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Items: 38

1.

A Beginner's Guide to Analysis of RNA Sequencing Data.

Koch CM, Chiu SF, Akbarpour M, Bharat A, Ridge KM, Bartom ET, Winter DR.

Am J Respir Cell Mol Biol. 2018 Aug;59(2):145-157. doi: 10.1165/rcmb.2017-0430TR.

PMID:
29624415
2.

Use of Serum Transthyretin as a Prognostic Indicator and Predictor of Outcome in Cardiac Amyloid Disease Associated With Wild-Type Transthyretin.

Hanson JLS, Arvanitis M, Koch CM, Berk JL, Ruberg FL, Prokaeva T, Connors LH.

Circ Heart Fail. 2018 Feb;11(2):e004000. doi: 10.1161/CIRCHEARTFAILURE.117.004000.

PMID:
29449366
3.

Inflammatory Monocytes Drive Influenza A Virus-Mediated Lung Injury in Juvenile Mice.

Coates BM, Staricha KL, Koch CM, Cheng Y, Shumaker DK, Budinger GRS, Perlman H, Misharin AV, Ridge KM.

J Immunol. 2018 Apr 1;200(7):2391-2404. doi: 10.4049/jimmunol.1701543. Epub 2018 Feb 14.

PMID:
29445006
4.

Knee Extensor Rate of Torque Development Before and After Arthroscopic Partial Meniscectomy, With Analysis of Neuromuscular Mechanisms.

Cobian DG, Koch CM, Amendola A, Williams GN.

J Orthop Sports Phys Ther. 2017 Dec;47(12):945-956. doi: 10.2519/jospt.2017.7310. Epub 2017 Oct 9.

PMID:
28992769
5.

Serum Proteomic Variability Associated with Clinical Phenotype in Familial Transthyretin Amyloidosis (ATTRm).

Chan GG, Koch CM, Connors LH.

J Proteome Res. 2017 Nov 3;16(11):4104-4112. doi: 10.1021/acs.jproteome.7b00479. Epub 2017 Sep 27.

PMID:
28922609
6.

Inhibition of the NOD-Like Receptor Protein 3 Inflammasome Is Protective in Juvenile Influenza A Virus Infection.

Coates BM, Staricha KL, Ravindran N, Koch CM, Cheng Y, Davis JM, Shumaker DK, Ridge KM.

Front Immunol. 2017 Jul 10;8:782. doi: 10.3389/fimmu.2017.00782. eCollection 2017.

7.

Lung Interstitial Macrophages: Establishing Identity and Uncovering Heterogeneity.

Koch CM, Chiu SF, Misharin AV, Ridge KM.

Am J Respir Cell Mol Biol. 2017 Jul;57(1):7-9. doi: 10.1165/rcmb.2017-0150ED. No abstract available.

PMID:
28665216
8.

Blood Proteomic Profiling in Inherited (ATTRm) and Acquired (ATTRwt) Forms of Transthyretin-Associated Cardiac Amyloidosis.

Chan GG, Koch CM, Connors LH.

J Proteome Res. 2017 Apr 7;16(4):1659-1668. doi: 10.1021/acs.jproteome.6b00998. Epub 2017 Feb 23.

PMID:
28196416
9.

Identification of Transthyretin Cardiac Amyloidosis Using Serum Retinol-Binding Protein 4 and a Clinical Prediction Model.

Arvanitis M, Koch CM, Chan GG, Torres-Arancivia C, LaValley MP, Jacobson DR, Berk JL, Connors LH, Ruberg FL.

JAMA Cardiol. 2017 Mar 1;2(3):305-313. doi: 10.1001/jamacardio.2016.5864.

10.

Children's interpretations of general quantifiers, specific quantifiers, and generics.

Gelman SA, Leslie SJ, Was AM, Koch CM.

Lang Cogn Neurosci. 2015 May 1;30(4):448-461.

11.

Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites.

Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W.

Clin Epigenetics. 2015 Mar 4;7:19. doi: 10.1186/s13148-015-0057-5. eCollection 2015.

12.

Proof of principle: quality control of therapeutic cell preparations using senescence-associated DNA-methylation changes.

Schellenberg A, Mauen S, Koch CM, Jans R, de Waele P, Wagner W.

BMC Res Notes. 2014 Apr 23;7:254. doi: 10.1186/1756-0500-7-254.

13.

Aging of blood can be tracked by DNA methylation changes at just three CpG sites.

Weidner CI, Lin Q, Koch CM, Eisele L, Beier F, Ziegler P, Bauerschlag DO, Jöckel KH, Erbel R, Mühleisen TW, Zenke M, Brümmendorf TH, Wagner W.

Genome Biol. 2014 Feb 3;15(2):R24. doi: 10.1186/gb-2014-15-2-r24.

14.

Induced pluripotent stem cell modeling of multisystemic, hereditary transthyretin amyloidosis.

Leung A, Nah SK, Reid W, Ebata A, Koch CM, Monti S, Genereux JC, Wiseman RL, Wolozin B, Connors LH, Berk JL, Seldin DC, Mostoslavsky G, Kotton DN, Murphy GJ.

Stem Cell Reports. 2013 Oct 31;1(5):451-63. doi: 10.1016/j.stemcr.2013.10.003. eCollection 2013.

15.

Epigenetic biomarker to determine replicative senescence of cultured cells.

Koch CM, Wagner W.

Methods Mol Biol. 2013;1048:309-21. doi: 10.1007/978-1-62703-556-9_20.

PMID:
23929112
16.

Pluripotent stem cells escape from senescence-associated DNA methylation changes.

Koch CM, Reck K, Shao K, Lin Q, Joussen S, Ziegler P, Walenda G, Drescher W, Opalka B, May T, Brümmendorf T, Zenke M, Saric T, Wagner W.

