Browse by Research Team

Allergy

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

American Journal of Respiratory and Critical Care Medicine

IL-33 expression is lower in current smokers at both transcriptomic and protein level.
Faiz, A. and Mahbub, R.M. and Boedijono, F.S. and Tomassen, M.I. and Kooistra, W. and Timens, W. and Nawijn, M. and Hansbro, P.M. and Johansen, M.D. and Pouwels, S.D. and Heijink, I.H. and Massip, F. and de Biase, M.S. and Schwarz, R.F. and Adcock, I.M. and Chung, K.F. and van der Does, A. and Hiemstra, P.S. and Goulaouic, H. and Xing, H. and Abdulai, R. and de Rinaldis, E. and Cunoosamy, D. and Harel, S. and Lederer, D. and Nivens, M.C. and Wark, P.A. and Kerstjens, H.A.M. and Hylkema, M.N. and Brandsma, C.A. and van den Berge, M.
American Journal of Respiratory and Critical Care Medicine 208 (10): 1075-1087. 15 November 2023

BIOspektrum

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

BMC Bioinformatics

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

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

BMC Proceedings

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

BMC Research Notes

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

BMC Systems Biology

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

Bioinformatics

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. and Kaufmann, T.L. and Schwarz, R.F.
Bioinformatics 39 (3): btad102. March 2023

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

Bioinformatics and Biology Insights

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

Cell

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

Cell Chemical Biology

The anti-amyloid compound DO1 decreases plaque pathology and neuroinflammation-related expression changes in 5xFAD transgenic mice.
Boeddrich, A. and Babila, J.T. and Wiglenda, T. and Diez, L. and Jacob, M. and Nietfeld, W. and Huska, M.R. and Haenig, C. and Groenke, N. and Buntru, A. and Blanc, E. and Meier, J.C. and Vannoni, E. and Erck, C. and Friedrich, B. and Martens, H. and Neuendorf, N. and Schnoegl, S. and Wolfer, D.P. and Loos, M. and Beule, D. and Andrade-Navarro, M.A. and Wanker, E.E.
Cell Chemical Biology 26 (1): 109-120. 17 January 2019

Cell Genomics

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

Cold Spring Harbor Perspectives in Medicine

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

EMBO Molecular Medicine

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

FEBS Letters

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

G3 : Genes Genomes Genetics

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

Genome Biology

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

Genome Medicine

Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk.
de Biase, M.S. and Massip, F. and Wei, T.T. and Giorgi, F.M. and Stark, R. and Stone, A. and Gladwell, A. and O'Reilly, M. and Schütte, D. and de Santiago, I. and Meyer, K.B. and Markowetz, F. and Ponder, B.A.J. and Rintoul, R.C. and Schwarz, R.F.
Genome Medicine 16 (1): 54. 8 April 2024

