Yanai I, Lercher M. The society of genes. Cambridge: Harvard University Press; 2016.
Science Magazine Book review by Joseph Swift
Avital G, Starvaggi França G, Yanai I. Bimodal evolutionary developmental miRNA program in animal embryogenesis. Mol Biol Evol. 2017 10.1093/molbev/msx316.
Avital G, Avraham R, Fan A, Hashimshony T, Hung DT, Yanai I. scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing. Genome Biol. 2017 Oct 27;18(1):200.
Zalts H and Yanai I. Developmental constraints shape the evolution of the nematode mid-developmental transition. Nature Ecology and Evolution 2017 doi:10.1038/s41559-017-0113
News & Views by Ronald E. Ellis
Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, and Yanai I. A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Systems 2016. S2405-4712(16)30266-6.
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, and Yanai I. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology 2016 17(1):77.
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, and Yanai I. The mid-developmental transition and the evolution of animal body plans. Nature 2016 531:637–641.
Hashimshony T, Feder M, Levin M, Hall BK, and Yanai I. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature 2015 519:219-22.
Hashimshony T, Wagner F, Sher N, and Yanai I. CEL-Seq: Single cell RNA-Seq by multiplexed linear amplification. Cell Reports 2012 2: 666-673.
Levin M, Hashimshony T, Wagner F, and Yanai I. Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Developmental Cell 2012 22:1101-8.
Kopelman, N, Lancet D, and Yanai I. Alternative splicing and gene duplication are inversely related evolutionary mechanisms. Nature Genetics 2005 37:588-589.
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, and Yaniv K. Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein. Nature 2015 522:56-61.
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. Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856. Genetics. 2015 200:975-89
Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM. Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Molecular Biology and Evolution 2015 32:2367-82
Schott D, Yanai I, Hunter CP. Natural RNA interference directs a heritable response to the environment. Scientific Reports 2014 4:1-10
Grishkevich V, Yanai I. Gene length and expression level shape genomic novelties. Genome Research 2014 24:1497-503.
Anavy L, Levin M, Khair S, Nakanishi N, Valverde SF, Degnan BM, and Yanai I. BLIND ordering of large-scale transcriptomic developmental time-courses. Development 2014 141:1161-6.
Silver DH, Ben-Elazar S, Bogoslavsky A, and Yanai I. ELOPER: Elongation of paired-end reads as a pre-processing tool to improve de novo genome assembly Bioinformatics 2013 29:1455-7.
Ben-Elazar S, Yakhini Z, and Yanai I. Spatial localization of co-regulated genes exceeds genomic gene clustering in the S. cerevisiae genome. Nucleic Acids Research 2013 41:2191-201.
Silver DH, Levin M, and Yanai I. Identifying functional links between genes by evolutionary transcriptomics. Molecular Biosystems 2012 8: 2585-92.
Grishkevich V, Ben-Elazar S, Hashimshony T, Schott D, Hunter CP, and Yanai I. A genomic bias for genotype-environment interactions in C. elegans. Molecular Systems Biology 2012 8:587.
Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, and Lindell D. A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proc Natl Acad Sci U S A 2012 109: 2037-42.
Grishkevich V, Hashimshony T, Yanai I. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Research 2011 21: 707-17.
Yanai I, Peshkin L, Jorgensen P, and Kirschner MW. Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. Developmental Cell 2011 20:483-96.
Yanai I and Hunter CP. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Research 2009 8: 651-658.
Yanai I, Baugh LB, Smith JJ, Roehrig C, Shen-Or SS, Claggett JM, Hill AA, Slonim DK, and Hunter CP. Pairing competitive and topologically distinct regulatory modules enhances patterned gene expression. Molecular Systems Biology 2008 4: 163.
Yanai I, Korbel J, Boue S, Bork P and Lercher M. Similar gene expression profiles do not imply similar tissue functions. Trends in Genetics 2006 22: 132-138.
Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, Berman J, and Barkai, N. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005 309:938-40.
Cohen-Gihon I, Lancet D, and Yanai I. Modular genes with metazoan-specific domains are enriched in tissue-specificity. Trends in Genetics 2005 21:210-213.
Yanai I, Benjamin-Rodrig H, Shmoish M, Chalifa-Caspi V, Ophir R, Bar-Even A, Shklar M, Horn-Saban S, Safran M, Domany E, Lancet D, and Shmueli O. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2005 5:650-659.
