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2018

DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis.
La Fortezza, M. and Grigolon, G. and Cosolo, A. and Pindyurin, A. and Breimann, L. and Blum, H. and van Steensel, B. and Classen, A.K.
Epigenetics & Chromatin 11 (1): 27. 5 June 2018

Deterministic evolutionary trajectories influence primary tumor growth: TRACERx renal.
Turajlic, S. and Xu, H. and Litchfield, K. and Rowan, A. and Horswell, S. and Chambers, T. and O'Brien, T. and Lopez, J.I. and Watkins, T.B.K. and Nicol, D. and Stares, M. and Challacombe, B. and Hazell, S. and Chandra, A. and Mitchell, T.J. and Au, L. and Eichler-Jonsson, C. and Jabbar, F. and Soultati, A. and Chowdhury, S. and Rudman, S. and Lynch, J. and Fernando, A. and Stamp, G. and Nye, E. and Stewart, A. and Xing, W. and Smith, J.C. and Escudero, M. and Huffman, A. and Matthews, N. and Elgar, G. and Phillimore, B. and Costa, M. and Begum, S. and Ward, S. and Salm, M. and Boeing, S. and Fisher, R. and Spain, L. and Navas, C. and Grönroos, E. and Hobor, S. and Sharma, S. and Aurangzeb, I. and Lall, S. and Polson, A. and Varia, M. and Horsfield, C. and Fotiadis, N. and Pickering, L. and Schwarz, R.F. and Silva, B. and Herrero, J. and Luscombe, N.M. and Jamal-Hanjani, M. and Rosenthal, R. and Birkbak, N.J. and Wilson, G.A. and Pipek, O. and Ribli, D. and Krzystanek, M. and Csabai, I. and Szallasi, Z. and Gore, M. and McGranahan, N. and Van Loo, P. and Campbell, P. and Larkin, J. and Swanton, C.
Cell 173 (3): 595-610. 19 April 2018

Phylogenetic quantification of intratumor heterogeneity.
Watkins, T.B.K. and Schwarz, R.F.
Cold Spring Harbor Perspectives in Medicine 8 (4): a028316. April 2018

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types.
Calabrese, C. and Davidson, N.R. and Fonseca, N.A. and He, Y. and Kahles, A. and Lehmann, K.V. and Liu, F. and Shiraishi, Y. and Soulette, C.M. and Urban, L. and Demircioğlu, D. and Greger, L. and Li, S. and Liu, D. and Perry, M.D. and Xiang, L. and Zhang, F. and Zhang, J. and Bailey, P. and Erkek, S. and Hoadley, K.A. and Hou, Y. and Kilpinen, H. and Korbel, J.O. and Marin, M.G. and Markowski, J. and Nandi, T. and Pan-Hammarström, Q. and Pedamallu, C.S. and Siebert, R. and Stark, S.G. and Su, H. and Tan, P. and Waszak, S.M. and Yung, C. and Zhu, S. and Awadalla, P. and Creighton, C.J. and Meyerson, M. and Ouellette, B.F.F. and Wu, K. and Yang, H. and Brazma, A. and Brooks, A.N. and Göke, J. and Rätsch, G. and Schwarz, R.F. and Stegle, O. and Zhang, Z.
bioRxiv : 183889. 12 March 2018

2017

Assessing the gene regulatory landscape in 1,188 human tumors.
Calabrese, C. and Lehmann, K.V. and Urban, L. and Liu, F. and Erkek, S. and Fonseca, N. and Kahles, A. and Kilpinen-Barrett, L.H. and Markowski, J. and Waszak, S. and Korbel, J. and Zhang, Z. and Brazma, A. and Raetsch, G. and Schwarz, R. and Stegle, O.
bioRxiv : 225441. 29 November 2017

