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Direct reprogramming of fibroblasts into antigen-presenting dendritic cells.

Rosa FF, Pires CF, Kurochkin I, Ferreira AG, Gomes AM, Palma LG, Shaiv K, Solanas L, Azenha C, Papatsenko D, Schulz O, Reis e Sousa C, Pereira CF.

Sci Immunol. 2018 Dec 7;3(30). pii: eaau4292. doi: 10.1126/sciimmunol.aau4292.


Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming.

Gomes AM, Kurochkin I, Chang B, Daniel M, Law K, Satija N, Lachmann A, Wang Z, Ferreira L, Ma'ayan A, Chen BK, Papatsenko D, Lemischka IR, Moore KA, Pereira CF.

Cell Rep. 2018 Dec 4;25(10):2821-2835.e7. doi: 10.1016/j.celrep.2018.11.032.


Feedback control of pluripotency in embryonic stem cells: Signaling, transcription and epigenetics.

Papatsenko D, Waghray A, Lemischka IR.

Stem Cell Res. 2018 May;29:180-188. doi: 10.1016/j.scr.2018.02.012. Epub 2018 Feb 20. Review.


HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ.

Nucleic Acids Res. 2018 Jan 4;46(D1):D252-D259. doi: 10.1093/nar/gkx1106.


High-throughput identification of small molecules that affect human embryonic vascular development.

Vazão H, Rosa S, Barata T, Costa R, Pitrez PR, Honório I, de Vries MR, Papatsenko D, Benedito R, Saris D, Khademhosseini A, Quax PH, Pereira CF, Mercader N, Fernandes H, Ferreira L.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E3022-E3031. doi: 10.1073/pnas.1617451114. Epub 2017 Mar 27.


Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.

Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D'Souza SL, Knowles JW, Patel A, Papatsenko D, Abbasi F, Reaven GM, Whalen S, Lee P, Shahbazi M, Henrion MYR, Zhu K, Wang S, Roussos P, Schadt EE, Pandey G, Chang R, Quertermous T, Lemischka I.

Cell Stem Cell. 2017 Apr 6;20(4):518-532.e9. doi: 10.1016/j.stem.2016.11.005. Epub 2016 Dec 22.


Emerging Modeling Concepts and Solutions in Stem Cell Research.

Papatsenko D, Lemischka IR.

Curr Top Dev Biol. 2016;116:709-21. doi: 10.1016/bs.ctdb.2015.11.040. Epub 2016 Feb 13. Review.


Hematopoietic Reprogramming In Vitro Informs In Vivo Identification of Hemogenic Precursors to Definitive Hematopoietic Stem Cells.

Pereira CF, Chang B, Gomes A, Bernitz J, Papatsenko D, Niu X, Swiers G, Azzoni E, de Bruijn MF, Schaniel C, Lemischka IR, Moore KA.

Dev Cell. 2016 Mar 7;36(5):525-39. doi: 10.1016/j.devcel.2016.02.011.


A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.

Liang R, Campreciós G, Kou Y, McGrath K, Nowak R, Catherman S, Bigarella CL, Rimmelé P, Zhang X, Gnanapragasam MN, Bieker JJ, Papatsenko D, Ma'ayan A, Bresnick E, Fowler V, Palis J, Ghaffari S.

PLoS Genet. 2015 Oct 9;11(10):e1005526. doi: 10.1371/journal.pgen.1005526. eCollection 2015 Oct.


Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal.

Papatsenko D, Darr H, Kulakovskiy IV, Waghray A, Makeev VJ, MacArthur BD, Lemischka IR.

Stem Cell Reports. 2015 Aug 11;5(2):207-20. doi: 10.1016/j.stemcr.2015.07.004.


Tbx3 Controls Dppa3 Levels and Exit from Pluripotency toward Mesoderm.

Waghray A, Saiz N, Jayaprakash AD, Freire AG, Papatsenko D, Pereira CF, Lee DF, Brosh R, Chang B, Darr H, Gingold J, Kelley K, Schaniel C, Hadjantonakis AK, Lemischka IR.

Stem Cell Reports. 2015 Jul 14;5(1):97-110. doi: 10.1016/j.stemcr.2015.05.009. Epub 2015 Jun 18.


Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming.