International Journal of Medical Microbiology

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

Journal of Bacteriology

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

Journal of Clinical Microbiology

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

Journal of Theoretical Biology

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

Nature

The evolution of lung cancer and impact of subclonal selection in TRACERx.
Frankell, A.M. and Dietzen, M. and Al Bakir, M. and Lim, E.L. and Karasaki, T. and Ward, S. and Veeriah, S. and Colliver, E. and Huebner, A. and Bunkum, A. and Hill, M.S. and Grigoriadis, K. and Moore, D.A. and Black, J.R.M. and Liu, W.K. and Thol, K. and Pich, O. and Watkins, T.B.K. and Naceur-Lombardelli, C. and Cook, D.E. and Salgado, R. and Wilson, G.A. and Bailey, C. and Angelova, M. and Bentham, R. and Martínez-Ruiz, C. and Abbosh, C. and Nicholson, A.G. and Le Quesne, J. and Biswas, D. and Rosenthal, R. and Puttick, C. and Hessey, S. and Lee, C. and Prymas, P. and Toncheva, A. and Smith, J. and Xing, W. and Nicod, J. and Price, G. and Kerr, K.M. and Naidu, B. and Middleton, G. and Blyth, K.G. and Fennell, D.A. and Forster, M.D. and Lee, S.M. and Falzon, M. and Hewish, M. and Shackcloth, M.J. and Lim, E. and Benafif, S. and Russell, P. and Boleti, E. and Krebs, M.G. and Lester, J.F. and Papadatos-Pastos, D. and Ahmad, T. and Thakrar, R.M. and Lawrence, D. and Navani, N. and Janes, S.M. and Dive, C. and Blackhall, F.H and Summers, Y. and Cave, J. and Marafioti, T. and Herrero, J. and Quezada, S.A. and Peggs, K.S. and Schwarz, R.F. and Van Loo, P. and Miedema, D.M. and Birkbak, N.J. and Hiley, C.T. and Hackshaw, A. and Zaccaria, S. and Jamal-Hanjani, M. and 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. and Frankell, A.M. and Harrison, T. and Kisistok, J. and Garnett, A. and Johnson, L. and Veeriah, S. and Moreau, M. and Chesh, A. and Chaunzwa, T.L. and Weiss, J. and Schroeder, M.R. and Ward, S. and Grigoriadis, K. and Shahpurwalla, A. and Litchfield, K. and Puttick, C. and Biswas, D. and Karasaki, T. and Black, J.R.M. and Martínez-Ruiz, C. and Bakir, M.A.l. and Pich, O. and Watkins, T.B.K. and Lim, E.L. and Huebner, A. and Moore, D.A. and Godin-Heymann, N. and L'Hernault, A. and Bye, H. and Odell, A. and Roberts, P. and Gomes, F. and Patel, A.J. and Manzano, E. and Hiley, C.T. and Carey, N. and Riley, J. and Cook, D.E. and Hodgson, D. and Stetson, D. and Barrett, J.C. and Kortlever, R.M. and Evan, G.I. and Hackshaw, A. and Daber, R.D. and Shaw, J.A. and Aerts, H.J.W.L. and Licon, A. and Stahl, J. and Jamal-Hanjani, M. and Birkbak, N.J. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 553-562. 20 April 2023

The evolution of non-small cell lung cancer metastases in TRACERx.
Al Bakir, M. and Huebner, A. and Martínez-Ruiz, C. and Grigoriadis, K. and Watkins, T.B.K. and Pich, O. and Moore, D.A. and Veeriah, S. and Ward, S. and Laycock, J. and Johnson, D. and Rowan, A. and Razaq, M. and Akther, M. and Naceur-Lombardelli, C. and Prymas, P. and Toncheva, A. and Hessey, S. and Dietzen, M. and Colliver, E. and Frankell, A.M. and Bunkum, A. and Lim, E.L. and Karasaki, T. and Abbosh, C. and Hiley, C.T. and Hill, M.S. and Cook, D.E. and Wilson, G.A. and Salgado, R. and Nye, E. and Stone, R.K. and Fennell, D.A. and Price, G. and Kerr, K.M. and Naidu, B. and Middleton, G. and Summers, Y. and Lindsay, C.R. and Blackhall, F.H. and Cave, J. and Blyth, K.G. and Nair, A. and Ahmed, A. and Taylor, M.N. and Procter, A.J. and Falzon, M. and Lawrence, D. and Navani, N. and Thakrar, R.M. and Janes, S.M. and Papadatos-Pastos, D. and Forster, M.D. and Lee, S.M. and Ahmad, T. and Quezada, S.A. and Peggs, K.S. and Van Loo, P. and Dive, C. and Hackshaw, A. and Birkbak, N.J. and Zaccaria, S. and Jamal-Hanjani, M. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 534-542. April 2023

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

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

Genomic basis for RNA alterations in cancer.
Calabrese, C. and Davidson, N.R. and Demircioğlu, D. 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 Greger, L. and Li, S. and Liu, D. and Perry, M.D. and Xiang, Q. and Zhang, F. and Zhang, J. and Bailey, P. and Erkek, S. and Hoadley, K.A. and Hou, Y. and Huska, M.R. 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.
Nature 578 (7793): 129-136. 6 February 2020

Pan-cancer analysis of whole genomes.