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes.
Waszak, S.M. and Tiao, G. and Zhu, B. and Rausch, T. and Muyas, F. and Rodriguez-Martin, B. and Rabionet, R. and Yakneen, S. and Escaramis, G. and Li, Y. and Saini, N. and Roberts, S.A. and Demidov, G.M. and Pitkanen, E. and Delaneau, O. and Heredia-Genestar, J.M. and Weischenfeldt, J. and Shringarpure, S.S. and Chen, J. and Nakagawa, H. and Alexandrov, L.B. and Drechsel, O. and Dursi, L.J. and Segre, A.V. and Garrison, E. and Erkek, S. and Habermann, N. and Urban, L. and Khurana, E. and Cafferkey, A. and Hayashi, S. and Imoto, S. and Aaltonen, L.A. and Alvarez, E.G. and Baez-Ortega, A. and Bailey, M. and Bosio, M. and Bruzos, A.L. and Buchhalter, I. and Bustamante, C.D. and Calabrese, C. and DiBiase, A. and Gerstein, M. and Holik, A.Z. and Hua, X. and Huang, K.l. and Letunic, I. and Klimczak, L.J. and Koster, R. and Kumar, S. and McLellan, M. and Mashl, J. and Mirabello, L. and Newhouse, S. and Prasad, A. and Raetsch, G. and Schlesner, M. and Schwarz, R. and Sharma, P. and Shmaya, T. and Sidiropoulos, N. and Song, L. and Susak, H. and Tanskanen, T. and Tojo, M. and Wedge, D.C. and Wright, M. and Wu, Y. and Ye, K. and Yellapantula, V. D. and Zamora, J. and Butte, A.J. and Getz, G. and Simpson, J. and Ding, L. and Marques-Bonet, T. and Navarro, A. and Brazma, A. and Campbell, P. and Chanock, S.J. and Chatterjee, N. and Stegle, O. and Siebert, R. and Ossowski, S. and Harismendy, O. and Gordenin, D.A. and Tubio, J.M.C. and De La Vega, F.M. and Easton, D.F. and Estivill, X. and Korbel, J.
bioRxiv : 208330. 1 November 2017

Pan-cancer study of heterogeneous RNA aberrations.
Fonseca, N.A. and Kahles, A. and Lehmann, K.V. and Calabrese, C. and Chateigner, A. and Davidson, N.R. and Demircioglu, D. and He, Y. and Lamaze, F.C. and Li, S. and Liu, D. and Liu, F. and Perry, M.D. and Su, H. and Xiang, L. and Zhang, J. and Amin, S.B. and Bailey, P. and Craft, B. and Frenkel-Morgenstern, M. and Goldman, M. and Greger, L. and Hoadley, K.A. and Hou, Y. and Khurana, E. and Korbel, J.O. and Li, C. and Li, X. and Li, X. and Liu, X. and Lu, Y. and Marin, M.G. and Meyerson, M. and Nandi, T. and Nielsen, M.M. and Ojesina, A.I. and Ouellette, B.F.F. and Pan-Hammarstroem, Q. and Pedamallu, C.S. and Pedersen, J.S. and Shiraishi, Y. and Siebert, R. and Soulette, C.M. and Stark, S.G. and Tan, P. and Teh, B.T. and Valencia, A. and Wang, J. and Xing, R. and Xiong, H. and Yakneen, S. and Ye, C. and Yung, C. and Zhang, F. and Zhang, X. and Zheng, L. and Zhu, J. and Zhu, S. and Awadalla, P. and Creighton, C.J. and Goeke, J. and Schwarz, R.F. and Stegle, O. and Wu, K. and Yang, H. and Zhang, Z. and Brazma, A. and Raetsch, G. and Brooks, A.N.
bioRxiv : 183889. 3 September 2017

