Publikationen im Rahmen der KFO 179

44
Bender C, Heyde S, Henjes F, Wiemann S, Korf U, Beißbarth T.
Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'.
BMC Bioinformatics 2011, 12:291.

43
Jung K, Friede T, Beißbarth T.
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes.
BMC Bioinformatics 2011, 12:288

42
Sprenger T, Rödel F, Beissbarth T, Conradi LC, Rothe H, Homayounfar K, Wolff HA, Ghadimi BM, Yildirim M, Becker H, Rödel C, Liersch T.
Failure of downregulation of survivin following neoadjuvant radiochemotherapy in rectal cancer is associated with distant metastases and shortened survival.
Clin Cancer Res. 2011 Mar 15;17(6):1623-31.

41
Wolff HA, Conradi LC, Schirmer M, Beissbarth T, Sprenger T, Rave-Fränk M, Hennies S, Hess CF, Becker H, Christiansen H, Liersch T.
Gender-specific acute organ toxicity during intensified preoperative radiochemotherapy for rectal cancer.
The Oncologist 2011c, 16(5):621-31

40
Jung K., Becker B., Brunner B., Beißbarth T.
Comparison of Global Tests for Functional Gene Sets in Two-Group Designs and Selection of Potentially Effect-causing Genes.
Bioinformatics 2011, 27(10): 1377-1383.

39
Leha A., Beißbarth T., Jung K.
Sequential Interim Analyses of Survival Data in DNA Microarray Experiments.
BMC Bioinformatics 2011, 12(1):127.

38
Conradi LC, Bleckmann A, Schirmer M, Sprenger T, Jo P, Homayounfar K, Wolff HA, Rothe H, Middel P, Becker H, Ghadimi MB, Beissbarth T, Liersch T.
Thymidylate Synthase as a Prognostic Biomarker for Locally Advanced Rectal Cancer after multimodal Treatment.
Ann Surg Oncol. 2011 Feb 23. [Epub ahead of print]

37
Ganslandt T, Mate S, Helbing K, Sax U, Prokosch1 HU.
TMF Special Issue: Unlocking Data for Clinical Research - The German i2b2 Experience
Applied Clinical Informatics (ACI). 2011;2(1):116-127.

36
Schirmer MA, Brockmöller J, Rave-Fränk M, Virsik P, Wilken B, Kühnle E, Campean R, Hoffmann AO, Müller K, Goetze1 RG, Neumann M, Janke JH, Nasser F, Wolff HA, Ghadimi BM, Schmidberger H, Hess CF, Christiansen H, Hille A.
A putatively functional haplotype in the gene encoding transforming growth factor-beta1 (TGF?1) as a potential biomarker for radiosensitivity.
Int J Radiat Oncol Biol Phys. 2011 Mar 1;79(3):866-74. Epub 2010 Dec 22.

35
Wolff HA, Hennies S, Herrmann MKA, Rave-Fränk M, Eickelmann D, Virsik P, Jung K, Schirmer M, Ghadimi M, Hess CF, Hermann RM, Christiansen H.
Comparison of micronucleus- and chromosome aberration technique for the documentation of cytogenetic damage in radiochemotherapy treated patients with rectal cancer.
Strahlenther Onkol. 2011 Jan;187(1):52-8. Epub 2010 Dec 23.

34
Meller B, Rave-Fränk M, Breunig C, Schirmer M, Baehre M, Nadrowitz R, Liersch T, Meller J.
Novel Carcinoembryonic-Antigen-(CEA)-Specific Pretargeting-system to Assess Tumor Cell Viability after Irradiation of Colorectal Cancer.
Strahlenther Onkol. 2011 Feb;187(2):120-6. Epub 2011 Jan 24.

33
Prokosch HU, Beck A, Ganslandt T, Hummel M, Kiehntopf M, Sax U, Ückert F, Semler S.
IT Infrastructure Components for Biobanking.
Applied Clinical Informatics (ACI). 2010;1(4):419-429.

32
Spitzner M, Emons G, Kramer F, Gaedcke J, Rave-Fränk M, Scharf J-G, Burfeind P, Becker H, Beissbarth T, Ghadimi BM, Ried T, Grade M.
A Gene Expression Signature for Chemoradiosensitivity of Colorectal Cancer Cells.
Int. J. Radiation Oncology Biol. Phys., Vol. 78, No. 4, pp. 1184-1192, 2010.

31
Helbing K, Demiroglu SY, Rakebrandt F, Pommerening K, Rienhoff O, Sax U.
A data protection scheme for medical research networks. Review after five years of operation.
Methods Inf Med. 2010 Jul 20;49(5). [Epub ahead of print]

30
Wolff HA, Raus I, Jung K, Schüler P, Herrmann MKA, Hennies S, Vorwerk H, Hille A, Hess CF, Christiansen H.
High-grade acute organ toxicity as positive prognostic factor in primary radiochemotherapy for anal carcinoma.
Int J Radiat Oncol Biol Phys. 2010 Jun 2. [Epub ahead of print]

29
Bang Y-J, Van Cutsem E, Feyereislova A, Chung HC, Shen L, Sawaki A, Lordick F, Ohtsu A, Omuro Y, Satoh T, Aprile G, Kulikov E, Hill J, Lehle M, Rüschoff J , Kang Y-K, for the ToGA Trial Investigators.
Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, andomised controlled trial.
Lancet 2010; 376: 687-97, epub 2010, Aug 20.

