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Items: 9

1.

A High Resolution Map of the Arabidopsis thaliana Developmental Transcriptome Based on RNA-seq Profiling.

Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA.

Plant J. 2016 Aug 23. doi: 10.1111/tpj.13312. [Epub ahead of print]

PMID:
27549386
2.

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D116-25. doi: 10.1093/nar/gkv1249. Epub 2015 Nov 19.

3.

Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes.

Zakharevich NV, Averina OV, Klimina KM, Kudryavtseva AV, Kasianov AS, Makeev VJ, Danilenko VN.

Microb Ecol. 2015 Oct;70(3):819-34. doi: 10.1007/s00248-015-0603-x. Epub 2015 Apr 17.

PMID:
25894918
4.

Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains.

Zakharevich NV, Averina OV, Klimina KM, Kudryavtseva AV, Kasianov AS, Makeev VJ, Danilenko VN.

Genome Announc. 2014 Dec 18;2(6). pii: e01348-14. doi: 10.1128/genomeA.01348-14.

5.

Draft Genome Sequence of Streptomyces fradiae ATCC 19609, a Strain Highly Sensitive to Antibiotics.

Bekker OB, Klimina KM, Vatlin AA, Zakharevich NV, Kasianov AS, Danilenko VN.

Genome Announc. 2014 Dec 4;2(6). pii: e01247-14. doi: 10.1128/genomeA.01247-14.

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.

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models.

Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D195-202. doi: 10.1093/nar/gks1089. Epub 2012 Nov 21.

8.

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.

Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ.

Bioinformatics. 2011 Oct 1;27(19):2621-4. doi: 10.1093/bioinformatics/btr453. Epub 2011 Aug 18.

9.

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum).

Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA.

BMC Genomics. 2011 Jan 13;12:30. doi: 10.1186/1471-2164-12-30.

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