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Items: 42

1.

Put science first and formatting later.

Khan A, Montenegro-Montero A, Mathelier A.

EMBO Rep. 2018 Apr 12. pii: e45731. doi: 10.15252/embr.201845731. [Epub ahead of print] No abstract available.

PMID:
29650529
2.

Characterization of the human RFX transcription factor family by regulatory and target gene analysis.

Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P.

BMC Genomics. 2018 Mar 6;19(1):181. doi: 10.1186/s12864-018-4564-6.

3.

JASPAR RESTful API: accessing JASPAR data from any programming language.

Khan A, Mathelier A.

Bioinformatics. 2017 Dec 15. doi: 10.1093/bioinformatics/btx804. [Epub ahead of print]

PMID:
29253085
4.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1284. doi: 10.1093/nar/gkx1188. No abstract available.

5.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. doi: 10.1093/nar/gkx1126.

6.

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B.

Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. doi: 10.1093/nar/gkx1092.

7.

DNA methylation at enhancers identifies distinct breast cancer lineages.

Fleischer T, Tekpli X, Mathelier A, Wang S, Nebdal D, Dhakal HP, Sahlberg KK, Schlichting E; Oslo Breast Cancer Research Consortium (OSBREAC), Børresen-Dale AL, Borgen E, Naume B, Eskeland R, Frigessi A, Tost J, Hurtado A, Kristensen VN.

Nat Commun. 2017 Nov 9;8(1):1379. doi: 10.1038/s41467-017-00510-x.

8.

An integrated expression atlas of miRNAs and their promoters in human and mouse.

de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL.

Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.

9.

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.

Khan A, Mathelier A.

BMC Bioinformatics. 2017 May 31;18(1):287. doi: 10.1186/s12859-017-1708-7.

10.

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR, Brown CJ, Wasserman WW.

Sci Rep. 2016 Nov 18;6:37324. doi: 10.1038/srep37324.

11.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H.

Nucleic Acids Res. 2017 Jan 4;45(D1):D737-D743. doi: 10.1093/nar/gkw995. Epub 2016 Oct 27.

12.

PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina.

Hickmott JW, Chen CY, Arenillas DJ, Korecki AJ, Lam SL, Molday LL, Bonaguro RJ, Zhou M, Chou AY, Mathelier A, Boye SL, Hauswirth WW, Molday RS, Wasserman WW, Simpson EM.

Mol Ther Methods Clin Dev. 2016 Aug 10;3:16051. doi: 10.1038/mtm.2016.51. eCollection 2016.

13.

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.

Mathelier A, Xin B, Chiu TP, Yang L, Rohs R, Wasserman WW.

Cell Syst. 2016 Sep 28;3(3):278-286.e4. doi: 10.1016/j.cels.2016.07.001. Epub 2016 Aug 18.

14.

Evaluating the impact of single nucleotide variants on transcription factor binding.

Shi W, Fornes O, Mathelier A, Wasserman WW.

Nucleic Acids Res. 2016 Dec 1;44(21):10106-10116. Epub 2016 Aug 4.

15.

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Arenillas DJ, Forrest AR, Kawaji H, Lassmann T; FANTOM Consortium, Wasserman WW, Mathelier A.

Bioinformatics. 2016 Sep 15;32(18):2858-60. doi: 10.1093/bioinformatics/btw337. Epub 2016 Jun 9.

16.

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.

Klein S, Dieterich LC, Mathelier A, Chong C, Sliwa-Primorac A, Hong YK, Shin JW, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E; FANTOM consortium, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M.

J Cell Sci. 2016 Jul 1;129(13):2573-85. doi: 10.1242/jcs.186767. Epub 2016 May 19.

17.

DNA methylation profiling in human Huntington's disease brain.

De Souza RA, Islam SA, McEwen LM, Mathelier A, Hill A, Mah SM, Wasserman WW, Kobor MS, Leavitt BR.

Hum Mol Genet. 2016 May 15;25(10):2013-2030. Epub 2016 Mar 6.

PMID:
26953320
18.

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.

Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Wasserman WW, Detmar M.

Cell Rep. 2015 Nov 17;13(7):1493-1504. doi: 10.1016/j.celrep.2015.10.002. Epub 2015 Nov 5.

19.

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

Mathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, Shi W, Shyr C, Tan G, Worsley-Hunt R, Zhang AW, Parcy F, Lenhard B, Sandelin A, Wasserman WW.

Nucleic Acids Res. 2016 Jan 4;44(D1):D110-5. doi: 10.1093/nar/gkv1176. Epub 2015 Nov 3.

