2025
PhytClust.
Ganesan, Katyayni 
ORCID: https://orcid.org/0009-0001-6849-0785, Kaufmann, Tom ORCID: https://orcid.org/0000-0003-4374-1338 and Schwarz, Roland ORCID: https://orcid.org/0000-0001-9155-4268
[Dataset]
11 December 2025
CNSistent integration and feature extraction from somatic copy number profiles.
Streck, Adam ORCID: https://orcid.org/0000-0002-7302-0147 and Schwarz, Roland F. ORCID: https://orcid.org/0000-0001-9155-4268
GigaScience 14
: giaf104.
13 September 2025
Extensive folding variability between homologous chromosomes in mammalian cells.
Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Markowski, J. ORCID: https://orcid.org/0000-0002-0573-7832, Loof, G. ORCID: https://orcid.org/0000-0003-3967-6115, Sparks, T.M. ORCID: https://orcid.org/0000-0002-9455-8309, Brookes, E. ORCID: https://orcid.org/0000-0003-2175-4349, Natarajan, K.N. ORCID: https://orcid.org/0000-0002-9264-1280, Sauer, S., Fisher, A.G. ORCID: https://orcid.org/0000-0003-3010-3644, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Ren, B., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular Systems Biology 21
(7): 735-775.
2 July 2025
Clonal driver neoantigen loss under EGFR TKI and immune selection pressures.
Al Bakir, M. ORCID: https://orcid.org/0000-0002-0846-8332, Reading, J.L. ORCID: https://orcid.org/0000-0001-5381-978X, Gamble, S., Rosenthal, R., Uddin, I., Rowan, A., Przewrocka, J., Rogers, A. ORCID: https://orcid.org/0000-0002-7071-7889, Wong, Y.N.S., Bentzen, A.K., Veeriah, S., Ward, S. ORCID: https://orcid.org/0000-0002-6777-5279, Garnett, A.T., Kalavakur, P., Martínez-Ruiz, C. ORCID: https://orcid.org/0000-0002-4817-0565, Puttick, C. ORCID: https://orcid.org/0009-0006-3022-8737, Huebner, A. ORCID: https://orcid.org/0000-0001-8009-4999, Cook, D.E. ORCID: https://orcid.org/0000-0003-3347-562X, Moore, D.A. ORCID: https://orcid.org/0000-0002-6296-1312, Abbosh, C., Hiley, C.T., Naceur-Lombardelli, C. ORCID: https://orcid.org/0000-0002-7097-0307, Watkins, T.B.K., Petkovic, M. ORCID: https://orcid.org/0000-0003-2875-216X, Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Gálvez-Cancino, F. ORCID: https://orcid.org/0000-0001-8417-1891, Litchfield, K. ORCID: https://orcid.org/0000-0002-3725-0914, Meldgaard, P. ORCID: https://orcid.org/0000-0002-5788-4463, Sorensen, B.S. ORCID: https://orcid.org/0000-0002-9472-8099, Madsen, L.B., Jäger, D., Forster, M.D., Arkenau, T., Domingo-Vila, C., Tree, T.I.M., Kadivar, M. ORCID: https://orcid.org/0000-0003-1499-191X, Hadrup, S.R. ORCID: https://orcid.org/0000-0002-5937-4344, Chain, B. ORCID: https://orcid.org/0000-0002-7417-3970, Quezada, S.A. ORCID: https://orcid.org/0000-0002-9763-1700, McGranahan, N. ORCID: https://orcid.org/0000-0001-9537-4045 and Swanton, C. ORCID: https://orcid.org/0000-0002-4299-3018
Nature 639
(639): 639.
27 March 2025
2024
Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma.
Burkert, M. ORCID: https://orcid.org/0000-0002-6721-9985, Blanc, E. ORCID: https://orcid.org/0000-0002-4369-0254, Thiessen, N., Weber, C., Toedling, J. ORCID: https://orcid.org/0000-0003-1471-1295, Monti, R. ORCID: https://orcid.org/0000-0002-6354-8319, Dombrowe, V.M. ORCID: https://orcid.org/0000-0002-1466-1518, de Biase, M.S. ORCID: https://orcid.org/0000-0003-0383-5161, Kaufmann, T.L. ORCID: https://orcid.org/0000-0003-4374-1338, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Waszak, S.M., Eggert, A., Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632, Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
iScience 27
(10): 110918.