Tracking the evolution of non-small-cell lung cancer.
Jamal-Hanjani, M. and Wilson, G.A. and McGranahan, N. and Birkbak, N.J. and Watkins, T.B.K. and Veeriah, S. and Shafi, S. and Johnson, D.H. and Mitter, R. and Rosenthal, R. and Salm, M. and Horswell, S. and Escudero, M. and Matthews, N. and Rowan, A. and Chambers, T. and Moore, D.A. and Turajlic, S. and Xu, H. and Lee, S.-M. and Forster, M.D. and Ahmad, T. and Hiley, C.T. and Abbosh, C. and Falzon, M. and Borg, E. and Marafioti, T. and Lawrence, D. and Hayward, M. and Kolvekar, S. and Panagiotopoulos, N. and Janes, S.M. and Thakrar, R. and Ahmed, A. and Blackhall, F. and Summers, Y. and Shah, R. and Joseph, L. and Quinn, A.M. and Crosbie, P.A. and Naidu, B. and Middleton, G. and Langman, G. and Trotter, S. and Nicolson, M. and Remmen, H. and Kerr, K. and Chetty, M. and Gomersall, L. and Fennell, D.A. and Nakas, A. and Rathinam, S. and Anand, G. and Khan, S. and Russell, P. and Ezhil, V. and Ismail, B. and Irvin-Sellers, M. and Prakash, V. and Lester, J.F. and Kornaszewska, M. and Attanoos, R. and Adams, H. and Davies, H. and Dentro, S. and Taniere, P. and O'Sullivan, B. and Lowe, H.L. and Hartley, J.A. and Iles, N. and Bell, H. and Ngai, Y. and Shaw, J.A. and Herrero, J. and Szallasi, Z. and Schwarz, R.F. and Stewart, A. and Quezada, S.A. and Le Quesne, J. and Van Loo, P. and Dive, C. and Hackshaw, A. and Swanton, C.
New England Journal of Medicine 376 (22): 2109-2121. 1 June 2017

Phylogenetic ctDNA analysis depicts early stage lung cancer evolution.
Abbosh, C. and Birkbak, N.J. and Wilson, G.A. and Jamal-Hanjani, M. and Constantin, T. and Salari, R. and Quesne, J.L. and Moore, D.A. and Veeriah, S. and Rosenthal, R. and Marafioti, T. and Kirkizlar, E. and Watkins, T.B.K. and McGranahan, N. and Ward, S. and Martinson, L. and Riley, J. and Fraioli, F. and Bakir, M.A. and Grönroos, E. and Zambrana, F. and Endozo, R. and Bi, W.L. and Fennessy, F.M. and Sponer, N. and Johnson, D. and Laycock, J. and Shafi, S. and Czyzewska-Khan, J. and Rowan, A. and Chambers, T. and Matthews, N. and Turajlic, S. and Hiley, C. and Lee, S.M. and Forster, M.D. and Ahmad, T. and Falzon, M. and Borg, E. and Lawrence, D. and Hayward, M. and Kolvekar, S. and Panagiotopoulos, N. and Janes, S.M. and Thakrar, R. and Ahmed, A. and Blackhall, F. and Summers, Y. and Hafez, D. and Naik, A. and Ganguly, A. and Kareht, S. and Shah, R. and Joseph, L. and Quinn, A.M. and Crosbie, P. and Naidu, B. and Middleton, G. and Langman, G. and Trotter, S. and Nicolson, M. and Remmen, H. and Kerr, K. and Chetty, M. and Gomersall, L. and Fennell, D.A. and Nakas, A. and Rathinam, S. and Anand, G. and Khan, S. and Russell, P. and Ezhil, V. and Ismail, B. and Irvin-Sellers, M. and Prakash, V. and Lester, J.F. and Kornaszewska, M. and Attanoos, R. and Adams, H. and Davies, H. and Oukrif, D. and Akarca, A.U. and Hartley, J.A. and Lowe, H.L. and Lock, S. and Iles, N. and Bell, H. and Ngai, Y. and Elgar, G. and Szallasi, Z. and Schwarz, R.F. and Herrero, J. and Stewart, A. and Quezada, S.A. and Van Loo, P. and Dive, C. and Lin, C.J. and Rabinowitz, M. and Aerts, H.J.W.L. and Hackshaw, A. and Shaw, J.A. and Zimmermann, B.G. and Swanton, C.
Nature 545 (7655): 446-451. 25 May 2017

2016

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz, R.F. and Tamuri, A.U. and Kultys, M. and King, J. and Godwin, J. and Florescu, A.M. and Schultz, J. and Goldman, N.
Nucleic Acids Research 44 (8): e77. 5 May 2016

