Bioinformatics Publications
- Dončević, Daria; Herrmann, Carl: Biologically informed variational autoencoders allow predictive modeling of genetic and drug-induced perturbations / Daria Doncevic and Carl Herrmann, June 2023. - 12 S. : Illustrationen
In: Bioinformatics, ISSN 1367-4811. 39(2023), 6 vom: Juni, Artikel-ID btad387, Seite 1-12
DOI: 10.1093/bioinformatics/btad387 - Rheinberger, Mona; Costa, Ana Luisa; Kampmann, Martin; Glavas, Dunja; Shytaj, Iart Luca; Sreeram, Sheetal; Penzo, Carlotta; Tibroni, Nadine; Garcia-Mesa, Yoelvis; Leskov, Konstantin; Fackler, Oliver Till; Vlahovicek, Kristian; Karn, Jonathan; Lucic, Bojana; Herrmann, Carl; Lusic, Marina: Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains / Mona Rheinberger, Ana Luisa Costa, Martin Kampmann, Dunja Glavas, Iart Luca Shytaj, Sheetal Sreeram,… , 13 February 2023. - 27 S.
In: Cell reports, ISSN 2211-1247. 42(2023), 2 vom: Feb., Artikel-ID 112110, Seite 1-27
DOI: 10.1016/j.celrep.2023.112110 - Alborzinia, Hamed; Flórez, Andrés F.; Kreth, Sina; Brückner, Lena M.; Yildiz, Umut; Gartlgruber, Moritz; Odoni, Dorett; Poschet, Gernot; Garbowicz, Karolina; Shao, Chunxuan; Klein, Corinna; Meier, Jasmin; Zeisberger, Petra; Nadler-Holly, Michal; Ziehm, Matthias; Paul, Franziska; Burhenne, Jürgen; Bell, Emma; Shaikhkarami, Marjan; Würth, Roberto; Stainczyk, Sabine A.; Wecht, Elisa M.; Kreth, Jochen; Büttner, Michael; Ishaque, Naveed; Schlesner, Matthias; Nicke, Barbara; Stresemann, Carlo; Llamazares-Prada, Maria; Reiling, Jan H.; Fischer, Matthias; Amit, Ido; Selbach, Matthias; Herrmann, Carl; Wölfl, Stefan; Henrich, Kai-Oliver; Höfer, Thomas; Trumpp, Andreas; Westermann, Frank: MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis / Hamed Alborzinia, Andrés F. Flórez, Sina Kreth, Lena M. Brückner, Umut Yildiz, Moritz Gartlgruber, D… , 28 April 2022. - 15 S.
In: Nature cancer, ISSN 2662-1347. 3(2022), 4, Seite 471-485
DOI: 10.1038/s43018-022-00355-4 - Cao, Han; Zhang, Youcheng; Baumbach, Jan; Burton, Paul R.; Dwyer, Dominic; Koutsouleris, Nikolaos; Matschinske, Julian; Marcon, Yannick; Rajan, Sivanesan; Rieger, Thilo; Ryser-Welch, Patricia; Späth, Julian; Herrmann, Carl; Schwarz, Emanuel: dsMTL : a computational framework for privacy-preserving, distributed multi-task machine learning : data and text mining / Han Cao, Youcheng Zhang, Jan Baumbach, Paul R Burton, Dominic Dwyer, Nikolaos Koutsouleris, Julian M… , 08 September 2022. - 8 S.
In: Bioinformatics, ISSN 1367-4811. 38(2022), 21 vom: Nov., Seite 4919-4926
DOI: 10.1093/bioinformatics/btac616 - Afanasyeva, Elena; Gartlgruber, Moritz; Ryl, Tatsiana; Decaesteker, Bieke; Denecker, Geertrui; Mönke, Gregor; Toprak, Umut; Flórez, Andrés; Torkov, Alica; Dreidax, Daniel; Herrmann, Carl; Okonechnikov, Konstantin; Ek, Sara; Sharma, Ashwini Kumar; Sagulenko, Vitaliya; Speleman, Frank; Henrich, Kai-Oliver; Westermann, Frank: Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma / Elena A Afanasyeva, Moritz Gartlgruber, Tatsiana Ryl, Bieke Decaesteker, Geertrui Denecker, Gregor M… , 3 March, 2021. - 25 S.
