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Items: 1 to 50 of 65

1.

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA.

Nat Commun. 2019 May 29;10(1):2415. doi: 10.1038/s41467-019-10557-7.

2.

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA.

Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Erratum in: Nat Commun. 2019 May 29;10(1):2415.

3.

A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.

Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T.

Cell. 2019 Apr 18;177(3):572-586.e22. doi: 10.1016/j.cell.2019.03.010. Epub 2019 Apr 4.

PMID:
30955884
4.

Mutation of chromatin regulators and focal hotspot alterations characterize human papillomavirus-positive oropharyngeal squamous cell carcinoma.

Haft S, Ren S, Xu G, Mark A, Fisch K, Guo TW, Khan Z, Pang J, Ando M, Liu C, Sakai A, Fukusumi T, Califano JA.

Cancer. 2019 Apr 1. doi: 10.1002/cncr.32068. [Epub ahead of print]

PMID:
30933315
5.

DNA methylation changes associated with Parkinson's disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood.

Henderson-Smith A, Fisch KM, Hua J, Liu G, Ricciardelli E, Jepsen K, Huentelman M, Stalberg G, Edland SD, Scherzer CR, Dunckley T, Desplats P.

Epigenetics. 2019 Apr;14(4):365-382. doi: 10.1080/15592294.2019.1588682. Epub 2019 Mar 14.

PMID:
30871403
6.

Biological Interpretation of Complex Genomic Data.

Fisch KM.

Methods Mol Biol. 2019;1908:61-71. doi: 10.1007/978-1-4939-9004-7_5.

PMID:
30649721
7.

Variations in HPV function are associated with survival in squamous cell carcinoma.

Gleber-Netto FO, Rao X, Guo T, Xi Y, Gao M, Shen L, Erikson K, Kalu NN, Ren S, Xu G, Fisch KM, Akagi K, Seiwert T, Gillison M, Frederick MJ, Johnson FM, Wang J, Myers JN, Califano J, Skinner HD, Pickering CR.

JCI Insight. 2019 Jan 10;4(1). pii: 124762. doi: 10.1172/jci.insight.124762. [Epub ahead of print]

8.

On entropy and information in gene interaction networks.

Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R.

Bioinformatics. 2019 Mar 1;35(5):815-822. doi: 10.1093/bioinformatics/bty691.

PMID:
30102349
9.

Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis.

Fisch KM, Gamini R, Alvarez-Garcia O, Akagi R, Saito M, Muramatsu Y, Sasho T, Koziol JA, Su AI, Lotz MK.

Osteoarthritis Cartilage. 2018 Nov;26(11):1531-1538. doi: 10.1016/j.joca.2018.07.012. Epub 2018 Aug 3.

PMID:
30081074
10.

A Conservation Hatchery Population of Delta Smelt Shows Evidence of Genetic Adaptation to Captivity After 9 Generations.

Finger AJ, Mahardja B, Fisch KM, Benjamin A, Lindberg J, Ellison L, Ghebremariam T, Hung TC, May B.

J Hered. 2018 Aug 24;109(6):689-699. doi: 10.1093/jhered/esy035.

PMID:
30016452
11.

Characterization of Alternative Splicing Events in HPV-Negative Head and Neck Squamous Cell Carcinoma Identifies an Oncogenic DOCK5 Variant.

Liu C, Guo T, Xu G, Sakai A, Ren S, Fukusumi T, Ando M, Sadat S, Saito Y, Khan Z, Fisch KM, Califano J.

Clin Cancer Res. 2018 Oct 15;24(20):5123-5132. doi: 10.1158/1078-0432.CCR-18-0752. Epub 2018 Jun 26.

PMID:
29945995
12.

Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48.

Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI.

Nat Commun. 2018 Jun 11;9(1):2280. doi: 10.1038/s41467-018-04649-z.

13.

Draft Genome Sequences of the Obligatory Marine Myxobacterial Strains Enhygromyxa salina SWB005 and SWB007.

Amiri Moghaddam J, Poehlein A, Fisch K, Alanjary M, Daniel R, König GM, Schäberle TF.

Genome Announc. 2018 Apr 26;6(17). pii: e00324-18. doi: 10.1128/genomeA.00324-18.

14.

Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of Matmata, Tunisia.

Nasfi Z, Poehlein A, Harms H, Goralski E, Fisch KM, Daniel R, König GM, Schäberle TF, Bachoual R.

