Article

Interpreting deep neural networks for the prediction of translation rates.
Korbel, F. ORCID: https://orcid.org/0009-0008-0080-0514, Eroshok, E. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
BMC Genomics 25 (1): 1061. 9 November 2024

Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks.
Proft, S. ORCID: https://orcid.org/0000-0002-1707-0625, Leiz, J. ORCID: https://orcid.org/0000-0002-6531-7047, Heinemann, U. ORCID: https://orcid.org/0000-0002-8191-3850, Seelow, D. ORCID: https://orcid.org/0000-0002-9746-4412, Schmidt-Ott, K.M. ORCID: https://orcid.org/0000-0002-7700-7142 and Rutkiewicz, M. ORCID: https://orcid.org/0000-0001-8339-3230
BMC Genomics 24 (1): 736. 4 December 2023

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
Miko, H. ORCID: https://orcid.org/0000-0001-5911-7586, Qiu, Y., Gaertner, B., Sander, M. ORCID: https://orcid.org/0000-0001-5308-7785 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
BMC Genomics 22 (1): 84. 28 January 2021

The effects of common structural variants on 3D chromatin structure.
Shanta, O., Noor, A. and Sebat, J. ORCID: https://orcid.org/0000-0002-9087-526X
BMC Genomics 21 (1): 95. 30 January 2020

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution.
Hansen, P., Ali, S., Blau, H., Danis, D., Hecht, J., Kornak, U., Lupiáñez, D.G. ORCID: https://orcid.org/0000-0002-3165-036X, Mundlos, S., Steinhaus, R. and Robinson, P.N. ORCID: https://orcid.org/0000-0002-0736-9199
BMC Genomics 20 (1): 40. 14 January 2019

First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data.
Genova, F., Longeri, M., Lyons, L.A., Bagnato, A. and Strillacci, M.G.
BMC Genomics 19 (1): 895. 10 December 2018

Finding RNA structure in the unstructured RBPome.
Orenstein, Y., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Berger, B.
BMC Genomics 19 (1): 154. 20 February 2018

Forward genetic screen of human transposase genomic rearrangements.
Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X, Jiang, E., Zhuang, J., Pinello, L., Socci, N.D., Koche, R., Gonen, M., Villasante, C.M., Armstrong, S.A., Bauer, D.E., Weng, Z. and Kentsis, A. ORCID: https://orcid.org/0000-0002-8063-9191
BMC Genomics 17 : 548. 4 August 2016

Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae).
Lamanna, F., Kirschbaum, F., Waurick, I., Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311 and Tiedemann, R.
BMC Genomics 16 (1): 668. 3 September 2015

Genomic landscape of rat strain and substrain variation.
Hermsen, R., de Ligt, J., Spee, W., Blokzijl, F., Schäfer, S., Adami, E. ORCID: https://orcid.org/0000-0002-1813-6681, Boymans, S., Flink, S, van Boxtel, R., van der Weide, R.H., Aitman, T., Hübner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Simonis, M., Tabakoff, B., Guryev, V. and Cuppen, E.
BMC Genomics 16 : 357. 6 May 2015

Induced pluripotent stem cell-derived neuronal cells from a sporadic Alzheimer's disease donor as a model for investigating AD-associated gene regulatory networks.
Hossini, A.M., Megges, M. ORCID: https://orcid.org/0000-0001-6537-0975, Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952, Lichtner, B., Toliat, M.R., Wruck, W., Schroeter, F., Nuernberg, P., Kroll, H., Makrantonaki, E., Zoubouliss, C.C. and Adjaye, J.
BMC Genomics 16 (1): 84. 14 February 2015

Whole genome sequencing and methylome analysis of the wild guinea pig.
Weyrich, A., Schuellermann, T., Heeger, F., Jeschek, M., Mazzoni, C.J., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Schumann, K. and Fickel, J.
BMC Genomics 15 (1): 1036. 28 November 2014

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples.
Risueño, A., Roson-Burgo, B., Dolnik, A., Hernandez-Rivas, J.M., Bullinger, L. ORCID: https://orcid.org/0000-0002-5890-5510 and De Las Rivas, J.
BMC Genomics 15 : 879. 8 October 2014