18 October 2024
Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity.
Stöber, M.C., Chamorro González, R. ORCID: https://orcid.org/0000-0002-5653-7259, Brückner, L. ORCID: https://orcid.org/0000-0002-6155-2277, Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Wittstruck, N. ORCID: https://orcid.org/0009-0000-4378-3226, Szymansky, A. ORCID: https://orcid.org/0000-0003-4797-4526, Eggert, A., Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201, Koche, R.P., Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X, Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268 and Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618
Cell Reports 43
(9): 114711.
24 September 2024
Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects.
Plavskin, Y. ORCID: https://orcid.org/0000-0002-6911-3009, de Biase, M.S. ORCID: https://orcid.org/0000-0003-0383-5161, Ziv, N., Janská, L., Zhu, Y.O., Hall, D.W., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Tranchina, D. and Siegal, M.L. ORCID: https://orcid.org/0000-0001-6930-2988
PLoS Biology 22
(7): e3002698.
1 July 2024
Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk.
de Biase, M.S. ORCID: https://orcid.org/0000-0003-0383-5161, Massip, F. ORCID: https://orcid.org/0000-0001-5855-0935, Wei, T.T. ORCID: https://orcid.org/0000-0001-5719-721X, Giorgi, F.M. ORCID: https://orcid.org/0000-0002-7325-9908, Stark, R., Stone, A., Gladwell, A., O'Reilly, M., Schütte, D., de Santiago, I., Meyer, K.B. ORCID: https://orcid.org/0000-0001-5906-1498, Markowetz, F., Ponder, B.A.J., Rintoul, R.C. ORCID: https://orcid.org/0000-0003-3875-3780 and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
Genome Medicine 16
(1): 54.
8 April 2024
2023
IL-33 expression is lower in current smokers at both transcriptomic and protein level.
Faiz, A. ORCID: https://orcid.org/0000-0003-1740-3538, Mahbub, R.M., Boedijono, F.S., Tomassen, M.I., Kooistra, W., Timens, W., Nawijn, M., Hansbro, P.M., Johansen, M.D., Pouwels, S.D. ORCID: https://orcid.org/0000-0001-7345-8061, Heijink, I.H., Massip, F. ORCID: https://orcid.org/0000-0001-5855-0935, de Biase, M.S. ORCID: https://orcid.org/0000-0003-0383-5161, Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Adcock, I.M. ORCID: https://orcid.org/0000-0003-2101-8843, Chung, K.F., van der Does, A., Hiemstra, P.S., Goulaouic, H., Xing, H., Abdulai, R., de Rinaldis, E., Cunoosamy, D., Harel, S., Lederer, D., Nivens, M.C., Wark, P.A. ORCID: https://orcid.org/0000-0001-5676-6126, Kerstjens, H.A.M., Hylkema, M.N., Brandsma, C.A. and van den Berge, M.
American Journal of Respiratory and Critical Care Medicine 208
(10): 1075-1087.
15 November 2023
Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, Colliver, E.C., Huska, M.R. ORCID: https://orcid.org/0000-0002-0912-745X, Kaufmann, T.L. ORCID: https://orcid.org/0000-0003-4374-1338, Lim, E.L., Duncan, C.B. ORCID: https://orcid.org/0000-0003-3127-228X, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Van Loo, P., Swanton, C., McGranahan, N. and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
PLoS Computational Biology 19
(10): e1011379.
23 October 2023
Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E. ORCID: https://orcid.org/0000-0002-2555-0178, Planas-Fèlix, M., Burkert, M. ORCID: https://orcid.org/0000-0002-6721-9985, Puiggròs, M., Toedling, J. ORCID: https://orcid.org/0000-0003-1471-1295, Thiessen, N., Blanc, E. ORCID: https://orcid.org/0000-0002-4369-0254, Szymansky, A. ORCID: https://orcid.org/0000-0003-4797-4526, Hertwig, F. ORCID: https://orcid.org/0000-0003-4784-6516, Ishaque, N. ORCID: https://orcid.org/0000-0002-8426-901X, Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632, Torrents, D., Eggert, A., Koche, R.P., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201 and Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X
Cell Genomics 3
(10): 100402.