Ding J, Huang X, Shao N, Zhou H, Lee DF, Faiola F, Fidalgo M, Guallar D, Saunders A, Shliaha PV, Wang H, Waghray A, Papatsenko D, Sánchez-Priego C, Li D, Yuan Y, Lemischka IR, Shen L, Kelley K, Deng H, Shen X, Wang J.

Cell Stem Cell. 2015 Jun 4;16(6):653-68. doi: 10.1016/j.stem.2015.04.001. Epub 2015 Apr 30.


Modeling familial cancer with induced pluripotent stem cells.

Lee DF, Su J, Kim HS, Chang B, Papatsenko D, Zhao R, Yuan Y, Gingold J, Xia W, Darr H, Mirzayans R, Hung MC, Schaniel C, Lemischka IR.

Cell. 2015 Apr 9;161(2):240-54. doi: 10.1016/j.cell.2015.02.045.


NetExplore: a web server for modeling small network motifs.

Papatsenko D, Lemischka IR.

Bioinformatics. 2015 Jun 1;31(11):1860-2. doi: 10.1093/bioinformatics/btv058. Epub 2015 Jan 30.


FOXO3-mTOR metabolic cooperation in the regulation of erythroid cell maturation and homeostasis.

Zhang X, Campreciós G, Rimmelé P, Liang R, Yalcin S, Mungamuri SK, Barminko J, D'Escamard V, Baron MH, Brugnara C, Papatsenko D, Rivella S, Ghaffari S.

Am J Hematol. 2014 Oct;89(10):954-63. doi: 10.1002/ajh.23786. Epub 2014 Jul 22.


Divisional history and hematopoietic stem cell function during homeostasis.

Qiu J, Papatsenko D, Niu X, Schaniel C, Moore K.

Stem Cell Reports. 2014 Mar 20;2(4):473-90. doi: 10.1016/j.stemcr.2014.01.016. eCollection 2014 Apr 8.


Expression of podocalyxin separates the hematopoietic and vascular potentials of mouse embryonic stem cell-derived mesoderm.

Zhang H, Nieves JL, Fraser ST, Isern J, Douvaras P, Papatsenko D, D'Souza SL, Lemischka IR, Dyer MA, Baron MH.

Stem Cells. 2014 Jan;32(1):191-203. doi: 10.1002/stem.1536.


Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.

Kim Y, Iagovitina A, Ishihara K, Fitzgerald KM, Deplancke B, Papatsenko D, Shvartsman SY.

Chaos. 2013 Jun;23(2):025105. doi: 10.1063/1.4808157.


Induction of a hemogenic program in mouse fibroblasts.

Pereira CF, Chang B, Qiu J, Niu X, Papatsenko D, Hendry CE, Clark NR, Nomura-Kitabayashi A, Kovacic JC, Ma'ayan A, Schaniel C, Lemischka IR, Moore K.

Cell Stem Cell. 2013 Aug 1;13(2):205-18. doi: 10.1016/j.stem.2013.05.024. Epub 2013 Jun 13.


The Drosophila gap gene network is composed of two parallel toggle switches.

Papatsenko D, Levine M.

PLoS One. 2011;6(7):e21145. doi: 10.1371/journal.pone.0021145. Epub 2011 Jul 1.


Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles.

Papatsenko D, Levine M, Goltsev Y.

PLoS Biol. 2011 Jan 25;9(1):e1000584. doi: 10.1371/journal.pbio.1000584.


Temporal waves of coherent gene expression during Drosophila embryogenesis.

Papatsenko I, Levine M, Papatsenko D.

Bioinformatics. 2010 Nov 1;26(21):2731-6. doi: 10.1093/bioinformatics/btq513. Epub 2010 Sep 6.


Time warping of evolutionary distant temporal gene expression data based on noise suppression.

Goltsev Y, Papatsenko D.

BMC Bioinformatics. 2009 Oct 26;10:353. doi: 10.1186/1471-2105-10-353.


Stripe formation in the early fly embryo: principles, models, and networks.

Papatsenko D.

Bioessays. 2009 Nov;31(11):1172-80. doi: 10.1002/bies.200900096. Review.


Organization of developmental enhancers in the Drosophila embryo.

Papatsenko D, Goltsev Y, Levine M.