Genome Res. 2013 Feb;23(2):248-59. doi: 10.1101/gr.141945.112. Epub 2012 Oct 18.

17.

Monitoring of cellular senescence by DNA-methylation at specific CpG sites.

Koch CM, Joussen S, Schellenberg A, Lin Q, Zenke M, Wagner W.

Aging Cell. 2012 Apr;11(2):366-9. doi: 10.1111/j.1474-9726.2011.00784.x. Epub 2012 Jan 19.

18.

Epigenetic-aging-signature to determine age in different tissues.

Koch CM, Wagner W.

Aging (Albany NY). 2011 Oct;3(10):1018-27.

19.

Replicative senescence of mesenchymal stem cells causes DNA-methylation changes which correlate with repressive histone marks.

Schellenberg A, Lin Q, Schüler H, Koch CM, Joussen S, Denecke B, Walenda G, Pallua N, Suschek CV, Zenke M, Wagner W.

Aging (Albany NY). 2011 Sep;3(9):873-88.

20.

Serum after autologous transplantation stimulates proliferation and expansion of human hematopoietic progenitor cells.

Walenda T, Bokermann G, Jost E, Galm O, Schellenberg A, Koch CM, Piroth DM, Drescher W, Brümmendorf TH, Wagner W.

PLoS One. 2011 Mar 18;6(3):e18012. doi: 10.1371/journal.pone.0018012.

21.

Specific age-associated DNA methylation changes in human dermal fibroblasts.

Koch CM, Suschek CV, Lin Q, Bork S, Goergens M, Joussen S, Pallua N, Ho AD, Zenke M, Wagner W.

PLoS One. 2011 Feb 8;6(2):e16679. doi: 10.1371/journal.pone.0016679.

22.

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution.

Dhami P, Saffrey P, Bruce AW, Dillon SC, Chiang K, Bonhoure N, Koch CM, Bye J, James K, Foad NS, Ellis P, Watkins NA, Ouwehand WH, Langford C, Andrews RM, Dunham I, Vetrie D.

PLoS One. 2010 Aug 23;5(8):e12339. doi: 10.1371/journal.pone.0012339.

23.

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.

Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J.

Nucleic Acids Res. 2010 Jul;38(13):4325-36. doi: 10.1093/nar/gkq175. Epub 2010 Mar 31.

24.

Windei, the Drosophila homolog of mAM/MCAF1, is an essential cofactor of the H3K9 methyl transferase dSETDB1/Eggless in germ line development.

Koch CM, Honemann-Capito M, Egger-Adam D, Wodarz A.

PLoS Genet. 2009 Sep;5(9):e1000644. doi: 10.1371/journal.pgen.1000644. Epub 2009 Sep 11.

25.

DNA methylation-histone modification relationships across the desmin locus in human primary cells.

Lindahl Allen M, Koch CM, Clelland GK, Dunham I, Antoniou M.

BMC Mol Biol. 2009 May 27;10:51. doi: 10.1186/1471-2199-10-51.

26.

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D.

Genome Res. 2009 Jun;19(6):994-1005. doi: 10.1101/gr.089086.108. Epub 2009 Apr 28.

27.

Epigenetic marking prepares the human HOXA cluster for activation during differentiation of pluripotent cells.

Atkinson SP, Koch CM, Clelland GK, Willcox S, Fowler JC, Stewart R, Lako M, Dunham I, Armstrong L.

Stem Cells. 2008 May;26(5):1174-85. doi: 10.1634/stemcells.2007-0497. Epub 2008 Feb 21.

28.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

29.

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.

De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, Dunham I, Gibbons RJ, Wood WG, Higgs DR.

Blood. 2007 Dec 15;110(13):4503-10. Epub 2007 Aug 22. Erratum in: Blood. 2008 Feb 15;111(4):1773.

30.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

31.

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.

Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C.

Genome Res. 2007 Jun;17(6):708-19.

32.

The landscape of histone modifications across 1% of the human genome in five human cell lines.

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I.

Genome Res. 2007 Jun;17(6):691-707.

33.

Genomic amplification and oncogenic properties of the KCNK9 potassium channel gene.

Mu D, Chen L, Zhang X, See LH, Koch CM, Yen C, Tong JJ, Spiegel L, Nguyen KC, Servoss A, Peng Y, Pei L, Marks JR, Lowe S, Hoey T, Jan LY, McCombie WR, Wigler MH, Powers S.

Cancer Cell. 2003 Mar;3(3):297-302.

34.

Effects of extensive resection of the small intestine in the pony.

Tate LP Jr, Ralston SL, Koch CM, Everitt JI.

Am J Vet Res. 1983 Jul;44(7):1187-91.

PMID:
6881658
35.

Genetic control of the spontaneous hypertension in the NZB/Cr strain of mice. Immunogenetic considerations.

Svendsen UG, Koch CM, Rubin B.

Acta Pathol Microbiol Scand C. 1979 Aug;87C(4):269-73.

PMID:
495103
36.

Perspectives on the development of dental hygiene in Germany.

Koch CM.

Dent Hyg (Chic). 1975 Oct;49(10):454. No abstract available.

PMID:
1073118
37.

Use of pipelines as aerobic biological reactors.

Koch CM, Zandi I.

J Water Pollut Control Fed. 1973 Dec;45(12):2537-48. No abstract available.

PMID:
4769858
38.

[The behaviour of d-glucosamine in aqueous solutions].

HEYNS K, KOCH CM, KOCH W.

Hoppe Seylers Z Physiol Chem. 1954;296(3-4):121-9. German. No abstract available.

PMID:
13221235

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