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Items: 39

1.

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing.

Nepal C, Hadzhiev Y, Balwierz P, Tarifeño-Saldivia E, Cardenas R, Wragg JW, Suzuki AM, Carninci P, Peers B, Lenhard B, Andersen JB, Müller F.

Nat Commun. 2020 Jan 10;11(1):168. doi: 10.1038/s41467-019-13687-0.

2.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M.

Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

3.

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways.

Gruber AJ, Grandy WA, Balwierz PJ, Dimitrova YA, Pachkov M, Ciaudo C, Nimwegen Ev, Zavolan M.

Nucleic Acids Res. 2014 Aug;42(14):9313-26. doi: 10.1093/nar/gku544. Epub 2014 Jul 16.

4.

Transcription and enhancer profiling in human monocyte subsets.

Schmidl C, Renner K, Peter K, Eder R, Lassmann T, Balwierz PJ, Itoh M, Nagao-Sato S, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y, Andreesen R, Hume DA, Hoffmann P, Forrest AR, Kreutz MP, Edinger M, Rehli M; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e90-9. doi: 10.1182/blood-2013-02-484188. Epub 2014 Mar 26.

PMID:
24671955
5.

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations.

Schmidl C, Hansmann L, Lassmann T, Balwierz PJ, Kawaji H, Itoh M, Kawai J, Nagao-Sato S, Suzuki H, Andreesen R, Hayashizaki Y, Forrest AR, Carninci P, Hoffmann P, Edinger M, Rehli M; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e68-78. doi: 10.1182/blood-2013-02-486944. Epub 2014 Mar 26.

PMID:
24671953
6.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

7.

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.

Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E.

Genome Res. 2014 May;24(5):869-84. doi: 10.1101/gr.169508.113. Epub 2014 Feb 10.

8.

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

Vigano MA, Ivanek R, Balwierz P, Berninger P, van Nimwegen E, Karjalainen K, Rolink A.

Eur J Immunol. 2014 Apr;44(4):1181-93. doi: 10.1002/eji.201344022. Epub 2014 Feb 1.

9.

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming.

Tiwari N, Tiwari VK, Waldmeier L, Balwierz PJ, Arnold P, Pachkov M, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G.

Cancer Cell. 2013 Jun 10;23(6):768-83. doi: 10.1016/j.ccr.2013.04.020.

10.

Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium.

Meier-Abt F, Milani E, Roloff T, Brinkhaus H, Duss S, Meyer DS, Klebba I, Balwierz PJ, van Nimwegen E, Bentires-Alj M.

Breast Cancer Res. 2013 Apr 29;15(2):R36. doi: 10.1186/bcr3419.

11.

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.

Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E.

Nucleic Acids Res. 2013 Jan;41(Database issue):D214-20. doi: 10.1093/nar/gks1145. Epub 2012 Nov 24.

12.

The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism.

Pérez-Schindler J, Summermatter S, Salatino S, Zorzato F, Beer M, Balwierz PJ, van Nimwegen E, Feige JN, Auwerx J, Handschin C.

Mol Cell Biol. 2012 Dec;32(24):4913-24. doi: 10.1128/MCB.00877-12. Epub 2012 Oct 1.

13.

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D.

Genome Res. 2013 Jan;23(1):60-73. doi: 10.1101/gr.142661.112. Epub 2012 Sep 10.

14.

Adipose tissue microRNAs as regulators of CCL2 production in human obesity.

Arner E, Mejhert N, Kulyté A, Balwierz PJ, Pachkov M, Cormont M, Lorente-Cebrián S, Ehrlund A, Laurencikiene J, Hedén P, Dahlman-Wright K, Tanti JF, Hayashizaki Y, Rydén M, Dahlman I, van Nimwegen E, Daub CO, Arner P.

Diabetes. 2012 Aug;61(8):1986-93. doi: 10.2337/db11-1508. Epub 2012 Jun 11.

15.

Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop.

Aceto N, Sausgruber N, Brinkhaus H, Gaidatzis D, Martiny-Baron G, Mazzarol G, Confalonieri S, Quarto M, Hu G, Balwierz PJ, Pachkov M, Elledge SJ, van Nimwegen E, Stadler MB, Bentires-Alj M.

Nat Med. 2012 Mar 4;18(4):529-37. doi: 10.1038/nm.2645.

PMID:
22388088
16.

The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing.

Kishore S, Khanna A, Zhang Z, Hui J, Balwierz PJ, Stefan M, Beach C, Nicholls RD, Zavolan M, Stamm S.

Hum Mol Genet. 2010 Apr 1;19(7):1153-64. doi: 10.1093/hmg/ddp585. Epub 2010 Jan 6.

17.

Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome.

Hutzinger R, Feederle R, Mrazek J, Schiefermeier N, Balwierz PJ, Zavolan M, Polacek N, Delecluse HJ, Hüttenhofer A.