Nucleic Acids Res. 2009 Sep;37(17):5665-77. doi: 10.1093/nar/gkp619. Epub 2009 Aug 3.


How the Dorsal gradient works: insights from postgenome technologies.

Hong JW, Hendrix DA, Papatsenko D, Levine MS.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20072-6. doi: 10.1073/pnas.0806476105. Epub 2008 Dec 22. Review.


Dual regulation by the Hunchback gradient in the Drosophila embryo.

Papatsenko D, Levine MS.

Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2901-6. doi: 10.1073/pnas.0711941105. Epub 2008 Feb 19.


A rationale for the enhanceosome and other evolutionarily constrained enhancers.

Papatsenko D, Levine M.

Curr Biol. 2007 Nov 20;17(22):R955-7. No abstract available.


Enhancer responses to similarly distributed antagonistic gradients in development.

Zinzen RP, Papatsenko D.

PLoS Comput Biol. 2007 May;3(5):e84. Epub 2007 Mar 29.


ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors.

Papatsenko D.

Bioinformatics. 2007 Apr 15;23(8):1032-4. Epub 2007 Feb 18.


Evolution of the ventral midline in insect embryos.

Zinzen RP, Cande J, Ronshaugen M, Papatsenko D, Levine M.

Dev Cell. 2006 Dec;11(6):895-902.


Computational models for neurogenic gene expression in the Drosophila embryo.

Zinzen RP, Senger K, Levine M, Papatsenko D.

Curr Biol. 2006 Jul 11;16(13):1358-65. Epub 2006 Jun 6.


Conservation patterns in different functional sequence categories of divergent Drosophila species.

Papatsenko D, Kislyuk A, Levine M, Dubchak I.

Genomics. 2006 Oct;88(4):431-42. Epub 2006 May 11.


Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.

Boeva V, Regnier M, Papatsenko D, Makeev V.

Bioinformatics. 2006 Mar 15;22(6):676-84. Epub 2006 Jan 10.


Computational identification of regulatory DNAs underlying animal development.

Papatsenko D, Levine M.

Nat Methods. 2005 Jul;2(7):529-34. No abstract available.


Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.

Papatsenko D, Levine M.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4966-71. Epub 2005 Mar 28.


The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila.

Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4960-5. Epub 2005 Mar 25.


A self-organizing system of repressor gradients establishes segmental complexity in Drosophila.

Clyde DE, Corado MS, Wu X, Paré A, Papatsenko D, Small S.

Nature. 2003 Dec 18;426(6968):849-53.


Otd/Crx, a dual regulator for the specification of ommatidia subtypes in the Drosophila retina.

Tahayato A, Sonneville R, Pichaud F, Wernet MF, Papatsenko D, Beaufils P, Cook T, Desplan C.

Dev Cell. 2003 Sep;5(3):391-402.


Distinction between color photoreceptor cell fates is controlled by Prospero in Drosophila.

Cook T, Pichaud F, Sonneville R, Papatsenko D, Desplan C.

Dev Cell. 2003 Jun;4(6):853-64.


Homotypic regulatory clusters in Drosophila.

Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA.

Genome Res. 2003 Apr;13(4):579-88.


Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.

Papatsenko DA, Makeev VJ, Lifanov AP, Régnier M, Nazina AG, Desplan C.

Genome Res. 2002 Mar;12(3):470-81.


Sequential arrangement, not transcriptional activity, determines conformational stability of nucleosomes.

Belikov S, Papatsenko D, Preobrazhenskaya O, Sushkov V, Karpov V.

J Biomol Struct Dyn. 1997 Apr;14(5):651-5.


[A simple and effective method of synthesis of chain-specific DNA probes].

Belikov SV, Papatsenko DA, Tsibulin KV, Karpov VL.

Dokl Akad Nauk. 1996 Nov;351(3):404-5. Russian. No abstract available.


A method to synthesize strand-specific probes.

Belikov SV, Papatsenko DA, Karpov VL.

Anal Biochem. 1996 Aug 15;240(1):152-4. No abstract available.


Mapping of DNA-binding proteins along the yeast genome by UV-induced DNA-protein crosslinking.

Papatsenko DA, Priporova IV, Belikov SV, Karpov VL.

FEBS Lett. 1996 Feb 26;381(1-2):103-5.

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