28
Gaedcke J, Grade M, Jung K, Camps J, Jo P, Emons G, Gehoff A, Sax U, Schirmer M, Becker H, Beißbarth T, Ried T, Ghadimi BM.
Mutated KRAS Results in Overexpression of DUSP4, a MAP-Kinase Phosphatase, and SMYD3, a Histone Methyltransferase, in Rectal Carcinomas.
Genes Chromosomes Cancer. 2010 Nov;49(11):1024-34.

27
Opitz L, Salinas-Riester G, Grade M, Jung K, Jo P, Emons G, Ghadimi BM, Beissbarth T, Gaedcke J.
Impact of RNA degradation on gene expression profiling.
BMC Med Genomics., 2010 Aug 9;3:36.

26
Liersch T, Gaedcke J, Grade M, Sprenger T, Conradi L, Becker H, Ghadimi BM.
Molekulare Marker zur Responseprädiktion beim lokal fortgeschrittenen Rektumkarzinom. Kommt die Individualisierung der Therapie?
Onkologe 2010, 16:779-788, epub 2010 July 8.

25
Demiroglu SY, Rienhoff O.
Die Rolle IT-gestützter Biobanken in der Personalisierten Medizin.
In: Niederlag W, Lemke HU, Rienhoff O (Hrsg.): Personalisierte Medizin und Informationstechnologie.
Health Academy, Band 15, Dresden 2010, 156-169.

24
Sax U, Helbing L, Gaedcke J.
Die (zentrale) Rolle der elektronischen Gesundheitsakte in der Personalisierten Medizin.
In: Niederlag W, Lemke HU, Rienhoff O (Hrsg.): Personalisierte Medizin und Informationstechnologie.
Health Academy, Band 15, Dresden 2010, 49-57.

23
Johannes M, Brase JC, Fröhlich H, Gade S, Gehrman M, Fälth M, Sültmann H, Beißbarth T.
Integration of Pathway Knowledge Into A Reweighted Recursive Feature Elimination Approach For Risk Stratification Of Cancer Patients.
Bioinformatics, 2010 Jun 30, epub ahead of print.

22
Grade M, Hummon AB, Camps J, Emons G, Spitzner M, Gaedcke J, Hoermann P, Ebner R, Becker H, Difilippantonio MJ, Ghadimi BM, Beissbarth T, Caplen NJ, Ried T.
A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets.
Int J Cancer, 2010 May 12, epub ahead of print.

21
Dangl A, Demiroglu SY, Gaedcke J, Helbing K, Jo P, Rienhoff O, Sax U.
The IT-infrastructure of a biobank for an academic medical center.
Stud Health Technol Inform 2010;160:1334-1338.

20
Sprenger T, Rothe H, Jung K, Christiansen H, Conradi LC, Ghadimi BM, Becker H, Liersch T.
Stage II/III rectal cancer with intermediate response to preoperative radiochemotherapy: do we have indications for individual risk stratification?
World J Surg Oncol., 2010 Apr 13;8:27.

19
Jung K, Grade M, Gaedcke J, Jo P, Opitz L, Becker H, Ghadimi B M, Beißbarth T.
A new sensitivity-preferred strategy to build prediction rules for therapy response of cancer patients using gene expression data.
Comput Methods Programs Biomed 2010;100(2):132-139.

18
Weiss C, Arnold D, Dellas K, Liersch, T, Hipp M, Fietkau R, Sauer R, Hinke A, Roedel C.
Preoperative radiotherapy of advanced rectal cancer with Capecitabine and Oxaliplatin with or without Cetuximab: a pooled analysis of three prospective phase I-II trials.
Int J Radiat Oncol Biol Phys., 2010 Feb 2, epub ahead of print.

17
Ghadimi BM, Grade M.
Cancer gene profiling for response prediction.
Methods Mol Biol., 2010;576:327-39.

16
Wolff HA, Gaedcke J, Jung K, Hermann RM, Rothe H, Schirmer M, Liersch T, Herrmann MK, Hennies S, Rave-Fränk M, Hess CF, Christiansen H.
High-grade acute organ toxicity during preoperative radiochemotherapy as positive predictor for complete histopathologic tumor regression in multimodal treatment of locally advanced rectal cancer.
Strahlenther Onkol., 2010 Jan;186(1):30-5, epub 2009 Dec 28.

15
Dittfeld C, Dietrich A, Peickert S, Hering S, Baumann M, Grade M, Ried T, Kunz-Schughart LA.
CD133 expression is not selective for tumor-initiating or radioresistant cell populations in the CRC cell line HCT-116.
Radiother Oncol 2010;94(3):375-383.