PLoS Pathog. 2009 Aug;5(8):e1000547. doi: 10.1371/journal.ppat.1000547. Epub 2009 Aug 14.

18.

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.

Genome Biol. 2009;10(7):R79. doi: 10.1186/gb-2009-10-7-r79. Epub 2009 Jul 22.

19.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.

Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.

20.

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.

Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.

Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19.

21.
22.

[Influence of family history of hypertension on blood pressure in young healthy men].

Balwierz P, Grzeszczak W.

Pol Arch Med Wewn. 2003 Jan;109(1):7-14. Polish.

PMID:
12879761
23.

Morphological transformation of Syrian hamster embryo cells at pH 6.7 by bemitradine, a nongenotoxic carcinogen.

Oshiro Y, Balwierz PS, Morris DL, Alden CL, Bunch RT.

In Vitr Mol Toxicol. 2001 Summer;14(2):121-7.

PMID:
11690565
24.

Micronucleus formation in mouse bone marrow cells in vivo in response to trans, trans-muconaldehyde.

Oshiro Y, Balwierz PS, Witz G.

Toxicol Lett. 2001 May 19;121(3):159-66.

PMID:
11369470
25.

Exploration of the transformation potential of a unique male rat protein alpha2u-globulin using hamster embryonic cells.

Oshiro Y, Balwierz PS, Eurell TE, Morris DL, Alden CL.

Toxicol Pathol. 1998 May-Jun;26(3):381-7.

PMID:
9608644
26.

Genetic toxicology studies with a tumor promoter.

Oshiro Y, Piper CE, Garriott ML, Balwierz PS, Soelter SG, Rohrbacher E.

J Appl Toxicol. 1993 Mar-Apr;13(2):91-101.

PMID:
8486916
27.

An in vitro system to screen for diarrheagenic chemicals.

Oshiro Y, Kachur JF, Balwierz PS, Won-Kim S.

Cell Biol Toxicol. 1993 Jan-Mar;9(1):85-94.

PMID:
8518972
28.

Myocardial structures over the coronary arteries and their branches.

Aleksandrowicz R, Balwierz P, Barczak R, Stryjewska-Makuch G.

Folia Morphol (Warsz). 1993;52(4):183-90.

PMID:
8175071
29.

Genetic toxicology studies of an anti-AIDS drug.

Oshiro Y, Guzzie PJ, Balwierz PS, Soelter SG, Rohrbacher E, Gad SC.

Toxicol Lett. 1992 May;60(3):275-80.

PMID:
1595086
30.

Genotoxic properties of (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU).

Oshiro Y, Piper CE, Soelter SG, Balwierz PS, Garriott ML.

Fundam Appl Toxicol. 1992 May;18(4):491-8.

PMID:
1526360
31.

Chinese hamster ovary cell assays for mutation and chromosome damage: data from non-carcinogens.

Oshiro Y, Piper CE, Balwierz PS, Soelter SG.

J Appl Toxicol. 1991 Jun;11(3):167-77.

PMID:
1918790
32.

Experimental design for the C3H/10T1/2 CL8 cell transformation assay.

Oshiro Y, Balwierz PS, Piper CE.

J Appl Toxicol. 1988 Aug;8(4):255-60.

PMID:
3183291
33.

Evaluation of the division arrest method of the CHO/HGPRT mutation assay.

Oshiro Y, Balwierz PS, Piper CE.

J Appl Toxicol. 1988 Apr;8(2):129-34.

PMID:
3379234
34.

Decision criteria for the in vitro rat hepatocyte UDS assay.

Oshiro Y, Balwierz PS, Falk RW, Piper CE.

J Appl Toxicol. 1987 Dec;7(6):379-85.

PMID:
3429763
35.

Absence of a genotoxic response from steroids in the rat primary hepatocyte unscheduled DNA synthesis assay.

Oshiro Y, Balwierz PS, Piper CE.

Environ Mutagen. 1986;8(3):461-5. No abstract available.

PMID:
3709428
36.

Selection of fetal bovine serum for use in the C3H/10T 1/2 CL8 cell transformation assay system.

Oshiro Y, Balwierz PS, Piper CE.

Environ Mutagen. 1982;4(5):569-74.

PMID:
7140676
37.

Morphological transformation of C3H/10T1/2 CL8 cells by procarcinogens.

Oshiro Y, Balwierz PS.

Environ Mutagen. 1982;4(2):105-8.

PMID:
6804225
38.

Morphological transformation of C3H/10T1/2 CL8 cells by alkylating agents.

Oshiro Y, Balwierz PS, Molinary SV.

Toxicol Lett. 1981 Dec;9(4):301-6.

PMID:
7330894
39.

Characteristics of hamster cells transformed by the combined action of chemical and virus.

Hatch GG, Balwierz PJ, Casto BC, DiPaolo JA.

Int J Cancer. 1978 Jan 15;21(1):121-7.

PMID:
624597

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