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Article

Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity.
Stöber, M.C., Chamorro González, R., Brückner, L., Conrad, T., Wittstruck, N., Szymansky, A., Eggert, A., Schulte, J.H., Koche, R.P., Henssen, A.G., Schwarz, R.F. and Haase, K.
Cell Reports 43 (9): 114711. 24 September 2024

Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects.
Plavskin, Y., de Biase, M.S., Ziv, N., Janská, L., Zhu, Y.O., Hall, D.W., Schwarz, R.F., Tranchina, D. and Siegal, M.L.
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., Massip, F., Wei, T.T., Giorgi, F.M., Stark, R., Stone, A., Gladwell, A., O'Reilly, M., Schütte, D., de Santiago, I., Meyer, K.B., Markowetz, F., Ponder, B.A.J., Rintoul, R.C. and Schwarz, R.F.
Genome Medicine 16 (1): 54. 8 April 2024

IL-33 expression is lower in current smokers at both transcriptomic and protein level.
Faiz, A., Mahbub, R.M., Boedijono, F.S., Tomassen, M.I., Kooistra, W., Timens, W., Nawijn, M., Hansbro, P.M., Johansen, M.D., Pouwels, S.D., Heijink, I.H., Massip, F., de Biase, M.S., Schwarz, R.F., Adcock, I.M., 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., 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., Colliver, E.C., Huska, M.R., Kaufmann, T.L., Lim, E.L., Duncan, C.B., Haase, K., Van Loo, P., Swanton, C., McGranahan, N. and Schwarz, R.F.
PLoS Computational Biology 19 (10): e1011379. 23 October 2023

Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E., Planas-Fèlix, M., Burkert, M., Puiggròs, M., Toedling, J., Thiessen, N., Blanc, E., Szymansky, A., Hertwig, F., Ishaque, N., Beule, D., Torrents, D., Eggert, A., Koche, R.P., Schwarz, R.F., Haase, K., Schulte, J.H. and Henssen, A.G.
Cell Genomics 3 (10): 100402. 11 October 2023

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R., Conrad, T., Stöber, M.C., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Kasack, K., Brückner, L., van Leen, E., Helmsauer, K., Dorado Garcia, H., Stefanova, M.E., Hung, K.L., Bei, Y., Schmelz, K., Lodrini, M., Mundlos, S., Chang, H.Y., Deubzer, H.E., Sauer, S., Eggert, A., Schulte, J.H., Schwarz, R.F., Haase, K., Koche, R.P. and Henssen, A.G.
Nature Genetics 55 (5): 880-890. May 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., 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., Weiss, J., Skrzypski, M., Lam, J.M., Karasaki, T., Zambrana, F., Kidd, A.C., Frankell, A.M., Watkins, T.B.K., Martínez-Ruiz, C., Puttick, C., Black, J.R.M., Huebner, A., Bakir, M.A., Sokač, M., Collins, S., Veeriah, S., Magno, N., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Ward, S., Jayanth, N., Salgado, R., Bridge, C.P., Christiani, D.C., Mak, R.H., Bay, C., Rosenthal, M., Sattar, N., Welsh, P., Liu, Y., Perrimon, N., Popuri, K., Beg, M.F., McGranahan, N., Hackshaw, A., Breen, D.M., O'Rahilly, S., Birkbak, N.J., Aerts, H.J.W.L., Jamal-Hanjani, M. and Swanton, C.
Nature Medicine 29 (4): 846-858. April 2023

Evolutionary characterization of lung adenocarcinoma morphology in TRACERx.
Karasaki, T., Moore, D.A., Veeriah, S., Naceur-Lombardelli, C., Toncheva, A., Magno, N., Ward, S., Bakir, M.A., Watkins, T.B.K., Grigoriadis, K., Huebner, A., Hill, M.S., Frankell, A.M., Abbosh, C., Puttick, C., Zhai, H., Gimeno-Valiente, F., Saghafinia, S., Kanu, N., Dietzen, M., Pich, O., Lim, E.., Martínez-Ruiz, C., Black, J.R.M., Biswas, D., Campbell, B.B., Lee, C., Colliver, E., Enfield, K.S.S., Hessey, S., Hiley, C.T., Zaccaria, S., Litchfield, K., Birkbak, N.J., Cadieux, E.L., Demeulemeester, J., Van Loo, P., Adusumilli, P.S., Tan, K.S., Cheema, W., Sanchez-Vega, F., Jones, D.R., Rekhtman, N., Travis, W.D., Hackshaw, A., Marafioti, T., Salgado, R., Le Quesne, J., Nicholson, A.G., McGranahan, N., Swanton, C. and Jamal-Hanjani, M.
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., Kaufmann, T.L. and Schwarz, R.F.
Bioinformatics 39 (3): btad102. March 2023

