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Items: 32

1.

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes.

Lewis MJ, Barnes MR, Blighe K, Goldmann K, Rana S, Hackney JA, Ramamoorthi N, John CR, Watson DS, Kummerfeld SK, Hands R, Riahi S, Rocher-Ros V, Rivellese F, Humby F, Kelly S, Bombardieri M, Ng N, DiCicco M, van der Heijde D, Landewé R, van der Helm-van Mil A, Cauli A, McInnes IB, Buckley CD, Choy E, Taylor PC, Townsend MJ, Pitzalis C.

Cell Rep. 2019 Aug 27;28(9):2455-2470.e5. doi: 10.1016/j.celrep.2019.07.091.

2.

IRF2 transcriptionally induces GSDMD expression for pyroptosis.

Kayagaki N, Lee BL, Stowe IB, Kornfeld OS, O'Rourke K, Mirrashidi KM, Haley B, Watanabe C, Roose-Girma M, Modrusan Z, Kummerfeld S, Reja R, Zhang Y, Cho V, Andrews TD, Morris LX, Goodnow CC, Bertram EM, Dixit VM.

Sci Signal. 2019 May 21;12(582). pii: eaax4917. doi: 10.1126/scisignal.aax4917.

PMID:
31113851
3.

Intrinsic apoptosis shapes the tumor spectrum linked to inactivation of the deubiquitinase BAP1.

He M, Chaurushiya MS, Webster JD, Kummerfeld S, Reja R, Chaudhuri S, Chen YJ, Modrusan Z, Haley B, Dugger DL, Eastham-Anderson J, Lau S, Dey A, Caothien R, Roose-Girma M, Newton K, Dixit VM.

Science. 2019 Apr 19;364(6437):283-285. doi: 10.1126/science.aav4902. Epub 2019 Apr 18.

PMID:
31000662
4.

The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification.

Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM.

PLoS One. 2019 Apr 5;14(4):e0214110. doi: 10.1371/journal.pone.0214110. eCollection 2019.

5.

Ubiquitin ligase COP1 coordinates transcriptional programs that control cell type specification in the developing mouse brain.

Newton K, Dugger DL, Sengupta-Ghosh A, Ferrando RE, Chu F, Tao J, Lam W, Haller S, Chan S, Sa S, Dunlap D, Eastham-Anderson J, Ngu H, Hung J, French DM, Webster JD, Bolon B, Liu J, Reja R, Kummerfeld S, Chen YJ, Modrusan Z, Lewcock JW, Dixit VM.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11244-11249. doi: 10.1073/pnas.1805033115. Epub 2018 Oct 15.

6.

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.

7.

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.

8.

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.

9.

β-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.

10.

Caspase-11 cleaves gasdermin D for non-canonical inflammasome signalling.

Kayagaki N, Stowe IB, Lee BL, O'Rourke K, Anderson K, Warming S, Cuellar T, Haley B, Roose-Girma M, Phung QT, Liu PS, Lill JR, Li H, Wu J, Kummerfeld S, Zhang J, Lee WP, Snipas SJ, Salvesen GS, Morris LX, Fitzgerald L, Zhang Y, Bertram EM, Goodnow CC, Dixit VM.

Nature. 2015 Oct 29;526(7575):666-71. doi: 10.1038/nature15541. Epub 2015 Sep 16.

PMID:
26375259
11.

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.

12.

PILRα negatively regulates mouse inflammatory arthritis.

Sun Y, Caplazi P, Zhang J, Mazloom A, Kummerfeld S, Quinones G, Senger K, Lesch J, Peng I, Sebrell A, Luk W, Lu Y, Lin Z, Barck K, Young J, Del Rio M, Lehar S, Asghari V, Lin W, Mariathasan S, DeVoss J, Misaghi S, Balazs M, Sai T, Haley B, Hass PE, Xu M, Ouyang W, Martin F, Lee WP, Zarrin AA.

J Immunol. 2014 Jul 15;193(2):860-70. doi: 10.4049/jimmunol.1400045. Epub 2014 Jun 16.

13.

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
14.

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
15.

Gene expression patterns of Th2 inflammation and intercellular communication in asthmatic airways.

Choy DF, Modrek B, Abbas AR, Kummerfeld S, Clark HF, Wu LC, Fedorowicz G, Modrusan Z, Fahy JV, Woodruff PG, Arron JR.

J Immunol. 2011 Feb 1;186(3):1861-9. doi: 10.4049/jimmunol.1002568. Epub 2010 Dec 27.

16.

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
17.

Protein domain organisation: adding order.

Kummerfeld SK, Teichmann SA.

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

18.

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
19.

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.

20.

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.

21.

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
22.

DBD: a transcription factor prediction database.

Kummerfeld SK, Teichmann SA.

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

23.

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, Schönbach 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.

24.

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.

25.

The genome of the social amoeba Dictyostelium discoideum.

Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A.

Nature. 2005 May 5;435(7038):43-57.

26.

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
27.

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
28.

AMID: autonomous modeler of intragenic duplication.

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

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

PMID:
15130804
29.

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.

30.

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.

31.

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
32.

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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