Haploinsufficiency of ETV6 and CDKN1B in patients with acute myeloid leukemia and complex karyotype.
Feurstein, S., Rücker, F.G., Bullinger, L. ORCID: https://orcid.org/0000-0002-5890-5510, Hofmann, W., Manukjan, G., Göhring, G., Lehmann, U., Heuser, M., Ganser, A., Döhner, K., Schlegelberger, B. and Steinemann, D.
BMC Genomics 15 : 784. 11 September 2014

Deciphering the genetic basis of microcystin tolerance.
Schwarzenberger, A., Sadler, T., Motameny, S., Ben-Khalifa, K., Frommolt, P., Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Konrad, K. and von Elert, E.
BMC Genomics 15 : 776. 9 September 2014

Relationship between genome and epigenome - challenges and requirements for future research.
Almouzni, G., Altucci, L. ORCID: https://orcid.org/0000-0002-7312-5387, Amati, B. ORCID: https://orcid.org/0000-0002-2958-1799, Ashley, N. ORCID: https://orcid.org/0000-0002-1655-5137, Baulcombe, D. ORCID: https://orcid.org/0000-0003-0780-6878, Beaujean, N. ORCID: https://orcid.org/0000-0003-0188-9190, Bock, C. ORCID: https://orcid.org/0000-0001-6091-3088, Bongcam-Rudloff, E. ORCID: https://orcid.org/0000-0002-1947-8288, Bousquet, J., Braun, S., Bressac-de Paillerets, B., Bussemakers, M., Clarke, L. ORCID: https://orcid.org/0000-0002-5989-6898, Conesa, A. ORCID: https://orcid.org/0000-0001-9597-311X, Estivill, X. ORCID: https://orcid.org/0000-0002-0723-2256, Fazeli, A. ORCID: https://orcid.org/0000-0003-0870-9914, Grgurević, N., Gut, I., Heijmans, B.T., Hermouet, S., Houwing-Duistermaat, J., Iacobucci, I., Ilaš, J. ORCID: https://orcid.org/0000-0002-0124-0474, Kandimalla, R. ORCID: https://orcid.org/0000-0002-0342-5229, Krauss-Etschmann, S. ORCID: https://orcid.org/0000-0001-5945-5702, Lasko, P. ORCID: https://orcid.org/0000-0002-4037-3501, Lehmann, S. ORCID: https://orcid.org/0000-0001-6117-562X, Lindroth, A. ORCID: https://orcid.org/0000-0002-8291-2745, Majdič, G., Marcotte, E., Martinelli, G., Martinet, N., Meyer, E. ORCID: https://orcid.org/0000-0002-3161-8597, Miceli, C. ORCID: https://orcid.org/0000-0002-7829-8471, Mills, K. ORCID: https://orcid.org/0000-0002-6362-4481, Moreno-Villanueva, M., Morvan, G., Nickel, D., Niesler, B., Nowacki, M. ORCID: https://orcid.org/0000-0003-4894-2905, Nowak, J., Ossowski, S. ORCID: https://orcid.org/0000-0002-7416-9568, Pelizzola, M. ORCID: https://orcid.org/0000-0001-6672-9636, Pochet, R. ORCID: https://orcid.org/0000-0001-9027-7916, Potočnik, U. ORCID: https://orcid.org/0000-0003-1624-9428, Radwanska, M. ORCID: https://orcid.org/0000-0002-0797-6001, Raes, J. ORCID: https://orcid.org/0000-0002-1337-041X, Rattray, M. ORCID: https://orcid.org/0000-0001-8196-5565, Robinson, M.D. ORCID: https://orcid.org/0000-0002-3048-5518, Roelen, B., Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693, Schinzer, D., Slagboom, E. ORCID: https://orcid.org/0000-0002-2875-4723, Spector, T., Stunnenberg, H.G. ORCID: https://orcid.org/0000-0002-0066-1576, Tiligada, E., Torres-Padilla, M.E., Tsonaka, R., Van Soom, A., Vidaković, M. ORCID: https://orcid.org/0000-0001-8410-6264 and Widschwendter, M.
BMC Genomics 15 : 487. 18 June 2014