The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y., de Biase, M.S., Schwarz, R.F. and Siegal, M.L.
G3 : Genes Genomes Genetics 13 (3): jkac330. March 2023

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L., Petkovic, M., Watkins, T.B.K., Colliver, E.C., Laskina, S., Thapa, N., Minussi, D.C., Navin, N., Swanton, C., Van Loo, P., Haase, K., Tarabichi, M. and Schwarz, R.F.
Genome Biology 23 (1): 241. 14 November 2022

A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer.
Wu, Y., Biswas, D., Usaite, I., Angelova, M., Boeing, S., Karasaki, T., Veeriah, S., Czyzewska-Khan, J., Morton, C., Joseph, M., Hessey, S., Reading, J., Georgiou, A., Al-Bakir, M., McGranahan, N., Jamal-Hanjani, M., Hackshaw, A., Quezada, S.A., Hayday, A.C. and Swanton, C.
Nature Cancer 3 (6): 696-709. June 2022

Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions.
Schmelz, K., Toedling, J., Huska, M., Cwikla, M.C., Kruetzfeldt, L.M., Proba, J., Ambros, P.F., Ambros, I.M., Boral, S., Lodrini, M., Chen, C.Y., Burkert, M., Guergen, D., Szymansky, A., Astrahantseff, K., Kuenkele, A., Haase, K., Fischer, M., Deubzer, H.E., Hertwig, F., Hundsdoerfer, P., Henssen, A.G., Schwarz, R.F., Schulte, J.H. and Eggert, A.
Nature Communications 12 (1): 6804. 23 November 2021

Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
Uhlitz, F., Bischoff, P., Peidli, S., Sieber, A., Trinks, A., Lüthen, M., Obermayer, B., Blanc, E., Ruchiy, Y., Sell, T., Mamlouk, S., Arsie, R., Wei, T.T., Klotz-Noack, K., Schwarz, R.F., Sawitzki, B., Kamphues, C., Beule, D., Landthaler, M., Sers, C., Horst, D., Blüthgen, N. and Morkel, M.
EMBO Molecular Medicine 13 (10): e14123. 7 October 2021

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Kehr, B., Pombo, A., Rahmann, S. and Schwarz, R.F.
Bioinformatics 37 (19): 3128–3135. 1 October 2021

Using DNA sequencing data to quantify T cell fraction and therapy response.
Bentham, R., Litchfield, K., Watkins, T.B.K., Lim, E.L., Rosenthal, R., Martínez-Ruiz, C., Hiley, C.T., Bakir, M.A., Salgado, R., Moore, D.A., Jamal-Hanjani, M., Swanton, C. and McGranahan, N.
Nature 597 (7877): 555-560. 23 September 2021

Locus specific epigenetic modalities of random allelic expression imbalance.
Marion-Poll, L., Forêt, B., Zielinski, D., Massip, F., Attia, M., Carter, A.C., Syx, L., Chang, H.Y., Gendrel, A.V. and Heard, E.
Nature Communications 12 (1): 5330. 9 September 2021

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.
Sheinman, M., Arkhipova, K., Arndt, P.F., Dutilh, B.E., Hermsen, R. and Massip, F.
eLife 10 : e62719. 9 July 2021

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus, C., Luecken, M.D., Eraslan, G., Sikkema, L., Waghray, A., Heimberg, G., Kobayashi, Y., Vaishnav, E.D., Subramanian, A., Smillie, C., Jagadeesh, K.A., Duong, E.T., Fiskin, E., Triglia, E.T., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A.L., Chung, H., Montoro, D.T., Adams, T., Aliee, H., Allon, S.J., Andrusivova, Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L.T., Callori, S., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T.M., Cuoco, M.S., Cuomo, A.S.E., Deprez, M., Duclos, G., Fine, D., Fischer, D.S., Ghazanfar, S., Gillich, A., Giotti, B., Gould, J., Guo, M., Gutierrez, A.J., Habermann, A.C., Harvey, T., He, P., Hou, X., Hu, L., Hu, Y., Jaiswal, A., Ji, L., Jiang, P., Kapellos, T.S., Kuo, C.S., Larsson, L., Leney-Greene, M.A., Lim, K., Litviňuková, M., Ludwig, L.S., Lukassen, S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Leroy, S., Mayr, C.H., Mbano, I.M., McAdams, A.M., Nabhan, A.N., Nyquist, S.K., Penland, L., Poirion, O.B., Poli, S., Qi, C.C., Queen, R., Reichart, D., Rosas, I., Schupp, J.C., Shea, C.V., Shi, X., Sinha, R., Sit, R.V., Slowikowski, K., Slyper, M., Smith, N.P., Sountoulidis, A., Strunz, M., Sullivan, T.B., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K.J., Tucker, N.R., Vernon, K.A., Wadsworth, M.H., Waldman, J., Wang, X., Xu, K., Yan, W., Zhao, W. and Ziegler, C.G.K.
Nature Medicine 27 (3): 546-559. 2 March 2021