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

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

Nature Cancer

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

Nature Cell Biology

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

Nature Communications

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

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

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

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

Nature Genetics

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R. and Conrad, T. and Stöber, M.C. and Xu, R. and Giurgiu, M. and Rodriguez-Fos, E. and Kasack, K. and Brückner, L. and van Leen, E. and Helmsauer, K. and Dorado Garcia, H. and Stefanova, M.E. and Hung, K.L. and Bei, Y. and Schmelz, K. and Lodrini, M. and Mundlos, S. and Chang, H.Y. and Deubzer, H.E. and Sauer, S. and Eggert, A. and Schulte, J.H. and Schwarz, R.F. and Haase, K. and Koche, R.P. and Henssen, A.G.
Nature Genetics 55 (5): 880-890. May 2023

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

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

Nature Medicine

Body composition and lung cancer-associated cachexia in TRACERx.
Al-Sawaf, O. and Weiss, J. and Skrzypski, M. and Lam, J.M. and Karasaki, T. and Zambrana, F. and Kidd, A.C. and Frankell, A.M. and Watkins, T.B.K. and Martínez-Ruiz, C. and Puttick, C. and Black, J.R.M. and Huebner, A. and Bakir, M.A. and Sokač, M. and Collins, S. and Veeriah, S. and Magno, N. and Naceur-Lombardelli, C. and Prymas, P. and Toncheva, A. and Ward, S. and Jayanth, N. and Salgado, R. and Bridge, C.P. and Christiani, D.C. and Mak, R.H. and Bay, C. and Rosenthal, M. and Sattar, N. and Welsh, P. and Liu, Y. and Perrimon, N. and Popuri, K. and Beg, M.F. and McGranahan, N. and Hackshaw, A. and Breen, D.M. and O'Rahilly, S. and Birkbak, N.J. and Aerts, H.J.W.L. and Jamal-Hanjani, M. and Swanton, C.
Nature Medicine 29 (4): 846-858. April 2023

Evolutionary characterization of lung adenocarcinoma morphology in TRACERx.
Karasaki, T. and Moore, D.A. and Veeriah, S. and Naceur-Lombardelli, C. and Toncheva, A. and Magno, N. and Ward, S. and Bakir, M.A. and Watkins, T.B.K. and Grigoriadis, K. and Huebner, A. and Hill, M.S. and Frankell, A.M. and Abbosh, C. and Puttick, C. and Zhai, H. and Gimeno-Valiente, F. and Saghafinia, S. and Kanu, N. and Dietzen, M. and Pich, O. and Lim, E.. and Martínez-Ruiz, C. and Black, J.R.M. and Biswas, D. and Campbell, B.B. and Lee, C. and Colliver, E. and Enfield, K.S.S. and Hessey, S. and Hiley, C.T. and Zaccaria, S. and Litchfield, K. and Birkbak, N.J. and Cadieux, E.L. and Demeulemeester, J. and Van Loo, P. and Adusumilli, P.S. and Tan, K.S. and Cheema, W. and Sanchez-Vega, F. and Jones, D.R. and Rekhtman, N. and Travis, W.D. and Hackshaw, A. and Marafioti, T. and Salgado, R. and Le Quesne, J. and Nicholson, A.G. and McGranahan, N. and Swanton, C. and Jamal-Hanjani, M.
Nature Medicine 29 (4): 833-845. April 2023

