., Sowada, N., Medeira, A., Gueneau, L., Thiele, H., Kousi, M., Lepri, F., Wenzeck, L., Blumenthal, I., Radicioni, A., Schwarzenberg, T.L., Mandriani, B., Fischetto, R., Morris-Rosendahl, D.J., Altmüller, J., Reymond, A., Nürnberg, P., Merla, G., Dallapiccola, B., Katsanis, N., Cramer, P. and Kubisch, C.
Genome Research 25 (2): 155-166. February 2015

Natural variation of histone modification and its impact on gene expression in the rat genome.
Rintisch, C., Heinig, M., Bauerfeind, A., Schafer, S., Mieth, C., Patone, G., Hummel, O., Chen, W., Cook, S., Cuppen, E., Colomé-Tatché, M., Johannes, F., Jansen, R.C., Neil, H., Werner, M., Pravenec, M., 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., Hadzhiev, Y., Previti, C., Haberle, V., Li, N., Takahashi, H., Suzuki, A.M.M., Sheng, Y., Abdelhamid, R.F., Anand, S., Gehrig, J., Akalin, A., Kockx, C.E.M., van der Sloot, A.A.J., van Ijcken, W.F.J., Armant, O., Rastegar, S., Watson, C., Strähle, U., Stupka, E., Carninci, P., 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., Liberman, L., Mukherjee, N., 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., Sunagawa, S., Kultima, J.R., Mende, D.R., Arumugam, M., 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., Yardimci, G.G., Sheffield, N.C., 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., Somel, M., Tang, L., Yan, Z., Jiang, X., Guo, S., Yuan, Y.P., He, L., Oleksiak, A., Zhang, Y., Li, N., Hu, Y., Chen, W., Qiu, Z., Paeaebo, S. and Khaitovich, P.
Genome Research 22 (4): 611-622. April 2012

Promoter architecture of mouse olfactory receptor genes.
Plessy, C., Pascarella, G., Bertin, N., Akalin, A., Carrieri, C., Vassalli, A., Lazarevic, D., Severin, J., Vlachouli, C., Simone, R., Faulkner, G.J., Kawai, J., Daub, C.O., Zucchelli, S., Hayashizaki, Y., Mombaerts, P., Lenhard, B., 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., Corcoran, D.L., Petricka, J.J., Shen, J., Sae-Seaw, J., Rubio-Somoza, I., Weigel, D., 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., Wang, Y., Gruen, D., Mastrobuoni, G., You, X., Tolle, D., Dodt, M., Mackowiak, S.D., Gogol-Doering, A., Oenal, P., Rybak, A., Ross, E., Alvarado, A.S., Kempa, S., Dieterich, C., 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., Guo, S., Fu, N., Yan, Z., Hu, H.Y., Xu, Y., Yuan, Y., Ning, Z., Hu, Y., Menzel, C., Hu, H., Lachmann, M., Zeng, R., Chen, W. and Khaitovich, P.
Genome Research 20 (9): 1207-1218. September 2010

Phenotypic annotation of the mouse X chromosome.
Cox, B.J., Vollmer, M., Tamplin, O., Lu, M., Biechele, S., Gertsenstein, M., van Campenhout, C., Floss, T., Kühn, R., Wurst, W., 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., Birol, I., Guryev, V., Hirst, M., Hummel, O., Morrissey, C., Behmoaras, J., Fernandez-Suarez, X.M., Johnson, M.D., McLaren, W.M., Patone, G., Petretto, E., Plessy, C., Rockland, K.S., Rockland, C., Saar, K., Zhao, Y., Carninci, P., Flicek, P., Kurtz, T., Cuppen, E., Pravenec, M., Huebner, N., Jones, S.J., 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., Dieterich, C., Krug, K., Schuetz, W., Jung, S., Nordheim, A., 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., Liska, F., Gosele, C., Sedova, L., Kren, V., Krenova, D., Ivics, Z., 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., Landthaler, M., Jaskiewicz, L., 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., Zien, A., Zeller, G., Behr, J., Dieterich, C., Ong, C.S., Philips, P., De Bona, F., Hartmann, L., Bohlen, A., Krueger, N., 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., Pereira, F., Jensen, S.T., Ohler, U. and Hatzigeorgiou, A.G.
Genome Research 19 (4): 644-656. April 2009

Mapping translocation breakpoints by next-generation sequencing.
Chen, W., Kalscheuer, V., Tzschach, A., Menzel, C., Ullmann, R., Schulz, M.H., Erdogan, F., Li, N., Kijas, Z., Arkesteijn, G., Pajares, I.L., Goetz-Sothmann, M., Heinrich, U., Rost, I., Dufke, A., Grasshoff, U., Glaeser, B., 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., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstroem, P.G., Fredman, D., Akalin, A., Caccamo, M., Sealy, I., Howe, K., Ghislain, J., Pezeron, G., Mourrain, P., Ellingsen, S., Oates, A.C., Thisse, C., Thisse, B., Foucher, I., Adolf, B., Geling, A., 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., von Mering, C., 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., Zdobnov, E.M., Bork, P., 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., von Mering, C., Suyama, M., Harrington, E.D., 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., Wallis, J., Gösele, C., Bosdet, I., Chiu, R., Graves, T., Hummel, O., Layman, D., Mathewson, C., Wye, N., Zhu, B., Albracht, D., Asano, J., Barber, S., Brown-John, M., Chan, S., Chand, S., Cloutier, A., Davito, J., Fjell, C., Gaige, T., Ganten, D., Girn, N., Guggenheimer, K., Himmelbauer, H., Kreitler, T., Leach, S., Lee, D., Lehrach, H., Mayo, M., Mead, K., Olson, T., Pandoh, P., Prabhu, A.L., Shin, H., Taenzer, S., Thompson, J., Tsai, M., Walker, J., Yang, G., Sekhon, M., Hillier, L., Zimdahl, H., Marziali, A., Osoegawa, K., Zhao, S., Siddiqui, A., de Jong, P.J., Warren, W., Mardis, E., McPherson, J.D., Wilson, R., Hübner, N., Jones, S., Marra, M. and Schein, J.
Genome Research 14 (4): 766-779. April 2004

A genome-wide survey of human pseudogenes.
Torrents, D., Suyama, M., 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., Kepper, P., Hoehe, M., Schmitt, C., Reinhardt, R., 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., 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., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., 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., Bult, C.J., Cremer, C., Grunze, M., Knowles, B.B., Langowski, J., McNally, J., Pederson, T., Politz, J.C., Pombo, A., Schmahl, G., 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., Schultz, J., 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., Socci, N.D., 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., Copley, R.R., Schultz, J., 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., 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., Mott, R., 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., Pickard, B., Walter, J., Jung, M., Pourcel, L., Reik, W., Gauguier, D., 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., Snel, B., 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., Hartzell, G., Harris, N.L., Ohler, U., 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., Jung, M., Daser, A., Weiher, M., Walter, J., 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., Kwitek-Black, A.E., Glenn, C., Gullings-Handley, J., Van Etten, W., Atkinson, O.S., Appel, D., Twigger, S., Muir, M., Mull, T., Granados, M., Kissebah, M., Russo, K., Crane, R., Popp, M., Peden, M., Matise, T., Brown, D.M., Lu, J., Kingsmore, S., Tonellato, P.J., Rozen, S., Slonim, D., Young, P., Knoblauch, M., Provoost, A., Ganten, D., Colman, S.D., Rothberg, J., Lander, E.S. and Jacob, H.J.
Genome Research 9 : 1-8. 1 January 1999

Editorial

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