The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda.
Schiffer, P.H., Kroiher, M., Kraus, C., Koutsovoulos, G.D., Kumar, S., Camps, J.I.R., Nsah, N.A., Stappert, D., Morris, K., Heger, P., Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Frommolt, P., Nürnberg, P., Thomas, W.K., Blaxter, M.L. and Schierenberg, E.
BMC Genomics 14 : 923. 27 December 2013

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.
Ni, T., Yang, Y., Hafez, D., Yang, W., Kiesewetter, K., Wakabayashi, Y., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Peng, W. and Zhu, J.
BMC Genomics 14 (1): 615. 11 September 2013

A systematic evaluation of hybridization-based mouse exome capture system.
Gao, Q. ORCID: https://orcid.org/0000-0002-9930-8499, Sun, W. ORCID: https://orcid.org/0000-0001-9607-1361, You, X., Froehler, S. ORCID: https://orcid.org/0000-0001-8000-2927 and Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627
BMC Genomics 14 (1): 492. 21 July 2013

Transcriptome based identification of mouse cumulus cell markers that predict the developmental competence of their enclosed antral oocytes.
Vigone, G., Merico, V., Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952, Mulas, F., Sacchi, L., Gabetta, M., Bellazzi, R., Redi, C.A., Mazzini, G., Adjaye, J., Garagna, S. and Zuccotti, M.
BMC Genomics 14 : 380. 7 June 2013

Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans.
Sinha, A., Sommer, R.J. and Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311
BMC Genomics 13 (1): 254. 19 June 2012

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.
Ding, J., Li, D., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Guan, J. and Zhou, S.
BMC Genomics 13 (Suppl 3): S3. 11 June 2012

Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii.
Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Irgang, S., Pietzke, M. ORCID: https://orcid.org/0000-0002-6901-8511, Wenzel, M., Assmus, H.E., Schulze, W.X. and Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299
BMC Genomics 13 (1): 215. 31 May 2012

Preimplantation development regulatory pathway construction through a text-mining approach.
Donnard, E., Barbosa-Silva, A. ORCID: https://orcid.org/0000-0002-5260-2607, Guedes, R.L., Fernandes, G.R., Velloso, H., Kohn, M.J., Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711 and Ortega, J.M.
BMC Genomics 12 (Suppl 4): S3. 22 December 2011

Gatekeeper of pluripotency: a common Oct4 transcriptional network operates in mouse eggs and embryonic stem cells.
Zuccotti, M., Merico, V., Bellone, M., Mulas, F., Sacchi, L., Rebuzzini, P., Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952, Redi, C.A., Bellazzi, R., Adjaye, J. and Garagna, S.
BMC Genomics 12 : 345. 5 July 2011

Orthology confers intron position conservation.
Henricson, A., Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
BMC Genomics 11 : 412. 2 July 2010

Comprehensive survey of human brain microRNA by deep sequencing.
Shao, N.Y., Hu, H.Y., Yan, Z., Xu, Y., Hu, H., Menzel, C., Li, N., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627 and Khaitovich, P.
BMC Genomics 11 (1): 409. 30 June 2010

Deciphering the porcine intestinal microRNA transcriptome.
Sharbati, S., Friedlaender, M.R. ORCID: https://orcid.org/0000-0001-6577-4363, Sharbati, J., Hoeke, L., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Keller, A., Stahler, P.F., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Einspanier, R.
BMC Genomics 11 (1): 275. 30 April 2010

3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Froehler, S. ORCID: https://orcid.org/0000-0001-8000-2927 and Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311
BMC Genomics 10 (1): 635. 29 December 2009

Sequence features associated with microRNA strand selection in humans and flies.
Hu, H.Y., Yan, Z., Xu, Y., Hu, H., Menzel, C., Zhou, Y.H., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627 and Khaitovich, P.
BMC Genomics 10 : 413. 4 September 2009

