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Items: 23

1.

ASC- and caspase-8-dependent apoptotic pathway diverges from the NLRC4 inflammasome in macrophages.

Lee BL, Mirrashidi KM, Stowe IB, Kummerfeld SK, Watanabe C, Haley B, Cuellar TL, Reichelt M, Kayagaki N.

Sci Rep. 2018 Feb 28;8(1):3788. doi: 10.1038/s41598-018-21998-3.

2.

Non-canonical reader modules of BAZ1A promote recovery from DNA damage.

Oppikofer M, Sagolla M, Haley B, Zhang HM, Kummerfeld SK, Sudhamsu J, Flynn EM, Bai T, Zhang J, Ciferri C, Cochran AG.

Nat Commun. 2017 Oct 11;8(1):862. doi: 10.1038/s41467-017-00866-0.

3.

Transcription factor Etv5 is essential for the maintenance of alveolar type II cells.

Zhang Z, Newton K, Kummerfeld SK, Webster J, Kirkpatrick DS, Phu L, Eastham-Anderson J, Liu J, Lee WP, Wu J, Li H, Junttila MR, Dixit VM.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):3903-3908. doi: 10.1073/pnas.1621177114. Epub 2017 Mar 28.

4.

╬▓-Cell Insulin Secretion Requires the Ubiquitin Ligase COP1.

Suriben R, Kaihara KA, Paolino M, Reichelt M, Kummerfeld SK, Modrusan Z, Dugger DL, Newton K, Sagolla M, Webster JD, Liu J, Hebrok M, Dixit VM.

Cell. 2015 Dec 3;163(6):1457-67. doi: 10.1016/j.cell.2015.10.076. Epub 2015 Nov 25.

5.

Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics.

Dennis G Jr, Holweg CT, Kummerfeld SK, Choy DF, Setiadi AF, Hackney JA, Haverty PM, Gilbert H, Lin WY, Diehl L, Fischer S, Song A, Musselman D, Klearman M, Gabay C, Kavanaugh A, Endres J, Fox DA, Martin F, Townsend MJ.

Arthritis Res Ther. 2014;16(2):R90. Epub 2014 Apr 30.

6.

gCMAP: user-friendly connectivity mapping with R.

Sandmann T, Kummerfeld SK, Gentleman R, Bourgon R.

Bioinformatics. 2014 Jan 1;30(1):127-8. doi: 10.1093/bioinformatics/btt592. Epub 2013 Oct 15.

PMID:
24132929
7.

Pretreatment synovial transcriptional profile is associated with early and late clinical response in rheumatoid arthritis patients treated with rituximab.

Hogan VE, Holweg CT, Choy DF, Kummerfeld SK, Hackney JA, Teng YK, Townsend MJ, van Laar JM.

Ann Rheum Dis. 2012 Nov;71(11):1888-94. doi: 10.1136/annrheumdis-2011-201115. Epub 2012 Jun 26.

PMID:
22736099
8.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538. Review.

PMID:
19274049
9.

Protein domain organisation: adding order.

Kummerfeld SK, Teichmann SA.

BMC Bioinformatics. 2009 Jan 29;10:39. doi: 10.1186/1471-2105-10-39.

10.

Sticking together? Falling apart? Exploring the dynamics of the interactome.

Wilkins MR, Kummerfeld SK.

Trends Biochem Sci. 2008 May;33(5):195-200. doi: 10.1016/j.tibs.2008.03.001. Epub 2008 Apr 20.

PMID:
18424047
11.

AGEMAP: a gene expression database for aging in mice.

Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, Carter A, Weeraratna AT, Taub DD, Gorospe M, Mazan-Mamczarz K, Lakatta EG, Boheler KR, Xu X, Mattson MP, Falco G, Ko MS, Schlessinger D, Firman J, Kummerfeld SK, Wood WH 3rd, Zonderman AB, Kim SK, Becker KG.

PLoS Genet. 2007 Nov;3(11):e201. Epub 2007 Oct 2.

12.

DBD--taxonomically broad transcription factor predictions: new content and functionality.

Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA.

Nucleic Acids Res. 2008 Jan;36(Database issue):D88-92. Epub 2007 Dec 11.

13.

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS.

RNA Biol. 2006 Jan-Mar;3(1):40-8. Epub 2006 Apr 3.

PMID:
17114936
14.

DBD: a transcription factor prediction database.

Kummerfeld SK, Teichmann SA.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D74-81.

15.

The transcriptional landscape of the mammalian genome.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Sch├Ânbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).

Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713.

16.

Comparative genomics of trypanosomatid parasitic protozoa.

El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N.

Science. 2005 Jul 15;309(5733):404-9.

17.

The evolution of domain arrangements in proteins and interaction networks.

Bornberg-Bauer E, Beaussart F, Kummerfeld SK, Teichmann SA, Weiner J 3rd.

Cell Mol Life Sci. 2005 Feb;62(4):435-45. Review.

PMID:
15719170
18.

Relative rates of gene fusion and fission in multi-domain proteins.

Kummerfeld SK, Teichmann SA.

Trends Genet. 2005 Jan;21(1):25-30.

PMID:
15680510
19.

AMID: autonomous modeler of intragenic duplication.

Kummerfeld SK, Weiss AS, Fekete A, Jermiin LS.

Appl Bioinformatics. 2003;2(3):169-76.

PMID:
15130804
20.

Tyramide signal amplification enhances the detectable distribution of connexin-43 positive gap junctions across the ventricular wall of the rabbit heart.

McLachlan CS, Jusuf PR, Rummery N, Kummerfeld SK, Hambly B, McGuire MA, Turner V.

Arch Histol Cytol. 2003 Oct;66(4):359-65.

21.

The SUPERFAMILY database in 2004: additions and improvements.

Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D235-9.

22.

Cross-sectional infarct edge jaggedness does not influence ventricular electrical stability in a rabbit model of late myocardial infarct healing.

McLachlan CS, Jelinek HF, Kummerfeld SK, Rummery NM, Jusuf PR, Hambly B, McGuire MA.

Redox Rep. 2000;5(2-3):122-3.

PMID:
10939289
23.

A method to determine the fractal dimension of the cross-sectional jaggedness of the infarct scar edge.

McLachlan CS, Jelinek HF, Kummerfeld SK, Rummery N, McLachlan PD, Jusuf P, Driussi C, Yin J.

Redox Rep. 2000;5(2-3):119-21.

PMID:
10939288

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