In: Life science alliance, ISSN 2575-1077. 4(2021), 5, Artikel-ID e201900332, Seite 1-25
DOI: 10.26508/lsa.201900332 - Derrien, Jennifer; Guérin-Charbonnel, Catherine; Gaborit, Victor; Campion, Loïc; Devic, Magali; Douillard, Elise; Roi, Nathalie; Avet-Loiseau, Hervé; Decaux, Olivier; Facon, Thierry; Mallm, Jan-Philipp; Eils, Roland; Munshi, Nikhil C.; Moreau, Philippe; Herrmann, Carl; Magrangeas, Florence; Minvielle, Stéphane: The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability / Jennifer Derrien, Catherine Guérin-Charbonnel, Victor Gaborit, Loïc Campion, Magali Devic, Elise Dou… , 09 August 2021. - 21 S.
In: Genome medicine, ISSN 1756-994X. 13(2021), Artikel-ID 127, Seite 1-21
DOI: 10.1186/s13073-021-00938-3 - Gartlgruber, Moritz; Sharma, Ashwini Kumar; Quintero, Andrés; Dreidax, Daniel; Jansky, Selina; Park, Young-Gyu; Kreth, Sina; Meder, Johanna; Dončević, Daria; Saary, Paul; Toprak, Umut H.; Ishaque, Naveed; Afanasyeva, Elena; Wecht, Elisa; Koster, Jan; Versteeg, Rogier; Grünewald, Thomas G. P.; Jones, David T. W.; Pfister, Stefan; Henrich, Kai-Oliver; van Nes, Johan; Herrmann, Carl; Westermann, Frank: Super enhancers define regulatory subtypes and cell identity in neuroblastoma / Moritz Gartlgruber, Ashwini Kumar Sharma, Andrés Quintero, Daniel Dreidax, Selina Jansky, Young-Gyu … , 2021. - 15 S.
In: Nature cancer, ISSN 2662-1347. 2(2021), 1, Seite 114-128
DOI: 10.1038/s43018-020-00145-w - Jansky, Selina; Sharma, Ashwini Kumar; Körber, Verena; Quintero, Andrés; Toprak, Umut; Wecht, Elisa M.; Gartlgruber, Moritz; Greco, Alessandro; Chomsky, Elad; Grünewald, Thomas G. P.; Henrich, Kai-Oliver; Tanay, Amos; Herrmann, Carl; Höfer, Thomas; Westermann, Frank: Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma / Selina Jansky, Ashwini Kumar Sharma, Verena Körber, Andrés Quintero, Umut H. Toprak, Elisa M. Wecht,… , 25 March 2021. - 11 S.
In: Nature genetics, ISSN 1546-1718. 53(2021), 5, Seite 683-693
DOI: 10.1038/s41588-021-00806-1 - Mika, Jagoda; Ottema, Sophie; Kiehlmeier, Sandra; Kruse, Sabrina; Smeenk, Leonie; Müller, Judith; Schweiggert, Sabrina; Herrmann, Carl; Sanders, Mathijs A.; Delwel, Ruud; Gröschel, Stefan: Derepression of retroelements in acute myeloid leukemia with 3q aberrations : letters to the editor / Jagoda Mika, Sophie Ottema, Sandra Kiehlmeier, Sabrina Kruse, Leonie Smeenk, Judith Müller, Sabrina … , August 2021. - 5 S.
In: Haematologica, ISSN 1592-8721. 106(2021), 8, Seite 2269-2273
DOI: 10.3324/haematol.2020.277400 - Ramirez, Carlos; Kee, Carmon; Sharma, Ashwini Kumar; Thomas, Leonie; Schmidt, Florian I.; Stanifer, Megan; Boulant, Steeve; Herrmann, Carl: The endogenous cellular protease inhibitor SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity / Carlos Ramirez Alvarez, Carmon Kee, Ashwini Kumar Sharma, Leonie Thomas, Florian I. Schmidt, Megan L… , June 28, 2021. - 24 S.