11 October 2023
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R. ORCID: https://orcid.org/0000-0002-5653-7259, Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Stöber, M.C. ORCID: https://orcid.org/0000-0002-6679-5577, Xu, R. ORCID: https://orcid.org/0000-0002-5618-246X, Giurgiu, M. ORCID: https://orcid.org/0000-0001-5007-7442, Rodriguez-Fos, E. ORCID: https://orcid.org/0000-0002-2555-0178, Kasack, K., Brückner, L. ORCID: https://orcid.org/0000-0002-6155-2277, van Leen, E., Helmsauer, K. ORCID: https://orcid.org/0000-0003-0773-4114, Dorado Garcia, H. ORCID: https://orcid.org/0000-0002-2578-3350, Stefanova, M.E. ORCID: https://orcid.org/0000-0002-4419-2839, Hung, K.L. ORCID: https://orcid.org/0000-0002-3662-4662, Bei, Y. ORCID: https://orcid.org/0000-0002-2104-8025, Schmelz, K., Lodrini, M., Mundlos, S., Chang, H.Y. ORCID: https://orcid.org/0000-0002-9459-4393, Deubzer, H.E. ORCID: https://orcid.org/0000-0002-6115-4893, Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693, Eggert, A. ORCID: https://orcid.org/0000-0003-3476-8184, Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201, Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Koche, R.P. ORCID: https://orcid.org/0000-0002-6820-5083 and Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X
Nature Genetics 55
(5): 880-890.
May 2023
Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, Elias ORCID: https://orcid.org/0000-0002-2555-0178, Planas-Fèlix, Mercè, Burkert, Martin ORCID: https://orcid.org/0000-0002-6721-9985, Puiggròs, Montserrat, Toedling, Joern, Thiessen, Nina, Blanc, Eric ORCID: https://orcid.org/0000-0002-4369-0254, Szymansky, Annabell ORCID: https://orcid.org/0000-0003-4797-4526, Hertwig, Falk ORCID: https://orcid.org/0000-0003-4784-6516, Ishaque, Naveed ORCID: https://orcid.org/0000-0002-8426-901X, Beule, Dieter ORCID: https://orcid.org/0000-0002-3284-0632, Torrents, David, Eggert, Angelika, Koche, Richard P., Schwarz, Roland F. ORCID: https://orcid.org/0000-0001-9155-4268, Haase, Kerstin ORCID: https://orcid.org/0000-0002-0944-5618, Schulte, Johannes H. ORCID: https://orcid.org/0000-0003-0671-1201 and Henssen, Anton G. ORCID: https://orcid.org/0000-0003-1534-778X
[Dataset]
27 April 2023
The evolution of lung cancer and impact of subclonal selection in TRACERx.
Frankell, A.M., Dietzen, M., Al Bakir, M., Lim, E.L., Karasaki, T., Ward, S., Veeriah, S., Colliver, E., Huebner, A., Bunkum, A., Hill, M.S., Grigoriadis, K., Moore, D.A., Black, J.R.M., Liu, W.K., Thol, K., Pich, O., Watkins, T.B.K., Naceur-Lombardelli, C., Cook, D.E., Salgado, R., Wilson, G.A., Bailey, C., Angelova, M., Bentham, R., Martínez-Ruiz, C., Abbosh, C., Nicholson, A.G., Le Quesne, J., Biswas, D., Rosenthal, R., Puttick, C., Hessey, S., Lee, C., Prymas, P., Toncheva, A., Smith, J., Xing, W., Nicod, J., Price, G., Kerr, K.M., Naidu, B., Middleton, G., Blyth, K.G., Fennell, D.A., Forster, M.D., Lee, S.M., Falzon, M., Hewish, M., Shackcloth, M.J., Lim, E., Benafif, S., Russell, P., Boleti, E., Krebs, M.G., Lester, J.F., Papadatos-Pastos, D., Ahmad, T., Thakrar, R.M., Lawrence, D., Navani, N., Janes, S.M., Dive, C., Blackhall, F.H, Summers, Y., Cave, J., Marafioti, T., Herrero, J., Quezada, S.A., Peggs, K.S., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Van Loo, P., Miedema, D.M., Birkbak, N.J., Hiley, C.T., Hackshaw, A., Zaccaria, S., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616
(7957): 525-533.