Genome Announc. 2018 Apr 26;6(17). pii: e00323-18. doi: 10.1128/genomeA.00323-18.

15.

Efficient population-scale variant analysis and prioritization with VAPr.

Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch KM.

Bioinformatics. 2018 Aug 15;34(16):2843-2845. doi: 10.1093/bioinformatics/bty192.

PMID:
29659724
16.

Heterogeneous muscle gene expression patterns in patients with massive rotator cuff tears.

Gibbons MC, Fisch KM, Pichika R, Cheng T, Engler AJ, Schenk S, Lane JG, Singh A, Ward SR.

PLoS One. 2018 Jan 2;13(1):e0190439. doi: 10.1371/journal.pone.0190439. eCollection 2018.

17.

The Potential of Indonesian Heterobranchs Found around Bunaken Island for the Production of Bioactive Compounds.

Fisch KM, Hertzer C, Böhringer N, Wuisan ZG, Schillo D, Bara R, Kaligis F, Wägele H, König GM, Schäberle TF.

Mar Drugs. 2017 Dec 7;15(12). pii: E384. doi: 10.3390/md15120384. Review.

18.

Draft Genome Sequence of Burkholderia contaminans 293K04B, an Endosymbiont of the Sponge-Derived Fungus Stachylidium bicolor.

Fisch KM, Silva Pereira C, Genilloud O, Almeida C, Schäberle TF.

Genome Announc. 2017 Nov 9;5(45). pii: e01142-17. doi: 10.1128/genomeA.01142-17.

19.

Interactive network visualization in Jupyter notebooks: visJS2jupyter.

Rosenthal SB, Len J, Webster M, Gary A, Birmingham A, Fisch KM.

Bioinformatics. 2018 Jan 1;34(1):126-128. doi: 10.1093/bioinformatics/btx581.

20.

Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate.

Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C.

Cell. 2017 Sep 21;171(1):103-119.e18. doi: 10.1016/j.cell.2017.09.001.

21.

Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification.

Widjaja CE, Olvera JG, Metz PJ, Phan AT, Savas JN, de Bruin G, Leestemaker Y, Berkers CR, de Jong A, Florea BI, Fisch K, Lopez J, Kim SH, Garcia DA, Searles S, Bui JD, Chang AN, Yates JR 3rd, Goldrath AW, Overkleeft HS, Ovaa H, Chang JT.

J Clin Invest. 2017 Oct 2;127(10):3609-3623. doi: 10.1172/JCI90895. Epub 2017 Aug 28.

22.

Occurrence of pharmaceuticals and UV-filters in riverine run-offs and waters of the German Baltic Sea.

Fisch K, Waniek JJ, Schulz-Bull DE.

Mar Pollut Bull. 2017 Nov 15;124(1):388-399. doi: 10.1016/j.marpolbul.2017.07.057. Epub 2017 Aug 9.

PMID:
28802657
23.

Antimicrobial Potential of Bacteria Associated with Marine Sea Slugs from North Sulawesi, Indonesia.

Böhringer N, Fisch KM, Schillo D, Bara R, Hertzer C, Grein F, Eisenbarth JH, Kaligis F, Schneider T, Wägele H, König GM, Schäberle TF.

Front Microbiol. 2017 Jun 14;8:1092. doi: 10.3389/fmicb.2017.01092. eCollection 2017.

24.

Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.

Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T.

Cancer Discov. 2017 Apr;7(4):410-423. doi: 10.1158/2159-8290.CD-16-1045. Epub 2017 Feb 10.

25.

Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples.

Cowell AN, Loy DE, Sundararaman SA, Valdivia H, Fisch K, Lescano AG, Baldeviano GC, Durand S, Gerbasi V, Sutherland CJ, Nolder D, Vinetz JM, Hahn BH, Winzeler EA.

MBio. 2017 Feb 7;8(1). pii: e02257-16. doi: 10.1128/mBio.02257-16.

26.

Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes.

Akagi R, Akatsu Y, Fisch KM, Alvarez-Garcia O, Teramura T, Muramatsu Y, Saito M, Sasho T, Su AI, Lotz MK.

Osteoarthritis Cartilage. 2017 Jun;25(6):943-951. doi: 10.1016/j.joca.2016.11.007. Epub 2016 Nov 22.

27.

Id3 Orchestrates Germinal Center B Cell Development.