20.

15 TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Yang L, Dror I, Zhou T, Mathelier A, Wasserman WW, Gordân R, Rohs R.

J Biomol Struct Dyn. 2015;33 Suppl 1:9. doi: 10.1080/07391102.2015.1032555. No abstract available.

PMID:
26103228
21.

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP.

Genome Biol. 2015 Apr 23;16:84. doi: 10.1186/s13059-015-0648-7.

22.

Identification of altered cis-regulatory elements in human disease.

Mathelier A, Shi W, Wasserman WW.

Trends Genet. 2015 Feb;31(2):67-76. doi: 10.1016/j.tig.2014.12.003. Epub 2015 Jan 27. Review.

PMID:
25637093
23.

The potential of microRNAs in personalized medicine against cancers.

Saumet A, Mathelier A, Lecellier CH.

Biomed Res Int. 2014;2014:642916. doi: 10.1155/2014/642916. Epub 2014 Aug 28. Review.

24.

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.

BMC Genomics. 2014 Jun 13;15:472. doi: 10.1186/1471-2164-15-472.

25.

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.

26.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R.

Nucleic Acids Res. 2014 Jan;42(Database issue):D148-55. doi: 10.1093/nar/gkt1087. Epub 2013 Nov 7.

27.

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7. doi: 10.1093/nar/gkt997. Epub 2013 Nov 4.

28.

The next generation of transcription factor binding site prediction.

Mathelier A, Wasserman WW.

PLoS Comput Biol. 2013;9(9):e1003214. doi: 10.1371/journal.pcbi.1003214. Epub 2013 Sep 5.

29.

Large scale chromosomal mapping of human microRNA structural clusters.

Mathelier A, Carbone A.

Nucleic Acids Res. 2013 Apr;41(8):4392-408. doi: 10.1093/nar/gkt112. Epub 2013 Feb 26.

30.

Retina restored and brain abnormalities ameliorated by single-copy knock-in of human NR2E1 in null mice.

Schmouth JF, Banks KG, Mathelier A, Gregory-Evans CY, Castellarin M, Holt RA, Gregory-Evans K, Wasserman WW, Simpson EM.

Mol Cell Biol. 2012 Apr;32(7):1296-311. doi: 10.1128/MCB.06016-11. Epub 2012 Jan 30.

31.

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.

Mathelier A, Carbone A.

Bioinformatics. 2010 Sep 15;26(18):2226-34. doi: 10.1093/bioinformatics/btq329. Epub 2010 Jun 30.

PMID:
20591903
32.

Chromosomal periodicity and positional networks of genes in Escherichia coli.

Mathelier A, Carbone A.

Mol Syst Biol. 2010 May 11;6:366. doi: 10.1038/msb.2010.21.

33.

Placenta previa and accreta complicated by amniotic fluid embolism.

Mathelier AC, Karachorlu K.

Int J Fertil Womens Med. 2006 Jan-Feb;51(1):28-32. Erratum in: Int J Fertil Womens Med. 2006 May-Jun;51(3):99.

PMID:
16596906
34.

Unusual late complications after two previous cesarean deliveries: a case report.

Mathelier AC.

Int J Fertil Womens Med. 2003 Mar-Apr;48(2):70-3.

PMID:
12779292
35.

Vanished twin and fetal alcohol syndrome in the surviving twin. A case report.

Mathelier AC, Karachorlu K.

J Reprod Med. 1999 Apr;44(4):394-8.

PMID:
10319316
36.

Radiopelvimetry after cesarean section.

Mathelier AC.

J Reprod Med. 1996 Jun;41(6):427-30.

PMID:
8799919
37.
39.

Hemoperitoneum from a tubal pregnancy mimicking abruptio placentae: an obstetrical enigma.

Mathelier AC, Jurado L, Karachorlu K.

Int J Fertil. 1992 Jan-Feb;37(1):29-32.

PMID:
1348732
40.

Fertility after bilateral tubal pregnancy--modern treatment considerations.

Mathelier AC.

Int J Fertil. 1990 May-Jun;35(3):160-3.

PMID:
1973921
41.

Vulvar hematoma secondary to a human bite. A case report.

Mathelier AC.

J Reprod Med. 1987 Aug;32(8):618-9.

PMID:
3656302
42.

Tubal pregnancy coexisting with retrocecal gangrenous appendicitis. A case report.

Mathelier AC.

J Reprod Med. 1983 Jan;28(1):45-6. No abstract available.

PMID:
6834347

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