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Items: 1 to 20 of 32

1.

Metagenomics and transcriptomics data from human colorectal cancer.

Visnovska T, Biggs PJ, Schmeier S, Frizelle FA, Purcell RV.

Sci Data. 2019 Jul 5;6(1):116. doi: 10.1038/s41597-019-0117-3.

2.

Differential Targeting of c-Maf, Bach-1, and Elmo-1 by microRNA-143 and microRNA-365 Promotes the Intracellular Growth of Mycobacterium tuberculosis in Alternatively IL-4/IL-13 Activated Macrophages.

Tamgue O, Gcanga L, Ozturk M, Whitehead L, Pillay S, Jacobs R, Roy S, Schmeier S, Davids M, Medvedeva YA, Dheda K, Suzuki H, Brombacher F, Guler R.

Front Immunol. 2019 Mar 19;10:421. doi: 10.3389/fimmu.2019.00421. eCollection 2019.

3.

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection.

Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S.

BMC Genomics. 2019 Jan 22;20(1):71. doi: 10.1186/s12864-019-5450-6.

4.

Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes.

Zhou H, Visnovska T, Gong H, Schmeier S, Hickford J, Ganley ARD.

Mol Phylogenet Evol. 2019 Apr;133:352-361. doi: 10.1016/j.ympev.2018.12.031. Epub 2018 Dec 30.

PMID:
30599197
5.

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB, Brombacher F, Suzuki H.

Sci Rep. 2018 Apr 30;8(1):6758. doi: 10.1038/s41598-018-24509-6.

6.

An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.

Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM.

Mol Biol Evol. 2018 Jun 1;35(6):1451-1462. doi: 10.1093/molbev/msy046.

7.

Genome-wide profiling of transcribed enhancers during macrophage activation.

Denisenko E, Guler R, Mhlanga MM, Suzuki H, Brombacher F, Schmeier S.

Epigenetics Chromatin. 2017 Oct 23;10(1):50. doi: 10.1186/s13072-017-0158-9.

8.

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.

Purcell RV, Visnovska M, Biggs PJ, Schmeier S, Frizelle FA.

Sci Rep. 2017 Sep 14;7(1):11590. doi: 10.1038/s41598-017-11237-6.

9.

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.

Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB.

RNA Biol. 2017 Jul 3;14(7):963-971. doi: 10.1080/15476286.2017.1312243. Epub 2017 Apr 7.

10.

An atlas of human long non-coding RNAs with accurate 5' ends.

Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.

Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.

PMID:
28241135
11.

TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions.

Schmeier S, Alam T, Essack M, Bajic VB.

Nucleic Acids Res. 2017 Jan 4;45(D1):D145-D150. doi: 10.1093/nar/gkw1007. Epub 2016 Oct 26.

12.

IRNdb: the database of immunologically relevant non-coding RNAs.

Denisenko E, Ho D, Tamgue O, Ozturk M, Suzuki H, Brombacher F, Guler R, Schmeier S.

Database (Oxford). 2016 Oct 25;2016. pii: baw138. doi: 10.1093/database/baw138.

13.

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, Guler R; Fantom Consortium, Brombacher F, Suzuki H.

Nucleic Acids Res. 2015 Aug 18;43(14):6969-82. doi: 10.1093/nar/gkv646. Epub 2015 Jun 27.

14.

Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.

Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, de Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H.

J Immunol. 2015 Jun 15;194(12):6035-44. doi: 10.4049/jimmunol.1402521. Epub 2015 May 8.

15.

IL-4Rα-dependent alternative activation of macrophages is not decisive for Mycobacterium tuberculosis pathology and bacterial burden in mice.

Guler R, Parihar SP, Savvi S, Logan E, Schwegmann A, Roy S, Nieuwenhuizen NE, Ozturk M, Schmeier S, Suzuki H, Brombacher F.

PLoS One. 2015 Mar 19;10(3):e0121070. doi: 10.1371/journal.pone.0121070. eCollection 2015.

16.

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.

17.

Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model.

Essack M, MacPherson CR, Schmeier S, Bajic VB.

BMC Syst Biol. 2012 Oct 26;6:135. doi: 10.1186/1752-0509-6-135.

18.

Network analysis of microRNAs and their regulation in human ovarian cancer.

Schmeier S, Schaefer U, Essack M, Bajic VB.

BMC Syst Biol. 2011 Nov 3;5:183. doi: 10.1186/1752-0509-5-183.

19.

In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer.

Kaur M, MacPherson CR, Schmeier S, Narasimhan K, Choolani M, Bajic VB.

BMC Syst Biol. 2011 Sep 19;5:144. doi: 10.1186/1752-0509-5-144.

20.

Simplified method to predict mutual interactions of human transcription factors based on their primary structure.

Schmeier S, Jankovic B, Bajic VB.

PLoS One. 2011;6(7):e21887. doi: 10.1371/journal.pone.0021887. Epub 2011 Jul 5.

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