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Items: 38

1.

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
2.

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
3.

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
4.

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]

5.

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
6.

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
7.

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
8.

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
9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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.

26.
27.

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.

28.

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
29.

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
30.

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
31.

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
32.

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
33.

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
34.

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
35.

Focal adhesion kinase regulates metastatic adhesion of carcinoma cells within liver sinusoids.

von Sengbusch A, Gassmann P, Fisch KM, Enns A, Nicolson GL, Haier J.

Am J Pathol. 2005 Feb;166(2):585-96.

36.

A new antioxidant isobenzofuranone derivative from the algicolous marine fungus Epicoccum sp.

Abdel-Lateff A, Fisch KM, Wright AD, König GM.

Planta Med. 2003 Sep;69(9):831-4.

PMID:
14598209
37.

Antioxidative meroterpenoids from the brown alga Cystoseira crinita.

Fisch KM, Böhm V, Wright AD, König GM.

J Nat Prod. 2003 Jul;66(7):968-75.

PMID:
12880316
38.

New antioxidant hydroquinone derivatives from the algicolous marine fungus Acremonium sp.

Abdel-Lateff A, König GM, Fisch KM, Höller U, Jones PG, Wright AD.

J Nat Prod. 2002 Nov;65(11):1605-11.

PMID:
12444684

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