In: PLoS pathogens, ISSN 1553-7374. 17(2021), 6, Artikel-ID e1009687, Seite 1-24
DOI: 10.1371/journal.ppat.1009687 - Schwarz, Emanuel; Alnæs, Dag; Andreassen, Ole A.; Cao, Han; Chen, Junfang; Degenhardt, Franziska; Dončević, Daria; Dwyer, Dominic; Eils, Roland; Erdmann, Jeanette; Herrmann, Carl; Hofmann-Apitius, Martin; Kaufmann, Tobias; Koutsouleris, Nikolaos; Kodamullil, Alpha T.; Khuntia, Adyasha; Mucha, Sören; Nöthen, Markus Maria; Paul, Riya; Pedersen, Mads L.; Quintero, Andrés; Schunkert, Heribert; Sharma, Ashwini Kumar; Tost, Heike; Westlye, Lars T.; Zhang, Youcheng; Meyer-Lindenberg, Andreas: Identifying multimodal signatures underlying the somatic comorbidity of psychosis : the COMMITMENT roadmap : guest editorial / Emanuel Schwarz, Dag Alnæs, Ole A. Andreassen, Han Cao, Junfang Chen, Franziska Degenhardt, Daria Do… , 2021. - 3 S.
In: Molecular psychiatry, ISSN 1476-5578. 26(2021), 3, Seite 722-724
DOI: 10.1038/s41380-020-00915-z - Stainczyk, Sabine; Sieverling, Lina; Nadler-Holly, Michal; Ziehm, Matthias; Toprak, Umut H.; Herrmann, Carl; Ishaque, Naveed; Okonechnikov, Konstantin; Gartlgruber, Moritz; Park, Young-Gyu; Wecht, Elisa Maria; Savelyeva, Larissa; Henrich, Kai-Oliver; Rosswog, Carolina; Fischer, Matthias; Hero, Barbara; Jones, David T. W.; Pfaff, Elke; Witt, Olaf; Pfister, Stefan; Volckmann, Richard; Koster, Jan; Kiesel, Katharina; Rippe, Karsten; Taschner-Mandl, Sabine; Ambros, Peter; Brors, Benedikt; Selbach, Matthias; Feuerbach, Lars; Westermann, Frank: Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome / Sabine A. Hartlieb, Lina Sieverling, Michal Nadler-Holly, Matthias Ziehm, Umut H. Toprak, Carl Herrm… , 24 February 2021. - 18 S.
In: Nature Communications, ISSN 2041-1723. 12(2021), Artikel-ID 1269, Seite 1-18
DOI: 10.1038/s41467-021-21247-8 - Triana, Sergio; Metz Zumarán, Camila; Ramirez, Carlos; Kee, Carmon; Doldan, Patricio; Shahraz, Mohammed; Schraivogel, Daniel; Gschwind, Andreas R; Sharma, Ashwini Kumar; Steinmetz, Lars M; Herrmann, Carl; Alexandrov, Theodore; Boulant, Steeve; Stanifer, Megan: Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut / Sergio Triana, Camila Metz-Zumaran, Carlos Ramirez, Carmon Kee, Patricio Doldan, Mohammed Shahraz, D… , 2021. - 25 S.
In: Molecular systems biology, ISSN 1744-4292. 17(2021), 4, Artikel-ID e10232, Seite 1-25
DOI: 10.15252/msb.202110232 - Wang, Qi; Wu, Yonghe; Vorberg, Tim; Eils, Roland; Herrmann, Carl: Integrative ranking of enhancer networks facilitates the discovery of epigenetic markers in cancer / Qi Wang, Yonghe Wu, Tim Vorberg, Roland Eils and Carl Herrmann, 31 May 2021. - 11 S.
In: Frontiers in genetics, ISSN 1664-8021. 12(2021) vom: 31. Mai, Artikel-ID 664654
DOI: 10.3389/fgene.2021.664654 - Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas-Ponte, David; Pedersen, Jakob Skou; Johnson, Rory: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis / Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen… , 05 February 2020. - 16 S.