Pervasive chromosomal instability and karyotype order in tumour evolution.
Watkins, T.B.K., Lim, E.L., Petkovic, M., Elizalde, S., Birkbak, N.J., Wilson, G.A., Moore, D.A., Grönroos, E., Rowan, A., Dewhurst, S.M., Demeulemeester, J., Dentro, S.C., Horswell, S., Au, L., Haase, K., Escudero, M., Rosenthal, R., Bakir, M.A., Xu, H., Litchfield, K., Lu, W.T., Mourikis, T.P., Dietzen, M., Spain, L., Cresswell, G.D., Biswas, D., Lamy, P., Nordentoft, I., Harbst, K., Castro-Giner, F., Yates, L.R., Caramia, F., Jaulin, F., Vicier, C., Tomlinson, I.P.M., Brastianos, P.K., Cho, R.J., Bastian, B.C., Dyrskjøt, L., Jönsson, G.B., Savas, P., Loi, S., Campbell, P.J., Andre, F., Luscombe, N.M., Steeghs, N., Tjan-Heijnen, V.C.G., Szallasi, Z., Turajlic, S., Jamal-Hanjani, M., Van Loo, P., Bakhoum, S.F., Schwarz, R.F., McGranahan, N. and Swanton, C.
Nature 587 (7832): 126-132. 5 November 2020

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey, M.H., Meyerson, W.U., Dursi, L.J., Wang, L.B., Dong, G., Liang, W.W., Weerasinghe, A., Li, S., Li, Y., Kelso, S., Saksena, G., Ellrott, K., Wendl, M.C., Wheeler, D.A., Getz, G., Simpson, J.T., Gerstein, M.B. and Ding, Li
Nature Communications 11 (1): 4748. 21 September 2020

Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution.
López, S., Lim, E.L., Horswell, S., Haase, K., Huebner, A., Dietzen, M., Mourikis, T.P., Watkins, T.B.K., Rowan, A., Dewhurst, S.M., Birkbak, N.J., Wilson, G.A., Van Loo, P., Jamal-Hanjani, M., Swanton, C. and McGranahan, N.
Nature Genetics 52 (3): 283-293. March 2020

covRNA: discovering covariate associations in large-scale gene expression data.
Urban, L., Remmele, C.W., Dittrich, M., Schwarz, R.F. and Müller, T.
BMC Research Notes 13 (1): 92. 24 February 2020

Genomic basis for RNA alterations in cancer.
Calabrese, C., Davidson, N.R., Demircioğlu, D., Fonseca, N.A., He, Y., Kahles, A., Lehmann, K.V., Liu, F., Shiraishi, Y., Soulette, C.M., Urban, L., Greger, L., Li, S., Liu, D., Perry, M.D., Xiang, Q., Zhang, F., Zhang, J., Bailey, P., Erkek, S., Hoadley, K.A., Hou, Y., Huska, M.R., Kilpinen, H., Korbel, J.O., Marin, M.G., Markowski, J., Nandi, T., Pan-Hammarström, Q., Pedamallu, C.S., Siebert, R., Stark, S.G., Su, H., Tan, P., Waszak, S.M., Yung, C., Zhu, S., Awadalla, P., Creighton, C.J., Meyerson, M., Ouellette, B.F.F., Wu, K., Yang, H., Brazma, A., Brooks, A.N., Göke, J., Rätsch, G., Schwarz, R.F., Stegle, O. and Zhang, Z.
Nature 578 (7793): 129-136. 6 February 2020

Pan-cancer analysis of whole genomes.

