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Night science.

Yanai I, Lercher M.

Genome Biol. 2019 Aug 28;20(1):179. doi: 10.1186/s13059-019-1800-6. No abstract available.


A periodic table of cell types.

Xia B, Yanai I.

Development. 2019 Jun 27;146(12). pii: dev169854. doi: 10.1242/dev.169854. Review.


CEL-Seq2-Single-Cell RNA Sequencing by Multiplexed Linear Amplification.

Yanai I, Hashimshony T.

Methods Mol Biol. 2019;1979:45-56. doi: 10.1007/978-1-4939-9240-9_4.


Dropouts in an Antidepressant Trial: How Do They Fare Afterwards?

Furukawa TA, Kato T, Akechi T, Shimodera S, Okada N, Yanai I, Ozaki K, Kinou K.

Psychother Psychosom. 2018;87(6):380-382. doi: 10.1159/000492434. Epub 2018 Aug 21. No abstract available.


Spatiotemporal Gene Expression Analysis of the Caenorhabditis elegans Germline Uncovers a Syncytial Expression Switch.

Tzur YB, Winter E, Gao J, Hashimshony T, Yanai I, Colaiácovo MP.

Genetics. 2018 Oct;210(2):587-605. doi: 10.1534/genetics.118.301315. Epub 2018 Aug 9.


The gene regulatory program of Acrobeloides nanus reveals conservation of phylum-specific expression.

Schiffer PH, Polsky AL, Cole AG, Camps JIR, Kroiher M, Silver DH, Grishkevich V, Anavy L, Koutsovoulos G, Hashimshony T, Yanai I.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4459-4464. doi: 10.1073/pnas.1720817115. Epub 2018 Apr 6.


Bimodal evolutionary developmental miRNA program in animal embryogenesis.

Avital G, Starvaggi França G, Yanai I.

Mol Biol Evol. 2017 Dec 11. doi: 10.1093/molbev/msx316. [Epub ahead of print]


Computational biologists: moving to the driver's seat.

Yanai I, Chmielnicki E.

Genome Biol. 2017 Nov 23;18(1):223. doi: 10.1186/s13059-017-1357-1.


A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.

Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, Nyman J, Sakuishi K, Kurtulus S, Gennert D, Xia J, Kwon JYH, Nevin J, Herbst RH, Yanai I, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC.

Cell. 2017 Nov 16;171(5):1221-1223. doi: 10.1016/j.cell.2017.11.006. No abstract available.


scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing.

Avital G, Avraham R, Fan A, Hashimshony T, Hung DT, Yanai I.

Genome Biol. 2017 Oct 27;18(1):200. doi: 10.1186/s13059-017-1340-x.


Development and Evolution through the Lens of Global Gene Regulation.

Yanai I.

Trends Genet. 2018 Jan;34(1):11-20. doi: 10.1016/j.tig.2017.09.011. Epub 2017 Oct 20. Review.


New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics.

Baron M, Yanai I.

Genome Biol. 2017 Aug 24;18(1):159. doi: 10.1186/s13059-017-1300-5.


Developmental constraints shape the evolution of the nematode mid-developmental transition.

Zalts H, Yanai I.

Nat Ecol Evol. 2017 Mar 27;1(5):113. doi: 10.1038/s41559-017-0113.


It's about time: studying gene regulatory programs across serial organs.

Baron M, Yanai I.

Genome Biol. 2017 Feb 16;18(1):30. doi: 10.1186/s13059-017-1166-6. No abstract available.


A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.

Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I.

Cell Syst. 2016 Oct 26;3(4):346-360.e4. doi: 10.1016/j.cels.2016.08.011. Epub 2016 Sep 22.


A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.

Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, Nyman J, Sakuishi K, Kurtulus S, Gennert D, Xia J, Kwon JYH, Nevin J, Herbst RH, Yanai I, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC.

Cell. 2016 Sep 8;166(6):1500-1511.e9. doi: 10.1016/j.cell.2016.08.052. Erratum in: Cell. 2017 Nov 16;171(5):1221-1223.


CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.

Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I.

Genome Biol. 2016 Apr 28;17:77. doi: 10.1186/s13059-016-0938-8.


Forty years of The Selfish Gene are not enough.

Yanai I, Lercher MJ.

Genome Biol. 2016 Mar 2;17:39. doi: 10.1186/s13059-016-0910-7. Review. No abstract available.


The mid-developmental transition and the evolution of animal body plans.

Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, Yanai I.

Nature. 2016 Mar 31;531(7596):637-641. doi: 10.1038/nature16994. Epub 2016 Feb 17.


Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.

Thompson OA, Snoek LB, Nijveen H, Sterken MG, Volkers RJ, Brenchley R, Van't Hof A, Bevers RP, Cossins AR, Yanai I, Hajnal A, Schmid T, Perkins JD, Spencer D, Kruglyak L, Andersen EC, Moerman DG, Hillier LW, Kammenga JE, Waterston RH.

Genetics. 2015 Jul;200(3):975-89. doi: 10.1534/genetics.115.175950. Epub 2015 May 19.


Lymphatic vessels arise from specialized angioblasts within a venous niche.

Nicenboim J, Malkinson G, Lupo T, Asaf L, Sela Y, Mayseless O, Gibbs-Bar L, Senderovich N, Hashimshony T, Shin M, Jerafi-Vider A, Avraham-Davidi I, Krupalnik V, Hofi R, Almog G, Astin JW, Golani O, Ben-Dor S, Crosier PS, Herzog W, Lawson ND, Hanna JH, Yanai I, Yaniv K.

Nature. 2015 Jun 4;522(7554):56-61.


Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity.

Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM.

Mol Biol Evol. 2015 Sep;32(9):2367-82. doi: 10.1093/molbev/msv117. Epub 2015 May 14.


Natural RNA interference directs a heritable response to the environment.

Schott D, Yanai I, Hunter CP.

Sci Rep. 2014 Dec 9;4:7387. doi: 10.1038/srep07387.


Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer.

Hashimshony T, Feder M, Levin M, Hall BK, Yanai I.

Nature. 2015 Mar 12;519(7542):219-22. doi: 10.1038/nature13996. Epub 2014 Dec 10.


Gene length and expression level shape genomic novelties.

Grishkevich V, Yanai I.

Genome Res. 2014 Sep;24(9):1497-503. doi: 10.1101/gr.169722.113. Epub 2014 Jul 11.


Seeing is believing: new methods for in situ single-cell transcriptomics.

Avital G, Hashimshony T, Yanai I.

Genome Biol. 2014 Mar 31;15(3):110. doi: 10.1186/gb4169. Review.


Apoptosis induced by islet amyloid polypeptide soluble oligomers is neutralized by diabetes-associated specific antibodies.

Bram Y, Frydman-Marom A, Yanai I, Gilead S, Shaltiel-Karyo R, Amdursky N, Gazit E.

Sci Rep. 2014 Mar 4;4:4267. doi: 10.1038/srep04267.


BLIND ordering of large-scale transcriptomic developmental timecourses.

Anavy L, Levin M, Khair S, Nakanishi N, Fernandez-Valverde SL, Degnan BM, Yanai I.

Development. 2014 Mar;141(5):1161-6. doi: 10.1242/dev.105288. Epub 2014 Feb 6.


An introduction to high-throughput sequencing experiments: design and bioinformatics analysis.

Normand R, Yanai I.

Methods Mol Biol. 2013;1038:1-26. doi: 10.1007/978-1-62703-514-9_1. Review.


The genomic determinants of genotype × environment interactions in gene expression.

Grishkevich V, Yanai I.

Trends Genet. 2013 Aug;29(8):479-87. doi: 10.1016/j.tig.2013.05.006. Epub 2013 Jun 13. Review.


ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.

Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.

Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169. Epub 2013 Apr 19.


Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome.

Ben-Elazar S, Yakhini Z, Yanai I.

Nucleic Acids Res. 2013 Feb 1;41(4):2191-201. doi: 10.1093/nar/gks1360. Epub 2013 Jan 8.


CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Hashimshony T, Wagner F, Sher N, Yanai I.

Cell Rep. 2012 Sep 27;2(3):666-73. doi: 10.1016/j.celrep.2012.08.003. Epub 2012 Aug 30.


Identifying functional links between genes by evolutionary transcriptomics.

Silver DH, Levin M, Yanai I.

Mol Biosyst. 2012 Oct;8(10):2585-92. doi: 10.1039/c2mb25054c.


A genomic bias for genotype-environment interactions in C. elegans.

Grishkevich V, Ben-Elazar S, Hashimshony T, Schott DH, Hunter CP, Yanai I.

Mol Syst Biol. 2012 Jun 5;8:587. doi: 10.1038/msb.2012.19.


Developmental milestones punctuate gene expression in the Caenorhabditis embryo.

Levin M, Hashimshony T, Wagner F, Yanai I.

Dev Cell. 2012 May 15;22(5):1101-8. doi: 10.1016/j.devcel.2012.04.004. Epub 2012 May 3.


A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans.

Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, Lindell D.

Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2037-42. doi: 10.1073/pnas.1115467109. Epub 2012 Jan 23.


Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks.

Beer R, Wagner F, Grishkevich V, Peshkin L, Yanai I.

Genesis. 2012 Mar;50(3):186-91. doi: 10.1002/dvg.20811. Epub 2012 Jan 5. Review.


Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility.

Yanai I, Peshkin L, Jorgensen P, Kirschner MW.

Dev Cell. 2011 Apr 19;20(4):483-96. doi: 10.1016/j.devcel.2011.03.015.


Core promoter T-blocks correlate with gene expression levels in C. elegans.

Grishkevich V, Hashimshony T, Yanai I.

Genome Res. 2011 May;21(5):707-17. doi: 10.1101/gr.113381.110. Epub 2011 Mar 2.


Revealing developmental networks by comparative transcriptomics.

Hashimshony T, Yanai I.

Transcription. 2010 Nov;1(3):154-158. Epub 2010 Jul 27.


Self-assembled organic nanostructures with metallic-like stiffness.

Adler-Abramovich L, Kol N, Yanai I, Barlam D, Shneck RZ, Gazit E, Rousso I.

Angew Chem Int Ed Engl. 2010 Dec 17;49(51):9939-42. doi: 10.1002/anie.201002037. No abstract available.


Long-term prognosis of patients with major depression and silent cerebral infarction.

Yamashita H, Fujikawa T, Takami H, Yanai I, Okamoto Y, Morinobu S, Yamawaki S.

Neuropsychobiology. 2010 Aug;62(3):177-81. doi: 10.1159/000319359. Epub 2010 Jul 22.


Getting started in gene expression microarray analysis.

Slonim DK, Yanai I.

PLoS Comput Biol. 2009 Oct;5(10):e1000543. doi: 10.1371/journal.pcbi.1000543. Epub 2009 Oct 30. Review. No abstract available.


Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved.

Yanai I, Hunter CP.

Genome Res. 2009 Dec;19(12):2214-20. doi: 10.1101/gr.093815.109. Epub 2009 Sep 10.


Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.

Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP.

Mol Syst Biol. 2008;4:163. doi: 10.1038/msb.2008.6. Epub 2008 Feb 12.


Widespread ectopic expression of olfactory receptor genes.

Feldmesser E, Olender T, Khen M, Yanai I, Ophir R, Lancet D.

BMC Genomics. 2006 May 22;7:121.


Similar gene expression profiles do not imply similar tissue functions.

Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ.

Trends Genet. 2006 Mar;22(3):132-8. Epub 2006 Feb 9. Review.


Rewiring of the yeast transcriptional network through the evolution of motif usage.

Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, Berman J, Barkai N.

Science. 2005 Aug 5;309(5736):938-40.


Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms.

Kopelman NM, Lancet D, Yanai I.

Nat Genet. 2005 Jun;37(6):588-9. Epub 2005 May 15.

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