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

A clonal expression biomarker associates with lung cancer mortality.
Biswas, D. and Birkbak, N.J. and Rosenthal, R. and Hiley, C.T. and Lim, E.L. and Papp, K. and Boeing, S. and Krzystanek, M. and Djureinovic, D. and La Fleur, L. and Greco, M. and Döme, B. and Fillinger, J. and Brunnström, H. and Wu, Y. and Moore, D.A. and Skrzypski, M. and Abbosh, C. and Litchfield, K. and Al Bakir, M. and Watkins, T.B.K. and Veeriah, S. and Wilson, G.A. and Jamal-Hanjani, M. and Moldvay, J. and Botling, J. and Chinnaiyan, A.M. and Micke, P. and Hackshaw, A. and Bartek, J. and Csabai, I. and Szallasi, Z. and Herrero, J. and 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. and Rothwell, D.G. and McGranahan, N. and Gulati, S. and Abbosh, C. and Pearce, S.P. and Zhou, C. and Wilson, G.A. and Jamal-Hanjani, M. and Birkbak, N. and Pierce, J. and Kim, C.S. and Ferdous, S. and Burt, D.J. and Slane-Tan, D. and Gomes, F. and Moore, D. and Shah, R. and Al Bakir, M. and Hiley, C. and Veeriah, S. and Summers, Y. and Crosbie, P. and Ward, S. and Mesquita, B. and Dynowski, M. and Biswas, D. and Tugwood, J. and Blackhall, F. and Miller, C. and Hackshaw, A. and Brady, G. and 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. and de Massy, M.R. and Ismail, M. and Reading, J.L. and Uddin, I. and Woolston, A. and Hatipoglu, E. and Oakes, T. and Rosenthal, R. and Peacock, T. and Ronel, T. and Noursadeghi, M. and Turati, V. and Furness, A.J.S. and Georgiou, A. and Wong, Y.N.S. and Ben Aissa, A. and Sunderland, M.W. and Jamal-Hanjani, M. and Veeriah, S. and Birkbak, N.J. and Wilson, G.A. and Hiley, C.T. and Ghorani, E. and Guerra-Assunção, J.A. and Herrero, J. and Enver, T. and Hadrup, S.R. and Hackshaw, A. and Peggs, K.S. and McGranahan, N. and Swanton, C. and Quezada, S.A. and Chain, B.
Nature Medicine 25 (10): 1549-1559. October 2019

Nature Microbiology

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

New England Journal of Medicine

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

Nucleic Acids Research

Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints.
Massip, F. and Laurent, M. and Brossas, C. and Fernández-Justel, J.M. and Gómez, M. and Prioleau, M.N. and Duret, L. and Picard, F.
Nucleic Acids Research 47 (10): 5114-5125. 4 June 2019

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 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

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

PLoS Computational Biology

Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity.
Watkins, T.B.K. and Colliver, E.C. and Huska, M.R. and Kaufmann, T.L. and Lim, E.L. and Duncan, C.B. and Haase, K. and Van Loo, P. and Swanton, C. and McGranahan, N. and Schwarz, R.F.
PLoS Computational Biology 19 (10): e1011379. 23 October 2023

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

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

PLoS Medicine

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

PLoS ONE

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

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

Pharmacogenomics

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

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

Proceedings of the National Academy of Sciences of the United States of America

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

Proteomics

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

Science Translational Medicine

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

Systematic Biology

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

bioRxiv

The rate of spontaneous mutations in yeast deficient for MutSβ function.
Plavskin, Y. and de Biase, M.S. and Schwarz, R.F. and Siegal, M.L.
bioRxiv : 2022.08.25.505291v2. 26 November 2022

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. and Kaufmann, T. and Schwarz, R.F.
bioRxiv : 2022.07.22.501136. 24 July 2022

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L. and Petkovic, M. and Watkins, T.B.K. and Colliver, E.C. and Laskina, S. and Thapa, N. and Minussi, D.C. and Navin, N. and Swanton, C. and Van Loo, P. and Haase, K. and Tarabichi, M. and Schwarz, R.F.
bioRxiv : 2021.02.28.433227. 6 September 2021

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

GAMIBHEAR: whole-genome haplotype reconstruction from genome architecture mapping data.
Markowski, J. and Kempfer, R. and Kukalev, A. and Irastorza-Azcarate, I. and Loof, G. and Pombo, A. and Schwarz, R.F.
bioRxiv : 2020.01.30.927061. 31 January 2020

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

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

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

eLife

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

medRxiv

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