Feldmesser E, Olender T, Khen M, Yanai I, Ophir R, and Lancet D. Widespread ectopic expression of olfactory receptor genes. BMC Genomics 2006 7:121.
Yanai I, Yu Y, Yu X, Cantor CR, and Weng Z. An avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin. Protein Science 2005 14: 417-423.
Chalifa-Caspi V, Shmueli O, Benjamin-Rodrig H, Rosen N, Shmoish M, Yanai I, Ophir R, Kats P, Safran M, and Lancet D. GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia. Briefings in Bioinformatics. 2003 4: 349-60.
Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, and Lancet D. GeneAnnot. Bioinformatics 2004 209:1457-8.
Yanai I, Graur D, and Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS 2004 8:15-24.
Yanai I and DeLisi C. The society of genes: networks of functional links between genes by comparative genomics. Genome Biology 2002 3:11.
Yanai I, Wolf YI, and Koonin EV. Evolution of gene fusions: horizontal transfer versus independent events. Genome Biology 2002 3:5.
Yanai I, Mellor JC, and DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends in Genetics 2002 18:176-179.
Mellor JC, Yanai I, Clodfelter KH, Mintseris J, and DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Research 2002 30:306-309.
Yanai I, Derti A, and DeLisi C. Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A. 2001 98:7940-7945.
Glusman G, Yanai I, Rubin I, and Lancet D. The complete human olfactory subgenome. Genome Research 2001 5:685-702.
Yanai I, Camacho CJ, and DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys Rev Lett. 2000 85:2641-2644.
Yanai I. Development and Evolution through the Lens of Global Gene Regulation. Trends in Genetics. 2017.
Baron M, Yanai I. It’s about time: studying gene regulatory programs across serial organs. Genome Biololgy. 2017 Feb 16;18(1):30.
Yanai I and Lercher MJ. Forty years of The Selfish Gene are not enough. Genome Biology 2016 17:39. Comment
Avital G, Hashimshony T, Yanai I. Seeing is believing: new methods for in situ single-cell transcriptomics. Genome Biology 2014 15:110 Research highlight
Grishkevich V and Yanai I. The genomic determinants of genotype-environment interactions on gene expression Trends in Genetics 2013 29:479-87.
Beer R, Wagner F, Grishkevich V, Peshkin L, and Yanai I. Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks. Genesis 2011 50:186-91.
Hashimshony T and Yanai I. Revealing developmental networks by comparative transcriptomics. Transcription 2010 Volume 1 Issue 3.
Slonim DK, Yanai I. Getting started in gene expression microarray analysis. PLoS Computational Biology 2009 5: e1000543.
Book chapters and other publications
Yanai I, Chmielnicki E. Computational biologists: moving to the driver’s seat. Genome Biol. 2017 Nov 23;18(1):223. doi: 10.1186/s13059-017-1357-1.
Yanai I. The Edge 2017 Annual Question. Somatic Evolution. WHAT SCIENTIFIC TERM OR CONCEPT OUGHT TO BE MORE WIDELY KNOWN?
I Yanai and M Lercher. Is our genome full of junk DNA? Aeon Magazine. Aug 25, 2014 .
Normand R and Yanai I. An introduction to high-throughput sequencing experiments: design and bioinformatics analysis. “Deep Sequencing Data Analysis” edited by Noam Shomron. Springer, 2012.
Yanai I and Tzezana R. Science’s white lie. Odyssey 2012 (in Hebrew) השקר הלבן של המדע PDF
Yanai I. Neutrality and selection in the evolution of gene family sizes. Power Laws, Scale-free Networks and Genome Biology. Editor: Koonin, Eugene 2005.
Yanai I. Encyclopedia entry: Connecting genes by comparative genomics. Encyclopedia of Genomics, Proteomics and Bioinformatics, edited by Michael Dunn, Lynn Jorde, Peter Little and Shankar Subramaniam 2004.
Yanai I. Meeting report: The integrated world of functional genomics. Genome Biology. 2002;4 (301).
Yanai I, Derti, A, and DeLisi, C. Beyond sequence similarity, or sequence analysis in the age of the genome. Functional Genomics, eds. Galas DJ and McCormack SJ 2002.
Yanai I. Brave New Patents: The Law of DNA Worship. Journal of BioLaw & Business, 2001 Vol. 4, No. 2.