The metabolic background is a global player in Saccharomyces gene expression epistasis.
Alam, M.T. and Zelezniak, A. and Mülleder, M. and Shliaha, P. and Schwarz, R. and Capuano, F. and Vowinckel, J. and Radmaneshfar, E. and Krüger, A. and Calvani, E. and Michel, S. and Börno, S. and Christen, S. and Patil, K.R. and Timmermann, B. and Lilley, K.S. and Ralser, M.
Nature Microbiology 1 : 15030. 1 February 2016

2015

Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion.
Schwarz, R.F. and Branicky, R. and Grundy, L.J. and Schafer, W.R. and Brown, A.E.X.
PLoS Computational Biology 11 (8): e1004322. 21 August 2015

Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion.
Schwarz, R.F. and Branicky, R. and Grundy, L.J. and Schafer, W.R. and Brown, A.E.X.
bioRxiv : 017707. 8 April 2015

Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.
Schwarz, R.F. and Ng, C.K.Y. and Cooke, S.L. and Newman, S. and Temple, J. and Piskorz, A.M. and Gale, D. and Sayal, K. and Murtaza, M. and Baldwin, P.J. and Rosenfeld, N. and Earl, H.M. and Sala, E. and Jimenez-Linan, M. and Parkinson, C.A. and Markowetz, F. and Brenton, J.D.
PLoS Medicine 12 (2): e1001789. 24 February 2015

Cancer evolution: mathematical models and computational inference.
Beerenwinkel, N. and Schwarz, R.F. and Gerstung, M. and Markowetz, F.
Systematic Biology 64 (1): e1-e25. January 2015

2014

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Kultys, M. and Nicholas, L. and Schwarz, R. and Goldman, N. and King, J.
BMC Proceedings 8 (Suppl 2): S8. 28 August 2014

Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz, R.F. and Trinh, A. and Sipos, B. and Brenton, J.D. and Goldman, N. and Markowetz, F.
PLoS Computational Biology 10 (4): e1003535. 17 April 2014

2012

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.
Yuan, Y. and Failmezger, H. and Rueda, O.M. and Ali, H.R. and Graef, S. and Chin, S.F. and Schwarz, R.F. and Curtis, C. and Dunning, M.J. and Bardwell, H. and Johnson, N. and Doyle, S. and Turashvili, G. and Provenzano, E. and Aparicio, S. and Caldas, C. and Markowetz, F.
Science Translational Medicine 4 (157): 157ra143. 24 October 2012

Diverse epigenetic strategies interact to control epidermal differentiation.
Mulder, K.W. and Wang, X. and Escriu, C. and Ito, Y. and Schwarz, R.F. and Gillis, J. and Sirokmany, G. and Donati, G. and Uribe-Lewis, S. and Pavlidis, P. and Murrell, A. and Markowetz, F. and Watt, F.M.
Nature Cell Biology 14 (7): 753-763. 24 June 2012

2011

Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data.
Liang, C. and Liebeke, M. and Schwarz, R. and Zuehlke, D. and Fuchs, S. and Menschner, L. and Engelmann, S. and Wolz, C. and Jaglitz, S. and Bernhardt, J. and Hecker, M. and Lalk, M. and Dandekar, T.
Proteomics 11 (10): 1915-1935. May 2011

Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome.
Joseph, B. and Schwarz, R.F. and Linke, B. and Blom, J. and Becker, A. and Claus, H. and Goesmann, A. and Frosch, M. and Mueller, T. and Vogel, U. and Schoen, C.
PLoS ONE 6 (4): e18441. 26 April 2011

Characterization of FarR as a highly specialized, growth phase-dependent transcriptional regulator in Neisseria meningitidis.
Schielke, S. and Spatz, C. and Schwarz, R.F. and Joseph, B. and Schoen, C. and Schulz, S.M. and Hubert, K. and Frosch, M. and Schubert-Unkmeir, A. and Kurzai, O.
International Journal of Medical Microbiology 301 (4): 325-333. April 2011