20 April 2023
Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.
Abbosh, C., Frankell, A.M., Harrison, T., Kisistok, J., Garnett, A., Johnson, L., Veeriah, S., Moreau, M., Chesh, A., Chaunzwa, T.L., Weiss, J., Schroeder, M.R., Ward, S., Grigoriadis, K., Shahpurwalla, A., Litchfield, K., Puttick, C., Biswas, D., Karasaki, T., Black, J.R.M., Martínez-Ruiz, C., Bakir, M.A.l., Pich, O., Watkins, T.B.K., Lim, E.L., Huebner, A., Moore, D.A., Godin-Heymann, N., L'Hernault, A., Bye, H., Odell, A., Roberts, P., Gomes, F., Patel, A.J., Manzano, E., Hiley, C.T., Carey, N., Riley, J., Cook, D.E., Hodgson, D., Stetson, D., Barrett, J.C., Kortlever, R.M., Evan, G.I., Hackshaw, A., Daber, R.D., Shaw, J.A., Aerts, H.J.W.L., Licon, A., Stahl, J., Jamal-Hanjani, M., Birkbak, N.J., McGranahan, N. and Swanton, C.
Nature 616
(7957): 553-562.
20 April 2023
Body composition and lung cancer-associated cachexia in TRACERx.
Al-Sawaf, O. ORCID: https://orcid.org/0000-0001-9895-0570, Weiss, J., Skrzypski, M., Lam, J.M. ORCID: https://orcid.org/0000-0001-9523-5029, Karasaki, T. ORCID: https://orcid.org/0000-0001-6863-2360, Zambrana, F., Kidd, A.C., Frankell, A.M. ORCID: https://orcid.org/0000-0002-0341-7878, Watkins, T.B.K., Martínez-Ruiz, C. ORCID: https://orcid.org/0000-0002-4817-0565, Puttick, C., Black, J.R.M., Huebner, A. ORCID: https://orcid.org/0000-0001-8009-4999, Bakir, M.A. ORCID: https://orcid.org/0000-0002-0846-8332, Sokač, M., Collins, S., Veeriah, S., Magno, N., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Ward, S. ORCID: https://orcid.org/0000-0002-6777-5279, Jayanth, N., Salgado, R. ORCID: https://orcid.org/0000-0002-1110-3801, Bridge, C.P. ORCID: https://orcid.org/0000-0002-2242-351X, Christiani, D.C. ORCID: https://orcid.org/0000-0002-0301-0242, Mak, R.H. ORCID: https://orcid.org/0000-0002-8754-0565, Bay, C., Rosenthal, M., Sattar, N., Welsh, P. ORCID: https://orcid.org/0000-0002-7970-3643, Liu, Y. ORCID: https://orcid.org/0000-0002-6419-1980, Perrimon, N. ORCID: https://orcid.org/0000-0001-7542-472X, Popuri, K., Beg, M.F., McGranahan, N., Hackshaw, A. ORCID: https://orcid.org/0000-0002-5570-5070, Breen, D.M., O'Rahilly, S. ORCID: https://orcid.org/0000-0003-2199-4449, Birkbak, N.J. ORCID: https://orcid.org/0000-0003-1613-9587, Aerts, H.J.W.L. ORCID: https://orcid.org/0000-0002-2122-2003, Jamal-Hanjani, M. ORCID: https://orcid.org/0000-0003-1212-1259 and Swanton, C. ORCID: https://orcid.org/0000-0002-4299-3018
Nature Medicine 29
(4): 846-858.
April 2023
Evolutionary characterization of lung adenocarcinoma morphology in TRACERx.
