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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and 2287=(select (case when (2287=6276) then 2287 else (select 6276 union select 8138) end))-- ovos] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 or row(8414,2309)>(select count(*),concat(0x716b7a6271,(select (elt(8414=8414,1))),0x7171787871,floor(rand(0)*2))x from (select 4075 union select 6472 union select 2615 union select 1242)a group by x)-- zkgv] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and extractvalue(8575,concat(0x5c,0x716b7a6271,(select (elt(8575=8575,1))),0x7171787871))] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and (select (case when (7625=7625) then null else ctxsys.drithsx.sn(1,7625) end) from dual) is null-- lswi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and extractvalue(8575,concat(0x5c,0x716b7a6271,(select (elt(8575=8575,1))),0x7171787871))-- mqqj] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and 5605=1381-- lzan] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and 6990=2891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and (select (case when (9223=6591) then null else ctxsys.drithsx.sn(1,9223) end) from dual) is null] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and (select (case when (7625=7625) then null else ctxsys.drithsx.sn(1,7625) end) from dual) is null] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 order by 1-- dumc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and 6414=(select (case when (6414=6414) then 6414 else (select 2996 union select 1656) end))-- cxqd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and row(6408,5347)>(select count(*),concat(0x716b7a6271,(select (elt(6408=6408,1))),0x7171787871,floor(rand(0)*2))x from (select 9322 union select 9085 union select 8760 union select 2880)a group by x)-- zsvf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and 6897=6897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 or extractvalue(4249,concat(0x5c,0x716b7a6271,(select (elt(4249=4249,1))),0x7171787871))-- achv] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 order by 1-- rdnu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 or row(8414,2309)>(select count(*),concat(0x716b7a6271,(select (elt(8414=8414,1))),0x7171787871,floor(rand(0)*2))x from (select 4075 union select 6472 union select 2615 union select 1242)a group by x)] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 order by 1#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and (select (case when (3119=6047) then null else ctxsys.drithsx.sn(1,3119) end) from dual) is null-- ymeg] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and 6897=6897-- ibes] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics 2014. [DOI: 10.1093/bioinformatics/btu393 and row(6408,5347)>(select count(*),concat(0x716b7a6271,(select (elt(6408=6408,1))),0x7171787871,floor(rand(0)*2))x from (select 9322 union select 9085 union select 8760 union select 2880)a group by x)] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Angelini C, Costa V. Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems. Front Cell Dev Biol 2014; 2:51. [PMID: 25364758 PMCID: PMC4207007 DOI: 10.3389/fcell.2014.00051] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 09/01/2014] [Indexed: 11/15/2022] Open
Abstract
The availability of omic data produced from international consortia, as well as from worldwide laboratories, is offering the possibility both to answer long-standing questions in biomedicine/molecular biology and to formulate novel hypotheses to test. However, the impact of such data is not fully exploited due to a limited availability of multi-omic data integration tools and methods. In this paper, we discuss the interplay between gene expression and epigenetic markers/transcription factors. We show how integrating ChIP-seq and RNA-seq data can help to elucidate gene regulatory mechanisms. In particular, we discuss the two following questions: (i) Can transcription factor occupancies or histone modification data predict gene expression? (ii) Can ChIP-seq and RNA-seq data be used to infer gene regulatory networks? We propose potential directions for statistical data integration. We discuss the importance of incorporating underestimated aspects (such as alternative splicing and long-range chromatin interactions). We also highlight the lack of data benchmarks and the need to develop tools for data integration from a statistical viewpoint, designed in the spirit of reproducible research.