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.
May, P., Christian, J.O., Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299 and Walther, D.
BMC Genomics 10 : 209. 4 May 2009

Estimating accuracy of RNA-Seq and microarrays with proteomics.
Fu, X., Fu, N., Guo, S., Yan, Z., Xu, Y., Hu, H., Menzel, C., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Li, Y., Zeng, R. and Khaitovich, P.
BMC Genomics 10 : 161. 16 April 2009

FragIdent - automatic identification and characterisation of cDNA-fragments.
Seelow, D. ORCID: https://orcid.org/0000-0002-9746-4412, Goehler, H. and Hoffmann, K.
BMC Genomics 10 : 95. 2 March 2009

Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives.
Trouillas, M., Saucourt, C., Guillotin, B., Gauthereau, X., Ding, L., Buchholz, F., Doss, M.X., Sachinidis, A., Hescheler, J., Hummel, O. ORCID: https://orcid.org/0009-0000-9986-8333, Huebner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Kolde, R., Vilo, J., Schulz, H. ORCID: https://orcid.org/0000-0002-0226-964X and Boeuf, H.
BMC Genomics 10 (1): 73. 9 February 2009

Differential RelA- and RelB-dependent gene transcription in LTbetaR-stimulated mouse embryonic fibroblasts.
Lovas, A., Radke, D., Albrecht, D., Yilmaz, Z.B., Moeller, U., Habenicht, A.J. and Weih, F.
BMC Genomics 9 : 606. 16 December 2008

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Palleja, A., Harrington, E.D. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
BMC Genomics 9 (1): 335. 15 July 2008

Non-random retention of protein-coding overlapping genes in Metazoa.
Solda', G., Suyama, M., Pelucchi, P., Boi, S., Guffanti, A., Rizzi, E., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Tenchini, M.L. and Ciccarelli, F.D.
BMC Genomics 9 (1): 174. 16 April 2008

A Caenorhabditis motif compendium for studying transcriptional gene regulation.
Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311 and Sommer, R.J.
BMC Genomics 9 : 30. 23 January 2008

Spatial preferences of microRNA targets in 3' untranslated regions.
Majoros, W.H. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
BMC Genomics 8 : 152. 7 June 2007

Large-scale mapping of mutations affecting zebrafish development.
Geisler, R., Rauch, G.J., Geiger-Rudolph, S., Albrecht, A., van Bebber, F., Berger, A., Busch-Nentwich, E., Dahm, R., Dekens, M.P., Dooley, C., Elli, A.F., Gehring, I., Geiger, H., Geisler, M., Glaser, S., Holley, S., Huber, M., Kerr, A., Kirn, A., Knirsch, M., Konantz, M., Kuechler, A.M., Maderspacher, F., Neuhauss, S.C., Nicolson, T., Ober, E.A., Praeg, E., Ray, R., Rentzsch, B., Rick, J.M., Rief, E., Schauerte, H.E., Schepp, C.P., Schoenberger, U., Schonthaler, H.B., Seiler, C., Sidi, S., Soellner, C., Wehner, A., Weiler, C. and Nuesslein-Volhard, C.
BMC Genomics 8 : 11. 9 January 2007

Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and altered Axin-1 expression during tumour progression.
Pospisil, H., Herrmann, A., Butherus, K., Pirson, S., Reich, J.G. and Kemmner, W. ORCID: https://orcid.org/0000-0002-1494-7225
BMC Genomics 7 : 148. 13 June 2006

Comparative promoter region analysis powered by CORG.
Dieterich, C., Grossmann, S., Tanzer, A., Roepcke, S., Arndt, P.F., Stadler, P.F. and Vingron, M.
BMC Genomics 6 (1): 24. 2005

Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
Englbrecht, C.C., Schoof, H. and Boehm, S.
BMC Genomics 5 (1): 39. 5 July 2004

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.
Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, Skovgaard, M., Sicheritz-Ponten, T., Jorgensen, M.K., Lundegaard, C., Pedersen, C.C., Petersen, N. and Ussery, D.
BMC Genomics 4 (1): 12. 2 April 2003