Nature 578 (7793): 82-93. 6 February 2020

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang, Y., Chen, F., Fonseca, N.A., He, Y., Fujita, M., Nakagawa, H., Zhang, Z., Brazma, A. and Creighton, C.J.
Nature Communications 11 (1): 736. 5 February 2020

Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche, R.P., Rodriguez-Fos, E., Helmsauer, K., Burkert, M., MacArthur, I.C., Maag, J., Chamorro, R., Munoz-Perez, N., Puiggròs, M., Dorado Garcia, H., Bei, Y., Röefzaad, C., Bardinet, V., Szymansky, A., Winkler, A., Thole, T., Timme, N., Kasack, K., Fuchs, S., Klironomos, F., Thiessen, N., Blanc, E., Schmelz, K., Künkele, A., Hundsdörfer, P., Rosswog, C., Theissen, J., Beule, D., Deubzer, H., Sauer, S., Toedling, J., Fischer, M., Hertwig, F., Schwarz, R.F., Eggert, A., Torrents, D., Schulte, J.H. and Henssen, A.G.
Nature Genetics 52 (1): 29-34. January 2020

A clonal expression biomarker associates with lung cancer mortality.
Biswas, D., Birkbak, N.J., Rosenthal, R., Hiley, C.T., Lim, E.L., Papp, K., Boeing, S., Krzystanek, M., Djureinovic, D., La Fleur, L., Greco, M., Döme, B., Fillinger, J., Brunnström, H., Wu, Y., Moore, D.A., Skrzypski, M., Abbosh, C., Litchfield, K., Al Bakir, M., Watkins, T.B.K., Veeriah, S., Wilson, G.A., Jamal-Hanjani, M., Moldvay, J., Botling, J., Chinnaiyan, A.M., Micke, P., Hackshaw, A., Bartek, J., Csabai, I., Szallasi, Z., Herrero, J., McGranahan, N. and Swanton, C.
Nature Medicine 25 (10): 1540-1548. October 2019

Pulmonary venous circulating tumor cell dissemination before tumor resection and disease relapse.
Chemi, F., Rothwell, D.G., McGranahan, N., Gulati, S., Abbosh, C., Pearce, S.P., Zhou, C., Wilson, G.A., Jamal-Hanjani, M., Birkbak, N., Pierce, J., Kim, C.S., Ferdous, S., Burt, D.J., Slane-Tan, D., Gomes, F., Moore, D., Shah, R., Al Bakir, M., Hiley, C., Veeriah, S., Summers, Y., Crosbie, P., Ward, S., Mesquita, B., Dynowski, M., Biswas, D., Tugwood, J., Blackhall, F., Miller, C., Hackshaw, A., Brady, G., Swanton, C. and Dive, C.
Nature Medicine 25 (10): 1534-1539. October 2019

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer.
Joshi, K., de Massy, M.R., Ismail, M., Reading, J.L., Uddin, I., Woolston, A., Hatipoglu, E., Oakes, T., Rosenthal, R., Peacock, T., Ronel, T., Noursadeghi, M., Turati, V., Furness, A.J.S., Georgiou, A., Wong, Y.N.S., Ben Aissa, A., Sunderland, M.W., Jamal-Hanjani, M., Veeriah, S., Birkbak, N.J., Wilson, G.A., Hiley, C.T., Ghorani, E., Guerra-Assunção, J.A., Herrero, J., Enver, T., Hadrup, S.R., Hackshaw, A., Peggs, K.S., McGranahan, N., Swanton, C., Quezada, S.A. and Chain, B.
Nature Medicine 25 (10): 1549-1559. October 2019

Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints.
Massip, F., 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., Babila, J.T., Wiglenda, T., Diez, L., Jacob, M., Nietfeld, W., Huska, M.R., Haenig, C., Groenke, N., Buntru, A., Blanc, E., Meier, J.C., Vannoni, E., Erck, C., Friedrich, B., Martens, H., Neuendorf, N., Schnoegl, S., Wolfer, D.P., Loos, M., Beule, D., Andrade-Navarro, M.A. and Wanker, E.E.
Cell Chemical Biology 26 (1): 109-120. 17 January 2019

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., 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., 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. and Schwarz, R.F.
Cold Spring Harbor Perspectives in Medicine 8 (4): a028316. April 2018

Tracking the evolution of non-small-cell lung cancer.
Jamal-Hanjani, M., Wilson, G.A., McGranahan, N., Birkbak, N.J., Watkins, T.B.K., 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., 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., 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., 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