2010

Evolutionary distances in the twilight zone-a rational kernel approach.
Schwarz, R.F. and Fletcher, W. and Foerster, F. and Merget, B. and Wolf, M. and Schultz, J. and Markowetz, F.
PLoS ONE 5 (12): e15788. 31 December 2010

Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.
Joseph, B. and Schneiker-Bekel, S. and Schramm-Glueck, A. and Blom, J. and Claus, H. and Linke, B. and Schwarz, R.F. and Becker, A. and Goesmann, A. and Frosch, M. and Schoen, C.
Journal of Bacteriology 192 (20): 5363-5377. October 2010

Evaluation of one- and two-color gene expression arrays for microbial comparative genome hybridization analyses in routine applications.
Schwarz, R. and Joseph, B. and Gerlach, G. and Schramm-Glueck, A. and Engelhard, K. and Frosch, M. and Mueller, T. and Schoen, C.
Journal of Clinical Microbiology 48 (9): 3105-3110. September 2010

The ITS2 Database III-sequences and structures for phylogeny.
Koetschan, C. and Foerster, F. and Keller, A. and Schleicher, T. and Ruderisch, B. and Schwarz, R. and Mueller, T. and Wolf, M. and Schultz, J.
Nucleic Acids Research 38 (Suppl 1): D275-D279. January 2010

2009

A kinome of 2600 in the ciliate Paramecium tetraurelia.
Bemm, F. and Schwarz, R. and Foerster, F. and Schultz, J.
FEBS Letters 583 (22): 3589-3592. 19 November 2009

Detecting species-site dependencies in large multiple sequence alignments.
Schwarz, R. and Seibel, P.N. and Rahmann, S. and Schoen, C. and Huenerberg, M. and Mueller-Reible, C. and Dandekar, T. and Karchin, R. and Schultz, J. and Mueller, T.
Nucleic Acids Research 37 (18): 5959-5968. October 2009

A probabilistic model of cell size reduction in Pseudo-nitzschia delicatissima (Bacillariophyta).
Schwarz, R. and Wolf, M. and Mueller, T.
Journal of Theoretical Biology 258 (2): 316-322. 21 May 2009

2008

Modelling phagosomal lipid networks that regulate actin assembly.
Kuehnel, M. and Mayorga, L.S. and Dandekar, T. and Thakar, J. and Schwarz, R. and Anes, E. and Griffiths, G. and Reich, J.
BMC Systems Biology 2 (1): 107. 5 December 2008

New trends in pharmacogenomic strategies against resistance development in microbial infections.
Ohlsen, K. and Dandekar, G. and Schwarz, R. and Dandekar, T.
Pharmacogenomics 9 (11): 1711-1723. November 2008

Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation.
Engelmann, J.C. and Schwarz, R. and Blenk, S. and Friedrich, T. and Seibel, P.N. and Dandekar, T. and Mueller, T.
Bioinformatics and Biology Insights 2 : 265-280. 26 May 2008

2007

Integrated network reconstruction, visualization and analysis using YANAsquare.
Schwarz, R. and Liang, C. and Kaleta, C. and Kuehnel, M. and Hoffmann, E. and Kuznetsov, S. and Hecker, M. and Griffiths, G. and Schuster, S. and Dandekar, T.
BMC Bioinformatics 8 : 313. 28 August 2007

2006

13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA.
Eisenreich, W. and Slaghuis, J. and Laupitz, R. and Bussemer, J. and Stritzker, J. and Schwarz, C. and Schwarz, R. and Dandekar, T. and Goebel, W. and Bacher, A.
Proceedings of the National Academy of Sciences of the United States of America 103 (7): 2040-2045. 14 February 2006

2005

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
Schwarz, R. and Musch, P. and von Kamp, A. and Engels, B. and Schirmer, H. and Schuster, S. and Dandekar, T.
BMC Bioinformatics 6 : 135. 1 June 2005

2004

Pharmacogenomic strategies against resistance development in microbial infections.
Ziebuhr, W. and Xiao, K. and Coulibaly, B. and Schwarz, R. and Dandekar, T.
Pharmacogenomics 5 (4): 361-379. June 2004

This list was generated on Sat Sep 22 02:23:32 2018 CEST.
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