Chen S, Miyazaki M, Chandra V, Fisch KM, Chang AN, Murre C.

Mol Cell Biol. 2016 Sep 26;36(20):2543-52. doi: 10.1128/MCB.00150-16. Print 2016 Oct 15.

28.

Toolbox for Antibiotics Discovery from Microorganisms.

Fisch KM, Schäberle TF.

Arch Pharm (Weinheim). 2016 Sep;349(9):683-91. doi: 10.1002/ardp.201600064. Epub 2016 Jun 17. Review.

PMID:
27311607
29.

Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy.

Alvarez-Garcia O, Olmer M, Akagi R, Akasaki Y, Fisch KM, Shen T, Su AI, Lotz MK.

Osteoarthritis Cartilage. 2016 Sep;24(9):1639-47. doi: 10.1016/j.joca.2016.04.015. Epub 2016 Apr 23.

30.

Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition.

Banno A, Garcia DA, van Baarsel ED, Metz PJ, Fisch K, Widjaja CE, Kim SH, Lopez J, Chang AN, Geurink PP, Florea BI, Overkleeft HS, Ovaa H, Bui JD, Yang J, Chang JT.

Oncotarget. 2016 Apr 19;7(16):21527-41. doi: 10.18632/oncotarget.7596.

31.

Increased DNA Methylation and Reduced Expression of Transcription Factors in Human Osteoarthritis Cartilage.

Alvarez-Garcia O, Fisch KM, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK.

Arthritis Rheumatol. 2016 Aug;68(8):1876-86. doi: 10.1002/art.39643.

32.

Organic polar pollutants in surface waters of inland seas.

Orlikowska A, Fisch K, Schulz-Bull DE.

Mar Pollut Bull. 2015 Dec 30;101(2):860-6. doi: 10.1016/j.marpolbul.2015.11.018. Epub 2015 Nov 12.

PMID:
26581813
33.

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing.

Meißner T, Fisch KM, Gioia L, Su AI.

BMC Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z.

34.

Omics Pipe: a community-based framework for reproducible multi-omics data analysis.

Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI.

Bioinformatics. 2015 Jun 1;31(11):1724-8. doi: 10.1093/bioinformatics/btv061. Epub 2015 Jan 30.

35.
36.

Tumor-infiltrating lymphocytes and response to neoadjuvant chemotherapy with or without carboplatin in human epidermal growth factor receptor 2-positive and triple-negative primary breast cancers.

Denkert C, von Minckwitz G, Brase JC, Sinn BV, Gade S, Kronenwett R, Pfitzner BM, Salat C, Loi S, Schmitt WD, Schem C, Fisch K, Darb-Esfahani S, Mehta K, Sotiriou C, Wienert S, Klare P, André F, Klauschen F, Blohmer JU, Krappmann K, Schmidt M, Tesch H, Kümmel S, Sinn P, Jackisch C, Dietel M, Reimer T, Untch M, Loibl S.

J Clin Oncol. 2015 Mar 20;33(9):983-91. doi: 10.1200/JCO.2014.58.1967. Epub 2014 Dec 22.

PMID:
25534375
37.

Oxidative stress diverts tRNA synthetase to nucleus for protection against DNA damage.

Wei N, Shi Y, Truong LN, Fisch KM, Xu T, Gardiner E, Fu G, Hsu YO, Kishi S, Su AI, Wu X, Yang XL.

Mol Cell. 2014 Oct 23;56(2):323-332. doi: 10.1016/j.molcel.2014.09.006. Epub 2014 Oct 2.

38.

Clinical validation of the EndoPredict test in node-positive, chemotherapy-treated ER+/HER2- breast cancer patients: results from the GEICAM 9906 trial.

Martin M, Brase JC, Calvo L, Krappmann K, Ruiz-Borrego M, Fisch K, Ruiz A, Weber KE, Munarriz B, Petry C, Rodriguez CA, Kronenwett R, Crespo C, Alba E, Carrasco E, Casas M, Caballero R, Rodriguez-Lescure A.

Breast Cancer Res. 2014 Apr 12;16(2):R38. doi: 10.1186/bcr3642.

39.

The EndoPredict score provides prognostic information on late distant metastases in ER+/HER2- breast cancer patients.