Karasaki, T. ORCID: https://orcid.org/0000-0001-6863-2360, Moore, D.A. ORCID: https://orcid.org/0000-0002-6296-1312, Veeriah, S., Naceur-Lombardelli, C., Toncheva, A., Magno, N., Ward, S. ORCID: https://orcid.org/0000-0002-6777-5279, Bakir, M.A. ORCID: https://orcid.org/0000-0002-0846-8332, Watkins, T.B.K., Grigoriadis, K. ORCID: https://orcid.org/0000-0002-8435-0176, Huebner, A. ORCID: https://orcid.org/0000-0001-8009-4999, Hill, M.S. ORCID: https://orcid.org/0000-0003-0718-8934, Frankell, A.M. ORCID: https://orcid.org/0000-0002-0341-7878, Abbosh, C. ORCID: https://orcid.org/0000-0002-8983-1382, Puttick, C., Zhai, H., Gimeno-Valiente, F., Saghafinia, S., Kanu, N., Dietzen, M. ORCID: https://orcid.org/0000-0002-6853-7563, Pich, O. ORCID: https://orcid.org/0000-0002-1956-1882, Lim, E.., Martínez-Ruiz, C. ORCID: https://orcid.org/0000-0002-4817-0565, Black, J.R.M., Biswas, D. ORCID: https://orcid.org/0000-0001-9141-5188, Campbell, B.B., Lee, C. ORCID: https://orcid.org/0000-0003-1715-2265, Colliver, E. ORCID: https://orcid.org/0000-0002-1497-0740, Enfield, K.S.S. ORCID: https://orcid.org/0000-0002-4551-6073, Hessey, S. ORCID: https://orcid.org/0000-0001-9856-424X, Hiley, C.T., Zaccaria, S. ORCID: https://orcid.org/0000-0002-5265-7392, Litchfield, K., Birkbak, N.J. ORCID: https://orcid.org/0000-0003-1613-9587, Cadieux, E.L., Demeulemeester, J. ORCID: https://orcid.org/0000-0002-2660-2478, Van Loo, P. ORCID: https://orcid.org/0000-0003-0292-1949, Adusumilli, P.S. ORCID: https://orcid.org/0000-0002-1699-2046, Tan, K.S., Cheema, W. ORCID: https://orcid.org/0000-0002-8000-7493, Sanchez-Vega, F. ORCID: https://orcid.org/0000-0002-2990-4893, Jones, D.R. ORCID: https://orcid.org/0000-0002-3318-0146, Rekhtman, N., Travis, W.D., Hackshaw, A. ORCID: https://orcid.org/0000-0002-5570-5070, Marafioti, T., Salgado, R. ORCID: https://orcid.org/0000-0002-1110-3801, Le Quesne, J. ORCID: https://orcid.org/0000-0003-3552-7446, Nicholson, A.G., McGranahan, N. ORCID: https://orcid.org/0000-0001-9537-4045, Swanton, C. ORCID: https://orcid.org/0000-0002-4299-3018 and Jamal-Hanjani, M. ORCID: https://orcid.org/0000-0003-1212-1259
Nature Medicine 29
(4): 833-845.
April 2023
The evolution of non-small cell lung cancer metastases in TRACERx.
Al Bakir, M., Huebner, A., Martínez-Ruiz, C., Grigoriadis, K., Watkins, T.B.K., Pich, O., Moore, D.A., Veeriah, S., Ward, S., Laycock, J., Johnson, D., Rowan, A., Razaq, M., Akther, M., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Hessey, S., Dietzen, M., Colliver, E., Frankell, A.M., Bunkum, A., Lim, E.L., Karasaki, T., Abbosh, C., Hiley, C.T., Hill, M.S., Cook, D.E., Wilson, G.A., Salgado, R., Nye, E., Stone, R.K., Fennell, D.A., Price, G., Kerr, K.M., Naidu, B., Middleton, G., Summers, Y., Lindsay, C.R., Blackhall, F.H., Cave, J., Blyth, K.G., Nair, A., Ahmed, A., Taylor, M.N., Procter, A.J., Falzon, M., Lawrence, D., Navani, N., Thakrar, R.M., Janes, S.M., Papadatos-Pastos, D., Forster, M.D., Lee, S.M., Ahmad, T., Quezada, S.A., Peggs, K.S., Van Loo, P., Dive, C., Hackshaw, A., Birkbak, N.J., Zaccaria, S., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616
(7957): 534-542.
