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Items: 23

1.

Comparison of single and module-based methods for modeling gene regulatory networks.

Hernaez M, Blatti C, Gevaert O.

Bioinformatics. 2019 Jul 9. pii: btz549. doi: 10.1093/bioinformatics/btz549. [Epub ahead of print]

PMID:
31287491
2.

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi).

Kapheim KM, Pan H, Li C, Blatti C 3rd, Harpur BA, Ioannidis P, Jones BM, Kent CF, Ruzzante L, Sloofman L, Stolle E, Waterhouse RM, Zayed A, Zhang G, Wcislo WT.

G3 (Bethesda). 2019 Mar 7;9(3):625-634. doi: 10.1534/g3.118.200865.

3.

Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge.

Saul MC, Blatti C, Yang W, Bukhari SA, Shpigler HY, Troy JM, Seward CH, Sloofman L, Chandrasekaran S, Bell AM, Stubbs L, Robinson GE, Zhao SD, Sinha S.

Genes Brain Behav. 2019 Jan;18(1):e12502. doi: 10.1111/gbb.12502. Epub 2018 Jul 16.

PMID:
29968347
4.

SigMat: a classification scheme for gene signature matching.

Xiao J, Blatti C, Sinha S.

Bioinformatics. 2018 Jul 1;34(13):i547-i554. doi: 10.1093/bioinformatics/bty251.

5.

Impaired T-cell migration to the CNS under fingolimod and dimethyl fumarate.

Mathias A, Perriot S, Canales M, Blatti C, Gaubicher C, Schluep M, Engelhardt B, Du Pasquier R.

Neurol Neuroimmunol Neuroinflamm. 2017 Oct 11;4(6):e401. doi: 10.1212/NXI.0000000000000401. eCollection 2017 Nov.

6.

Correction to 'Transcriptional regulation of brain gene expression in response to a territorial intrusion in sticklebacks'.

Sanogo YO, Band M, Blatti C, Sinha S, Bell AM.

Proc Biol Sci. 2016 Oct 26;283(1841). pii: 20162082. No abstract available.

7.

Postarrest stalling rather than crawling favors CD8(+) over CD4(+) T-cell migration across the blood-brain barrier under flow in vitro.

Rudolph H, Klopstein A, Gruber I, Blatti C, Lyck R, Engelhardt B.

Eur J Immunol. 2016 Sep;46(9):2187-203. doi: 10.1002/eji.201546251. Epub 2016 Jul 22.

8.

Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.

Blatti C, Sinha S.

Bioinformatics. 2016 Jul 15;32(14):2167-75. doi: 10.1093/bioinformatics/btw151. Epub 2016 Mar 19.

9.

Migration of encephalitogenic CD8 T cells into the central nervous system is dependent on the α4β1-integrin.

Martin-Blondel G, Pignolet B, Tietz S, Yshii L, Gebauer C, Perinat T, Van Weddingen I, Blatti C, Engelhardt B, Liblau R.

Eur J Immunol. 2015 Dec;45(12):3302-12. doi: 10.1002/eji.201545632. Epub 2015 Oct 6.

10.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G.

Science. 2015 Jun 5;348(6239):1139-43. doi: 10.1126/science.aaa4788. Epub 2015 May 14.

11.

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism.

Blatti C, Kazemian M, Wolfe S, Brodsky M, Sinha S.

Nucleic Acids Res. 2015 Apr 30;43(8):3998-4012. doi: 10.1093/nar/gkv195. Epub 2015 Mar 19.

12.

Core and region-enriched networks of behaviorally regulated genes and the singing genome.

Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256780. doi: 10.1126/science.1256780.

13.

Motif enrichment tool.

Blatti C, Sinha S.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W20-5. doi: 10.1093/nar/gku456. Epub 2014 May 23.

14.

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.

Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S.

PLoS Genet. 2013;9(8):e1003571. doi: 10.1371/journal.pgen.1003571. Epub 2013 Aug 1.

15.

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA.

Genome Res. 2013 Jun;23(6):928-40. doi: 10.1101/gr.151472.112. Epub 2013 Mar 7.

16.

Transcriptional regulation of brain gene expression in response to a territorial intrusion.

Sanogo YO, Band M, Blatti C, Sinha S, Bell AM.

Proc Biol Sci. 2012 Dec 22;279(1749):4929-38. doi: 10.1098/rspb.2012.2087. Epub 2012 Oct 24. Erratum in: Proc Biol Sci. 2016 Oct 26;283(1841):.

17.

New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior.

Ament SA, Blatti CA, Alaux C, Wheeler MM, Toth AL, Le Conte Y, Hunt GJ, Guzmán-Novoa E, Degrandi-Hoffman G, Uribe-Rubio JL, Amdam GV, Page RE Jr, Rodriguez-Zas SL, Robinson GE, Sinha S.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1801-10. doi: 10.1073/pnas.1205283109. Epub 2012 Jun 12.

18.

The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression.

Ament SA, Wang Y, Chen CC, Blatti CA, Hong F, Liang ZS, Negre N, White KP, Rodriguez-Zas SL, Mizzen CA, Sinha S, Zhong S, Robinson GE.

PLoS Genet. 2012;8(3):e1002596. doi: 10.1371/journal.pgen.1002596. Epub 2012 Mar 29.

19.

Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor.

Janes DE, Chapus C, Gondo Y, Clayton DF, Sinha S, Blatti CA, Organ CL, Fujita MK, Balakrishnan CN, Edwards SV.

Genome Biol Evol. 2011;3:102-13. doi: 10.1093/gbe/evq087. Epub 2010 Dec 23.

20.

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.

He X, Samee MA, Blatti C, Sinha S.

PLoS Comput Biol. 2010 Sep 16;6(9). pii: e1000935. doi: 10.1371/journal.pcbi.1000935.

21.

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials.

Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S.

PLoS Biol. 2010 Aug 17;8(8). pii: e1000456. doi: 10.1371/journal.pbio.1000456. Erratum in: PLoS Biol. 2013 Oct;11(10). doi: 10.1371/annotation/e38f4ae8-0776-42e6-b912-50800f54436e.

22.

A novel classification of quiescent and transit amplifying adult neural stem cells by surface and metabolic markers permits a defined simultaneous isolation.

Obermair FJ, Fiorelli R, Schroeter A, Beyeler S, Blatti C, Zoerner B, Thallmair M.

Stem Cell Res. 2010 Sep;5(2):131-43. doi: 10.1016/j.scr.2010.05.001. Epub 2010 May 16.

23.

The genome of a songbird.

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.

Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819.

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