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz, R.F., 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., 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

Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion.
Schwarz, R.F., 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., 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., Gerstung, M. and Markowetz, F.
Systematic Biology 64 (1): e1-e25. January 2015

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

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

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., 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., 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

Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data.
Liang, C., Liebeke, M., Schwarz, R., 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., 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., 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

Evolutionary distances in the twilight zone-a rational kernel approach.
Schwarz, R.F., 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., 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., 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., Mueller, T., Wolf, M. and Schultz, J.
Nucleic Acids Research 38 (Suppl 1): D275-D279. January 2010

A kinome of 2600 in the ciliate Paramecium tetraurelia.
Bemm, F., Schwarz, R., 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., 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., Wolf, M. and Mueller, T.
Journal of Theoretical Biology 258 (2): 316-322. 21 May 2009

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

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

Integrated network reconstruction, visualization and analysis using YANAsquare.
Schwarz, R., 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

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., 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

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

Review

Karzinogenese: Big Bang oder kontinuierliche Evolution?
Haase, K. and Schwarz, R.F.
BIOspektrum 26 (7): 718-720. November 2020

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

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

Letter

Determinants of expression of SARS-CoV-2 entry related genes in upper and lower airways.
Aliee, H., Massip, F., Qi, C., de Biase, M.S., van Nijnatten, J., Kersten, E.T.G., Kermani, N.Z., Khuder, B., Vonk, J.M., Vermeulen, R.C.H., Neighbors, M., Tew, G.W., Grimbaldeston, M.A., Ten Hacken, N.H.T., Hu, S., Guo, Y., Zhang, X., Sun, K., Hiemstra, P.S., Ponder, B.A., Mäkelä, M.J., Malmström, K., Rintoul, R.C., Reyfman, P.A., Theis, F.J., Brandsma, C.A., Adcock, I.M., Timens, W., Xu, C.J., van den Berge, M., Schwarz, R.F., Koppelman, G.H., Nawijn, M.C. and Faiz, A.
Allergy 77 (2): 690-694. February 2022

Preprint

Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways.
Aliee, H., Massip, F., Qi, C., de Biase, M.S., van Nijnatten, J.L., Kersten, E.T.G., Kermani, N.Z., Khuder, B., Vonk, J.M., Vermeulen, R.C.H., Neighbors, M., Tew, G.W., Grimbaldeston, M., Ten Hacken, N.H.T., Hu, S., Guo, Y., Zhang, X., Sun, K., Hiemstra, P.S., Ponder, B.A., Makela, M.J., Malmstrom, K., Rintoul, R.C., Reyfman, P.A., Theis, F.J., Brandsma, C.A., Adcock, I., Timens, W., Xu, C.J., van den Berge, M., Schwarz, R.F., Koppelman, G.H., Nawijn, M.C. and Faiz, A.
medRxiv : 2020.08.31.20169946. 2 September 2020

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells.
Muus, C., Luecken, M.D., Eraslan, G., Waghray, A., Heimberg, G., Sikkema, L., Kobayashi, Y., Vaishnav, E.D., Subramanian, A., Smilie, C., Jagadeesh, K., Thu Duong, E., Fiskin, E., Torlai Triglia, E., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A.L., Chung, H., Montoro, D.T., Adams, T., Aliee, H., Allon, S.J., Andrusivova, A.Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L.T., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T.M., Cuoco, M.S., Deprez, M., Fischer, D.S., Gillich, A., Gould, J., Guo, M., Gutierrez, A.J., Habermann, A.C., Harvey, T., He, P., Hou, X., Hu, L., Jaiswal, A., Jiang, P., Kapellos, T., Kuo, C.S., Larsson, L., Leney-Greene, M.A., Lim, K., Litviňuková, M., Lu, J., Ludwig, L.S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Marquette, C.H., Mbano, I., McAdams, A.M., Metzger, R.J., Nabhan, A.N., Nyquist, S.K., Penland, L., Poirion, O.B., Poli, S., Qi, C.C., Queen, R., Reichart, D., Rosas, I., Schupp, J., Sinha, R., Sit, R.V., Slowikowski, K., Slyper, M., Smith, N., Sountoulidis, A., Strunz, M., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K.J., Tucker, N.R., Vernon, K., Wadsworth, M.H., Waldman, J., Wang, X., Yan, W., Zhao, W. and Ziegler, C.G.K.
bioRxiv : 2020.04.19.049254. 21 April 2020

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

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