In: Communications biology, ISSN 2399-3642. 3(2020) Artikel-Nummer 56, 16 Seiten
DOI: 10.1038/s42003-019-0741-7 - Eismann, Björn; Krieger, Teresa G.; Beneke, Jürgen; Bulkescher, Ruben; Adam, Lukas; Erfle, Holger; Herrmann, Carl; Eils, Roland; Conrad, Christian: Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes / Björn Eismann, Teresa G. Krieger, Jürgen Beneke, Ruben Bulkescher, Lukas Adam, Holger Erfle, Carl He… , 1 June 2020. - 11 S.
In: Journal of cell science, ISSN 1477-9137. 133(2020,11) Artikel-Nummer jcs245043, 11 Seiten
DOI: 10.1242/jcs.245043 - Kumar, Sushant; Warrell, Jonathan; Li, Shantao; McGillivray, Patrick D.; Meyerson, William; Salichos, Leonidas; Harmanci, Arif; Martinez-Fundichely, Alexander; Chan, Calvin Wing Yiu; Nielsen, Morten Muhlig; Lochovsky, Lucas; Zhang, Yan; Li, Xiaotong; Lou, Shaoke; Pedersen, Jakob Skou; Herrmann, Carl; Getz, Gad; Khurana, Ekta; Gerstein, Mark B.: Passenger mutations in more than 2,500 cancer genomes : overall molecular functional impact and consequences / Sushant Kumar, Jonathan Warrell, Shantao Li, Patrick D. McGillivray, William Meyerson, Leonidas Sali… , 20 February 2020. - 29 S.
In: Cell, ISSN 1097-4172. 180(2020), 5, Seite 915-927,e1-e16
DOI: 10.1016/j.cell.2020.01.032 - Raffel, Simon; Klimmeck, Daniel; Falcone, Mattia; Demir, Aykut; Pouya, Alireza; Zeisberger, Petra; Lutz, Christoph; Tinelli, Marco; Bischel, Oliver E.; Bullinger, Lars; Thiede, Christian; Flörcken, Anne; Westermann, Jörg; Ehninger, Gerhard; Ho, Anthony Dick; Müller-Tidow, Carsten; Gu, Zuguang; Herrmann, Carl; Krijgsveld, Jeroen; Trumpp, Andreas; Hansson, Jenny: Quantitative proteomics reveals specific metabolic features of acute myeloid leukemia stem cells / Simon Raffel, Daniel Klimmeck, Mattia Falcone, Aykut Demir, Alireza Pouya, Petra Zeisberger, Christo… , June 18, 2020. - 13 S.
In: Blood, ISSN 1528-0020. 136(2020), 13, Seite 1507-1519
DOI: 10.1182/blood.2019003654 - Rheinbay, Esther; Herrmann, Carl; Sieverling, Lina Katharine: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes / Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao… , 05 February 2020. - 10 S.
In: Nature, ISSN 1476-4687. 578(2020), 7793, Seite 102-111
DOI: 10.1038/s41586-020-1965-x - Wu, Yonghe; Fletcher, Michael; Gu, Zuguang; Wang, Qi; Costa, Barbara; Bertoni, Anna; Man, Ka-Hou; Schlotter, Magdalena; Felsberg, Jörg; Mangei, Jasmin; Barbus, Martje; Gaupel, Ann-Christin; Wang, Wei; Weiss, Tobias; Eils, Roland; Weller, Michael; Liu, Hai-Kun; Reifenberger, Guido; Korshunov, Andrey; Angel, Peter; Lichter, Peter; Herrmann, Carl; Radlwimmer, Bernhard: Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype / Yonghe Wu, Michael Fletcher, Zuguang Gu, Qi Wang, Barbara Costa, Anna Bertoni, Ka-Hou Man, Magdalena… , 18 December 2020. - 19 S.