April 2023
SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. ORCID: https://orcid.org/0000-0002-7302-0147, Kaufmann, T.L. ORCID: https://orcid.org/0000-0003-4374-1338 and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
Bioinformatics 39
(3): btad102.
March 2023
The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y. ORCID: https://orcid.org/0000-0002-6911-3009, de Biase, M.S. ORCID: https://orcid.org/0000-0003-0383-5161, Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268 and Siegal, M.L. ORCID: https://orcid.org/0000-0001-6930-2988
G3 : Genes Genomes Genetics 13
(3): jkac330.
March 2023
2022
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
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(10): 1549-1559.
October 2019
Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints.
Massip, F. ORCID: https://orcid.org/0000-0001-5855-0935, Laurent, M., Brossas, C., Fernández-Justel, J.M., Gómez, M., Prioleau, M.N., Duret, L. and Picard, F.
Nucleic Acids Research 47
(10): 5114-5125.
4 June 2019
The anti-amyloid compound DO1 decreases plaque pathology and neuroinflammation-related expression changes in 5xFAD transgenic mice.
Boeddrich, A. ORCID: https://orcid.org/0000-0001-9118-050X, Babila, J.T., Wiglenda, T. ORCID: https://orcid.org/0000-0002-8460-9459, Diez, L. ORCID: https://orcid.org/0000-0003-3101-0191, Jacob, M., Nietfeld, W., Huska, M.R. ORCID: https://orcid.org/0000-0002-0912-745X, Haenig, C. ORCID: https://orcid.org/0000-0003-1973-7646, Groenke, N. ORCID: https://orcid.org/0000-0002-6927-3774, Buntru, A., Blanc, E. ORCID: https://orcid.org/0000-0002-4369-0254, Meier, J.C. ORCID: https://orcid.org/0000-0001-5574-3336, Vannoni, E., Erck, C., Friedrich, B., Martens, H., Neuendorf, N., Schnoegl, S., Wolfer, D.P., Loos, M., Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632, Andrade-Navarro, M.A. and Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630
Cell Chemical Biology 26
(1): 109-120.
17 January 2019
2018
Deterministic evolutionary trajectories influence primary tumor growth: TRACERx renal.
Turajlic, S., Xu, H., Litchfield, K., Rowan, A., Horswell, S., Chambers, T., O'Brien, T., Lopez, J.I., Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, Nicol, D., Stares, M., Challacombe, B., Hazell, S., Chandra, A., Mitchell, T.J., Au, L., Eichler-Jonsson, C., Jabbar, F., Soultati, A., Chowdhury, S., Rudman, S., Lynch, J., Fernando, A., Stamp, G., Nye, E., Stewart, A., Xing, W., Smith, J.C., Escudero, M., Huffman, A., Matthews, N., Elgar, G., Phillimore, B., Costa, M., Begum, S., Ward, S., Salm, M., Boeing, S., Fisher, R., Spain, L., Navas, C., Grönroos, E., Hobor, S., Sharma, S., Aurangzeb, I., Lall, S., Polson, A., Varia, M., Horsfield, C., Fotiadis, N., Pickering, L., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Silva, B., Herrero, J., Luscombe, N.M., Jamal-Hanjani, M., Rosenthal, R., Birkbak, N.J., Wilson, G.A., Pipek, O., Ribli, D., Krzystanek, M., Csabai, I., Szallasi, Z., Gore, M., McGranahan, N., Van Loo, P., Campbell, P., Larkin, J. and Swanton, C.
Cell 173
(3): 595-610.
19 April 2018
Phylogenetic quantification of intratumor heterogeneity.
Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
Cold Spring Harbor Perspectives in Medicine 8
(4): a028316.
April 2018
2017
Assessing the gene regulatory landscape in 1,188 human tumors.