Dubsky P, Brase JC, Jakesz R, Rudas M, Singer CF, Greil R, Dietze O, Luisser I, Klug E, Sedivy R, Bachner M, Mayr D, Schmidt M, Gehrmann MC, Petry C, Weber KE, Fisch K, Kronenwett R, Gnant M, Filipits M; Austrian Breast and Colorectal Cancer Study Group (ABCSG).

Br J Cancer. 2013 Dec 10;109(12):2959-64. doi: 10.1038/bjc.2013.671. Epub 2013 Oct 24.

40.

Channel noise from both slow adaptation currents and fast currents is required to explain spike-response variability in a sensory neuron.

Fisch K, Schwalger T, Lindner B, Herz AV, Benda J.

J Neurosci. 2012 Nov 28;32(48):17332-44. doi: 10.1523/JNEUROSCI.6231-11.2012.

41.

Evaluating the performance of captive breeding techniques for conservation hatcheries: a case study of the delta smelt captive breeding program.

Fisch KM, Ivy JA, Burton RS, May B.

J Hered. 2013 Jan-Feb;104(1):92-104. doi: 10.1093/jhered/ess084. Epub 2012 Nov 1.

PMID:
23125405
42.

Decentral gene expression analysis: analytical validation of the Endopredict genomic multianalyte breast cancer prognosis test.

Kronenwett R, Bohmann K, Prinzler J, Sinn BV, Haufe F, Roth C, Averdick M, Ropers T, Windbergs C, Brase JC, Weber KE, Fisch K, Müller BM, Schmidt M, Filipits M, Dubsky P, Petry C, Dietel M, Denkert C.

BMC Cancer. 2012 Oct 5;12:456. doi: 10.1186/1471-2407-12-456.

43.

Regio- and stereoselective oxidative phenol coupling in Aspergillus niger.

Gil Girol C, Fisch KM, Heinekamp T, Günther S, Hüttel W, Piel J, Brakhage AA, Müller M.

Angew Chem Int Ed Engl. 2012 Sep 24;51(39):9788-91. doi: 10.1002/anie.201203603. Epub 2012 Sep 3.

PMID:
22945023
44.

Rational domain swaps decipher programming in fungal highly reducing polyketide synthases and resurrect an extinct metabolite.

Fisch KM, Bakeer W, Yakasai AA, Song Z, Pedrick J, Wasil Z, Bailey AM, Lazarus CM, Simpson TJ, Cox RJ.

J Am Chem Soc. 2011 Oct 19;133(41):16635-41. doi: 10.1021/ja206914q. Epub 2011 Sep 26.

PMID:
21899331
45.

How noisy adaptation of neurons shapes interspike interval histograms and correlations.

Schwalger T, Fisch K, Benda J, Lindner B.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001026. doi: 10.1371/journal.pcbi.1001026.

46.

Catalytic role of the C-terminal domains of a fungal non-reducing polyketide synthase.

Fisch KM, Skellam E, Ivison D, Cox RJ, Bailey AM, Lazarus CM, Simpson TJ.

Chem Commun (Camb). 2010 Aug 7;46(29):5331-3. doi: 10.1039/c0cc01162b. Epub 2010 Jun 16.

PMID:
20552126
47.

Trichopyrone and other constituents from the marine sponge-derived fungus Trichoderma sp.

Abdel-Lateff A, Fisch K, Wright AD.

Z Naturforsch C. 2009 Mar-Apr;64(3-4):186-92.

PMID:
19526710
48.

Chemical induction of silent biosynthetic pathway transcription in Aspergillus niger.

Fisch KM, Gillaspy AF, Gipson M, Henrikson JC, Hoover AR, Jackson L, Najar FZ, Wägele H, Cichewicz RH.

J Ind Microbiol Biotechnol. 2009 Sep;36(9):1199-213. doi: 10.1007/s10295-009-0601-4. Epub 2009 Jun 12.

PMID:
19521728
49.

Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting.

Fisch KM, Gurgui C, Heycke N, van der Sar SA, Anderson SA, Webb VL, Taudien S, Platzer M, Rubio BK, Robinson SJ, Crews P, Piel J.

Nat Chem Biol. 2009 Jul;5(7):494-501. doi: 10.1038/nchembio.176.

PMID:
19448639
50.

Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family.

Fisch KM, Petersen JL, Baerwald MR, Pedroia JK, May B.

Mol Ecol Resour. 2009 Jan;9(1):405-8. doi: 10.1111/j.1755-0998.2008.02254.x.

PMID:
21564663

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