In: Nature Communications, ISSN 2041-1723. 11(2020), Artikel-ID 6434, Seite 1-19
DOI: 10.1038/s41467-020-20225-w - Chan, Calvin Wing Yiu; Gu, Zuguang; Bieg, Matthias; Eils, Roland; Herrmann, Carl: Impact of cancer mutational signatures on transcription factor motifs in the human genome / Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann. -
London: BioMed Central, 20 May 2019. - 1 Online-Ressource
DOI: 10.1186/s12920-019-0525-4 - Chan, Calvin Wing Yiu; Gu, Zuguang; Bieg, Matthias; Eils, Roland; Herrmann, Carl: Impact of cancer mutational signatures on transcription factor motifs in the human genome / Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann, 20 May 2019
In: BMC medical genomics, ISSN 1755-8794. 12(2019) Artikel-Nummer 64, 14 Seiten
DOI: 10.1186/s12920-019-0525-4 - Liu, Longqi; Quintero, Andrés; Herrmann, Carl; Eils, Roland: Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity / Longqi Liu, Chuanyu Liu, Andrés Quintero, Liang Wu, Yue Yuan, Mingyue Wang, Mengnan Cheng, Lizhi Len… , 28 January 2019. - 10 S.
In: Nature Communications, ISSN 2041-1723. 10(2019) Artikel-Nummer 470, 10 Seiten
DOI: 10.1038/s41467-018-08205-7 - Thier, Marc Christian; Pinna, Roberta; García-González, Diego; Assenov, Yassen; Milsom, Michael; Jauch, Anna; Utikal, Jochen; Herrmann, Carl; Monyer, Hannah; Trumpp, Andreas: Identification of embryonic neural plate border stem cells and their generation by direct reprogramming from adult human blood cells / Marc Christian Thier, Oliver Hommerding, Jasper Panten, Roberta Pinna, Diego García-González, Thomas… , December 20, 2018. - 17 S.
In: Cell stem cell, ISSN 1875-9777. 24(2019), 1, Seite 166-182.e13
DOI: 10.1016/j.stem.2018.11.015 - Decaesteker, Bieke; Denecker, Denecker; Van Neste, Christophe; Dolman, Emmy M.; Gartlgruber, Moritz; Nunes, Carolina; Essing, Anke H. W.; Herrmann, Carl; Dreidax, Daniel; Henssen, Anton George; Schulte, Johannes Hubertus; Westermann, Frank: TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets / Bieke Decaesteker, Denecker Denecker, Christophe Van Neste, Emmy M. Dolman, Wouter Van Loocke, Morit… , 19 November 2018. - 17 S.
In: Nature Communications, ISSN 2041-1723. 9(2018) Artikel-Nummer 4866, 17 Seiten
DOI: 10.1038/s41467-018-06699-9 - Raffel, Simon; Lutz, Christoph; Poschet, Gernot; Jensen, Patrizia; Fröhling, Stefan; Wuchter, Patrick; Lichter, Peter; Hell, Rüdiger; Herrmann, Carl; Ho, Anthony Dick; Krijgsveld, Jeroen: Author Correction: BCAT1 restricts αKG levels in AML stem cells leading to IDHmut -like DNA hypermethylation / Simon Raffel, Mattia Falcone, Niclas Kneisel, Jenny Hansson, Wei Wang, Christoph Lutz, Lars Bullinge… , 01 August 2018. - 1 S.
In: Nature, ISSN 1476-4687. 560(2018), 7718, Seite E28
DOI: 10.1038/s41586-018-0403-9 - Delacher, Michael; Imbusch, Charles; Weichenhan, Dieter; Breiling, Achim; Hotz-Wagenblatt, Agnes; Träger, Ulrike; Herrmann, Carl; Brors, Benedikt; Plass, Christoph; Feuerer, Markus: Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues / Michael Delacher, Charles D Imbusch, Dieter Weichenhan, Achim Breiling, Agnes Hotz-Wagenblatt, Ulrik… , 07 August 2017. - 13 S.
In: Nature immunology, ISSN 1529-2916. 18(2017), 10, Seite 1160-1172
DOI: 10.1038/ni.3799 - Raffel, Simon; Lutz, Christoph; Poschet, Gernot; Jensen, Patrizia; Fröhling, Stefan; Wuchter, Patrick; Lichter, Peter; Hell, Rüdiger; Herrmann, Carl; Ho, Anthony Dick; Krijgsveld, Jeroen: BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation / Simon Raffel, Mattia Falcone, Niclas Kneisel, Jenny Hansson, Wei Wang, Christoph Lutz, Lars Bullinge… , 16 November 2017. - 5 S.
In: Nature, ISSN 1476-4687. 551(2017), 7680, Seite 384-388
DOI: 10.1038/nature24294