Calabrese, C. ORCID: https://orcid.org/0000-0002-8941-2620, Lehmann, K.V. ORCID: https://orcid.org/0000-0002-1936-298X, Urban, L. ORCID: https://orcid.org/0000-0002-5445-9314, Liu, F., Erkek, S., Fonseca, N. ORCID: https://orcid.org/0000-0003-4832-578X, Kahles, A. ORCID: https://orcid.org/0000-0002-3411-0692, Kilpinen-Barrett, L.H. ORCID: https://orcid.org/0000-0001-6692-6154, Markowski, J. ORCID: https://orcid.org/0000-0002-0573-7832, Waszak, S. ORCID: https://orcid.org/0000-0003-3042-9521, Korbel, J. ORCID: https://orcid.org/0000-0002-2798-3794, Zhang, Z. ORCID: https://orcid.org/0000-0003-3789-6536, Brazma, A. ORCID: https://orcid.org/0000-0001-5988-7409, Raetsch, G. ORCID: https://orcid.org/0000-0001-5486-8532, Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268 and Stegle, O. ORCID: https://orcid.org/0000-0002-8818-7193
bioRxiv
: 225441.
29 November 2017
Tracking the evolution of non-small-cell lung cancer.
Jamal-Hanjani, M., Wilson, G.A., McGranahan, N., Birkbak, N.J., Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, Veeriah, S., Shafi, S., Johnson, D.H., Mitter, R., Rosenthal, R., Salm, M., Horswell, S., Escudero, M., Matthews, N., Rowan, A., Chambers, T., Moore, D.A., Turajlic, S., Xu, H., Lee, S.-M., Forster, M.D., Ahmad, T., Hiley, C.T., Abbosh, C., Falzon, M., Borg, E., Marafioti, T., Lawrence, D., Hayward, M., Kolvekar, S., Panagiotopoulos, N., Janes, S.M., Thakrar, R., Ahmed, A., Blackhall, F., Summers, Y., Shah, R., Joseph, L., Quinn, A.M., Crosbie, P.A., Naidu, B., Middleton, G., Langman, G., Trotter, S., Nicolson, M., Remmen, H., Kerr, K., Chetty, M., Gomersall, L., Fennell, D.A., Nakas, A., Rathinam, S., Anand, G., Khan, S., Russell, P., Ezhil, V., Ismail, B., Irvin-Sellers, M., Prakash, V., Lester, J.F., Kornaszewska, M., Attanoos, R., Adams, H., Davies, H., Dentro, S., Taniere, P., O'Sullivan, B., Lowe, H.L., Hartley, J.A., Iles, N., Bell, H., Ngai, Y., Shaw, J.A., Herrero, J., Szallasi, Z., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Stewart, A., Quezada, S.A., Le Quesne, J., Van Loo, P., Dive, C., 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., Birkbak, N.J., Wilson, G.A., Jamal-Hanjani, M., Constantin, T., Salari, R., Quesne, J.L., Moore, D.A., Veeriah, S., Rosenthal, R., Marafioti, T., Kirkizlar, E., Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, McGranahan, N., Ward, S., Martinson, L., Riley, J., Fraioli, F., Bakir, M.A., Grönroos, E., Zambrana, F., Endozo, R., Bi, W.L., Fennessy, F.M., Sponer, N., Johnson, D., Laycock, J., Shafi, S., Czyzewska-Khan, J., Rowan, A., Chambers, T., Matthews, N., Turajlic, S., Hiley, C., Lee, S.M., Forster, M.D., Ahmad, T., Falzon, M., Borg, E., Lawrence, D., Hayward, M., Kolvekar, S., Panagiotopoulos, N., Janes, S.M., Thakrar, R., Ahmed, A., Blackhall, F., Summers, Y., Hafez, D., Naik, A., Ganguly, A., Kareht, S., Shah, R., Joseph, L., Quinn, A.M., Crosbie, P., Naidu, B., Middleton, G., Langman, G., Trotter, S., Nicolson, M., Remmen, H., Kerr, K., Chetty, M., Gomersall, L., Fennell, D.A., Nakas, A., Rathinam, S., Anand, G., Khan, S., Russell, P., Ezhil, V., Ismail, B., Irvin-Sellers, M., Prakash, V., Lester, J.F., Kornaszewska, M., Attanoos, R., Adams, H., Davies, H., Oukrif, D., Akarca, A.U., Hartley, J.A., Lowe, H.L., Lock, S., Iles, N., Bell, H., Ngai, Y., Elgar, G., Szallasi, Z., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Herrero, J., Stewart, A., Quezada, S.A., Van Loo, P., Dive, C., Lin, C.J., Rabinowitz, M., Aerts, H.J.W.L., Hackshaw, A., Shaw, J.A., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Tamuri, A.U., Kultys, M., King, J., Godwin, J., Florescu, A.M., 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., Zelezniak, A., Mülleder, M., Shliaha, P., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Capuano, F., Vowinckel, J., Radmaneshfar, E., Krüger, A., Calvani, E., Michel, S., Börno, S., Christen, S., Patil, K.R., Timmermann, B., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Branicky, R., Grundy, L.J., Schafer, W.R. and Brown, A.E.X.