14
Gaedcke J, Grade M, Jung K, Schirmer M, Jo P, Obermeyer C, Wolff HA, Herrmann MK, Beissbarth T, Becker H, Ried T, Ghadimi M.
KRAS and BRAF mutations in patients with rectal cancer treated with preoperative chemoradiotherapy.
Radiother Oncol., 2010 Jan;94(1):76-81, epub 2009 Nov 11.

13
Sprenger T, Rothe H, Homayounfar K, Beissbarth T, Ghadimi BM, Becker H, Liersch T.
Preoperative chemoradiotherapy does not necessarily reduce lymph node retrieval in rectal cancer specimens--results from a prospective evaluation with extensive pathological work-up.
J Gastrointest Surg., 2010 Jan;14(1):96-103, epub 2009 Oct 15.

12
Grade M, Gaedcke J, Wangsa D, Varma S, Beckmann J, Liersch T, Hess C, Becker H, Difilippantonio MJ, Ried T, Ghadimi BM.
Chromosomal copy number changes of locally advanced rectal cancers treated with preoperative chemoradiotherapy.
Cancer Genet Cytogenet., 2009 Aug;193(1):19-28.

11
Liersch T, Grade M, Gaedcke J, Varma S, Difilippantonio MJ, Langer C, Hess CF, Becker H, Ried T, Ghadimi BM.
Preoperative chemoradiotherapy in locally advanced rectal cancer: correlation of a gene expression-based response signature with recurrence.
Cancer Genet Cytogenet., 2009 Apr 15;190(2):57-65.

10
Liersch T, Rothe H, Ghadimi BM, Becker H.
Therapie beim lokal fortgeschrittenen Rektumkarzinom - Ansätze zur Individualisierung.
Chirurg., 2009 Apr;80(4):281-93, epub 2009 Apr 8.

9
Kaulfuß S, Burfeind P, Gaedcke J, Scharf J-G.
Dual silencing of insulin-like growth factor receptor type 1 and epidermal growth factor receptor in colorectal cancer cell lines is associated with decreased proliferation and enhanced apoptosis.
Mol Cancer Ther., 2009 Apr;8(4):821-33.

8
Vorwerk H, Liersch T, Rothe H, Ghadimi M, Christiansen H, Hess CF, Hermann RM.
Gold markers for tumor localization and target volume delineation in radiotherapy for rectal cancer.
Strahlenther Onkol., 2009 Feb;185(2):127-133, epub 2009 Feb 25.

7
Christiansen H, Hermann RM, Rothe H, Liersch T.
Die Infiltration des CRM bestimmt entscheidend die Prognose. Journal Club Rektumkarzinom zu: Nagtegaal ID, Quirke P: What is the role for the circumferential margin in the modern treatment of rectal cancer? In: J Clin Oncol. 2009;26:303-12.
In|Fo|Onkologie, 2009;12:32-34 (Nr.1).

6
Schirmer M, Hoffmann AO, Campean R, Janke JH, Zidek LM, Hoffmann M, Kruse M, Sehrt D, Tzvetkov MV, Rave-Fränk M, Brockmöller J.
Bioinformatic and functional analysis of TGFBR1 polymorphisms.
Pharmacogenetics and Genomics 2009; 19:249-259.

5
Stoehlmacher J, Goekkurt E, Mogck U, Aust DE, Kramer M, Baretton GB, Liersch T, Ehninger G, Jakob C.
Thymidylate synthase genotypes and tumour regression in stage II/III rectal cancer patients after neoadjuvant fluorouracil-based chemoradiation.
Cancer Lett 2008;272(2):221-225.

4
Garman KS, Acharya CR, Edelman E, Grade M, Gaedcke J, Sud S, Barry W, Diehl AM, Provenzale D, Ginsburg SG, Ghadimi BM, Ried T, Nevins JR, Mukherjee S, Hsu D, Potti A.
A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities.
Proc Natl Acad Sci U S A., 2008 Dec 9;105(49):19432-7, epub 2008 Dec 2.

3
Christiansen H, Hermann RM, Rothe H, Liersch T.
Welche Rolle spielt der zirkumferentielle Resektionsrand nach präoperativer multimodaler Therapie beim lokal fortgeschrittenen Rektumkarzinom? Kommentar zu: Nagtegaal ID, Quirke P: What is the role for the circumferential margin in the modern treatment of rectal cancer? In: J Clin Oncol. 2008;26:303-12.
Strahlenther Onkol., 2008;184:693-694.

2
Camps J, Grade M, Nguyen QT, Hörmann P, Becker S, Hummon AB, Rodriguez V, Chandrasekharappa S, Chen Y, Difilippantonio MJ, Becker H, Ghadimi BM, Ried T.
Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome.
Cancer Res, 2008 Mar 1;68(5):1284-95.

1
Hermann RM, Liersch T, Sahlmann CO, Meller B, Meller J.
FDG-PET und FDG-PET / CT: Möglicher Stellenwert im Rahmen der Strahlentherapie des Rektumkarzinoms.
Der Nuklearmediziner, 2008; 31:65-68.