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Affiliation(s)
- Claudia Angelini
- Istituto per le Applicazioni del Calcolo "M. Picone" - CNR Napoli, Italy ; Computational and Biology Open Laboratory (ComBOlab) Napoli, Italy
| | - Valerio Costa
- Computational and Biology Open Laboratory (ComBOlab) Napoli, Italy ; Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR Napoli, Italy
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Fu X, Creighton CJ, Biswal NC, Kumar V, Shea M, Herrera S, Contreras A, Gutierrez C, Wang T, Nanda S, Giuliano M, Morrison G, Nardone A, Karlin KL, Westbrook TF, Heiser LM, Anur P, Spellman P, Guichard SM, Smith PD, Davies BR, Klinowska T, Lee AV, Mills GB, Rimawi MF, Hilsenbeck SG, Gray JW, Joshi A, Osborne CK, Schiff R. Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase. Breast Cancer Res 2014; 16:430. [PMID: 25212826 PMCID: PMC4303114 DOI: 10.1186/s13058-014-0430-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/20/2014] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Activation of the phosphatidylinositol 3-kinase (PI3K) pathway in estrogen receptor α (ER)-positive breast cancer is associated with reduced ER expression and activity, luminal B subtype, and poor outcome. Phosphatase and tensin homolog (PTEN), a negative regulator of this pathway, is typically lost in ER-negative breast cancer. We set out to clarify the role of reduced PTEN levels in endocrine resistance, and to explore the combination of newly developed PI3K downstream kinase inhibitors to overcome this resistance. METHODS Altered cellular signaling, gene expression, and endocrine sensitivity were determined in inducible PTEN-knockdown ER-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer cell and/or xenograft models. Single or two-agent combinations of kinase inhibitors were examined to improve endocrine therapy. RESULTS Moderate PTEN reduction was sufficient to enhance PI3K signaling, generate a gene signature associated with the luminal B subtype of breast cancer, and cause endocrine resistance in vitro and in vivo. The mammalian target of rapamycin (mTOR), protein kinase B (AKT), or mitogen-activated protein kinase kinase (MEK) inhibitors, alone or in combination, improved endocrine therapy, but the efficacy varied by PTEN levels, type of endocrine therapy, and the specific inhibitor(s). A single-agent AKT inhibitor combined with fulvestrant conferred superior efficacy in overcoming resistance, inducing apoptosis and tumor regression. CONCLUSIONS Moderate reduction in PTEN, without complete loss, can activate the PI3K pathway to cause endocrine resistance in ER-positive breast cancer, which can be overcome by combining endocrine therapy with inhibitors of the PI3K pathway. Our data suggests that the ER degrader fulvestrant, to block both ligand-dependent and -independent ER signaling, combined with an AKT inhibitor is an effective strategy to test in patients.
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Streit M, Lex A, Gratzl S, Partl C, Schmalstieg D, Pfister H, Park PJ, Gehlenborg N. Guided visual exploration of genomic stratifications in cancer. Nat Methods 2014; 11:884-885. [PMID: 25166867 PMCID: PMC4196637 DOI: 10.1038/nmeth.3088] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marc Streit
- Institute of Computer Graphics, Johannes Kepler University Linz, Linz, Austria
| | - Alexander Lex
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Samuel Gratzl
- Institute of Computer Graphics, Johannes Kepler University Linz, Linz, Austria
| | - Christian Partl
- Institute for Computer Graphics and Vision, Graz University of Technology, Graz, Austria
| | - Dieter Schmalstieg
- Institute for Computer Graphics and Vision, Graz University of Technology, Graz, Austria
| | - Hanspeter Pfister
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Peter J Park
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nils Gehlenborg
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
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Celiku O, Johnson S, Zhao S, Camphausen K, Shankavaram U. Visualizing molecular profiles of glioblastoma with GBM-BioDP. PLoS One 2014; 9:e101239. [PMID: 25010047 PMCID: PMC4091869 DOI: 10.1371/journal.pone.0101239] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/04/2014] [Indexed: 12/11/2022] Open
Abstract
Validation of clinical biomarkers and response to therapy is a challenging topic in cancer research. An important source of information for virtual validation is the datasets generated from multi-center cancer research projects such as The Cancer Genome Atlas project (TCGA). These data enable investigation of genetic and epigenetic changes responsible for cancer onset and progression, response to cancer therapies, and discovery of the molecular profiles of various cancers. However, these analyses often require bulk download of data and substantial bioinformatics expertise, which can be intimidating for investigators. Here, we report on the development of a new resource available to scientists: a data base called Glioblastoma Bio Discovery Portal (GBM-BioDP). GBM-BioDP is a free web-accessible resource that hosts a subset of the glioblastoma TCGA data and enables an intuitive query and interactive display of the resultant data. This resource provides visualization tools for the exploration of gene, miRNA, and protein expression, differential expression within the subtypes of GBM, and potential associations with clinical outcome, which are useful for virtual biological validation. The tool may also enable generation of hypotheses on how therapies impact GBM molecular profiles, which can help in personalization of treatment for optimal outcome. The resource can be accessed freely at http://gbm-biodp.nci.nih.gov (a tutorial is included).
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Affiliation(s)
- Orieta Celiku
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Seth Johnson
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shuping Zhao
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Camphausen
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Uma Shankavaram
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize Implements and enhances circular visualization in R. ACTA ACUST UNITED AC 2014; 30:2811-2. [PMID: 24930139 DOI: 10.1093/bioinformatics/btu393] [Citation(s) in RCA: 1936] [Impact Index Per Article: 193.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUMMARY Circular layout is an efficient way for the visualization of huge amounts of genomic information. Here we present the circlize package, which provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding genomic patterns behind multi-dimensional data. AVAILABILITY AND IMPLEMENTATION circlize is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/circlize/
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Affiliation(s)
- Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Lei Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, 69120 Heidelberg, Germany
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