PLoS Computational Biology 11
(8): e1004322.
21 August 2015
Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.
Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Ng, C.K.Y., Cooke, S.L., Newman, S., Temple, J., Piskorz, A.M., Gale, D., Sayal, K., Murtaza, M., Baldwin, P.J., Rosenfeld, N., Earl, H.M., Sala, E., Jimenez-Linan, M., Parkinson, C.A., Markowetz, F. and Brenton, J.D.
PLoS Medicine 12
(2): e1001789.
24 February 2015
Cancer evolution: mathematical models and computational inference.
Beerenwinkel, N., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, 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., Nicholas, L., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Goldman, N. and King, J.
BMC Proceedings 8
(Suppl 2): S8.
28 August 2014
Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Trinh, A., Sipos, B., Brenton, J.D., 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., Failmezger, H., Rueda, O.M., Ali, H.R., Graef, S., Chin, S.F., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Curtis, C., Dunning, M.J., Bardwell, H., Johnson, N., Doyle, S., Turashvili, G., Provenzano, E., Aparicio, S., 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., Wang, X., Escriu, C., Ito, Y., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Gillis, J., Sirokmany, G., Donati, G., Uribe-Lewis, S., Pavlidis, P., Murrell, A., 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., Liebeke, M., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Zuehlke, D., Fuchs, S., Menschner, L., Engelmann, S., Wolz, C., Jaglitz, S., Bernhardt, J., Hecker, M., 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., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Linke, B., Blom, J., Becker, A., Claus, H., Goesmann, A., Frosch, M., Mueller, T., 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., Spatz, C., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Joseph, B., Schoen, C., Schulz, S.M., Hubert, K., Frosch, M., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Fletcher, W., Foerster, F., Merget, B., Wolf, M., 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., Schneiker-Bekel, S., Schramm-Glueck, A., Blom, J., Claus, H., Linke, B., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Becker, A., Goesmann, A., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Joseph, B., Gerlach, G., Schramm-Glueck, A., Engelhard, K., Frosch, M., 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., Foerster, F., Keller, A., Schleicher, T., Ruderisch, B., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Mueller, T., 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., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, 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. ORCID: https://orcid.org/0000-0001-9155-4268, Seibel, P.N., Rahmann, S., Schoen, C., Huenerberg, M., Mueller-Reible, C., Dandekar, T., Karchin, R., 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. ORCID: https://orcid.org/0000-0001-9155-4268, 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., Mayorga, L.S., Dandekar, T., Thakar, J., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Anes, E., 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., Dandekar, G., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268 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., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Blenk, S., Friedrich, T., Seibel, P.N., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Liang, C., Kaleta, C., Kuehnel, M., Hoffmann, E., Kuznetsov, S., Hecker, M., Griffiths, G., 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., Slaghuis, J., Laupitz, R., Bussemer, J., Stritzker, J., Schwarz, C., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, Dandekar, T., 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. ORCID: https://orcid.org/0000-0001-9155-4268, Musch, P., von Kamp, A., Engels, B., Schirmer, H., Schuster, S. and Dandekar, T.
BMC Bioinformatics 6
: 135.
1 June 2005
2004
Pharmacogenomic strategies against resistance development in microbial infections.
Ziebuhr, W., Xiao, K., Coulibaly, B., Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268 and Dandekar, T.
Pharmacogenomics 5
(4): 361-379.
June 2004
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