Publications

Selected publications

Image
  1. França GS, Baron M, Pour M, King BR, Rao A, Misirlioglu S, Barkley D, Dolgalev I, Ho-Tang K, Avital G, Kuperwaser F, Patel A, Levine DA, Lionnet T, Yanai I. Drug-induced adaptation along a resistance continuum in cancer cells. bioRxiv 2022.06.21.496830v1.
  2. Xia B, Zhang W, Wudzinska A, Huang E, Brosh R, Pour M, Miller A, Dasen JS, Maurano MT, Kim SY, Boeke JD, Yanai I. The genetic basis of tail-loss evolution in humans and apes
    bioRxiv 2021.09.14.460388. New York Times piece. Science news story.
  3. Barkley D, Moncada R, Pour M, Liberman DA, Dryg I, Werba G, Wang W., Baron M, Rao A, Xia B, França GS, Weil A, Delair DF, Hajdu C, Lund AW, Osman I, Yanai I. Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment. Nature Genetics 2022 54: 1192-1201
  4. Rao A*, Barkley D*, Franca GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature 2021 596: 211-220.
  5. Xia B, Yan Y, Baron M, Wagner F, Barkley, D, Chiodin, M, Kim SY, Keefe DL, Alukal JP, Boeke JD, Yanai I. Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell 2020 180: 248-262.
              Preview by Bluma Lesch
  6. Moncada R, Barkley D, Wagner F, Chiodin M, Devlin JC, Baron M, Hajdu CH, Simeone D, Yanai I. Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nature Biotechnology 2020 38: 333-342.
  7. 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. The mid-developmental transition and the evolution of animal body plans. Nature 2016 531: 637–641.
  8. Hashimshony T, Feder M, Levin M, Hall BK, Yanai I. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature 2015 519: 219-22.

Book

society-genes

Itai Yanai & Martin Lercher. The Society of Genes. Harvard University Press (2016).
       Book Website
       Science review by Joseph Swift

Night Science project – Yanai & Lercher

  1. Night science. Genome Biology. Volume 20, Article number: 179 (2019).
  2. What is the question? Genome Biology. Volume 20, Article number: 289 (2019).
  3. Renaissance minds in 21st century science. Genome Biology. Volume 21, Article number: 67 (2020).
  4. The two languages of science. Genome Biology. Volume 21, Article number: 147 (2020).
  5. A hypothesis is a liability. Genome Biology. Volume 21, Article number: 231 (2020). [63rd most discussed publication of 2020 according to www.altmetric.com/top100/2020/]
  6. The data-hypothesis conversation. Genome Biology. Volume 22, Article number: 58 (2021).
  7. Novel predictions arise from contradictions. Genome Biology. Volume 22, Article number: 153 (2021).
  8. Improvisational science. Genome Biology. Volume 23, Article number: 4 (2022).
  9. What puzzle are you in? Genome Biology. Volume 23, Article number: 179 (2022).

All research publications

  1. Kuperwaser F, Avital G, Vaz MJ, Noble KN, Dammann AN, Randis TM, Aronoff DM, Ratner AJ, Yanai I. Host inflammatory dynamics reveal placental immune modulation by Group B Streptococcus during pregnancy. Molecular Systems Biology. 2023 202211021.
  2. Avital G*, Kuperwaser F*, Pountain AW, Lacey KA, Zwack EE, Podkowik M, Shopsin B, Torres VJ, Yanai I. The tempo and mode of gene regulatory programs during bacterial infection. Cell Reports 2022 41(2):111477.
  3. Barkley D, Moncada R, Pour M, Liberman DA, Dryg I, Werba G, Wang W., Baron M, Rao A, Xia B, França GS, Weil A, Delair DF, Hajdu C, Lund AW, Osman I, Yanai I. Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment. Nature Genetics 2022 54: 1192-1201
    1. News & Views by Roden & Swarbrick.
    2. Additional materials including R scripts and Seurat objects.
  4. Hunter MV*, Moncada R*, Weiss JM, Yanai I+, White RM+. Spatial transcriptomics reveals the architecture of the tumor/microenvironment interface. Nature Communications 2021 12:6278.
  5. Campbell N, Rao A, Zhang M, Baron M, Heilmann S, Deforet M, Kenny C, Ferretti L, Huang T-H, Garg M, Nsengimana J, Montal E, Tagore M, Hunter M, Newton-Bishop J, Middleton MR, Corrie P, Adams DJ, Rabbie R, Levesque MP, Cornell RA, Yanai I, Xavier JB, White RM. Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation. Developmental Cell. 2021 56:2808-2825.
  6. Xia B, Yanai I. Gene expression levels modulate germline mutation rates through the compound effects of transcription-coupled repair and damage. Human Genetics 2022 141:1211-1222.
  7. Baron M, Tagore M, Hunter MV, Kim IS, Moncada R, Yan Y, Campbell NR, White RM*, Yanai I*. The Stress-Like Cancer Cell State Is a Consistent Component of Tumorigenesis. Cell Systems 2020 11: 536-546.
  8. Levin M*, Zalts H*, Mostov N*, Hashimshony T, Yanai I. Developmental dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms. Nucleic Acids Research 2020 48: 486-499.
  9. Xia B, Yan Y, Baron M, Wagner F, Barkley, D, Chiodin, M, Kim SY, Keefe DL, Alukal JP, Boeke JD, Yanai I. Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell 2020 180: 248-262.
              Preview by Bluma Lesch
  10. Moncada R, Barkley D, Wagner F, Chiodin M, Devlin JC, Baron M, Hajdu CH, Simeone D, Yanai I. Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nature Biotechnology 2020 38: 333-342.
    1. Additional material: https://drive.google.com/drive/folders/1y2Sjr-u_hX5nPjEu0Zq3rAAscB3easkV?usp=sharing
  11. Baron T, Grossman RI, Abramson SB, Pusic MV, Rivera R, Triola MM, Yanai I. Signatures of medical student applicants and academic success. PLoS One 2020 15(1):e0227108. 
  12. Agmon N, Temple J, Tang Z, Schraink T, Baron M, Chen J, Mita P, Martin JA, Tu BP, Yanai I, Fenyö D, Boeke JD. Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast. Nucleic Acids Research 2020 48: 486-499. 
  13. Schiffer PH*, Polsky AL*, Cole AG, Camps JIR, Kroiher M, Silver DH, Grishkevich V, Anavy L, Koutsovoulos G, Hashimshony T, Yanai I. The gene regulatory program of Acrobeloides nanus reveals conservation of phylum-specific expression. Proc Natl Acad Sci U S A. 2018 115: 4459-4464.
  14. Tzur YB, Winter E, Gao J, Hashimshony T, Yanai I, Colaiácovo MP. Spatiotemporal Gene Expression Analysis of the Caenorhabditis elegans Germline Uncovers a Syncytial Expression Switch. Genetics 2018 210: 587-605. 
  15. Avital G, Starvaggi França G, Yanai I. Bimodal evolutionary developmental miRNA program in animal embryogenesis. Molecular Biology and Evolution 2017 35: 646–654.
  16. 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 Biology 2017 18: 200-210.
  17. 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. A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Cell 2017 171:1221-1223. 
  18. Zalts H, Yanai I. Developmental constraints shape the evolution of the nematode mid-developmental transition. Nature Ecology and Evolution 2017 Article number: 0113.
              News & Views by Ronald E. Ellis
  19. 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. A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Systems 2016 16: 30266-6.
              Preview by David Harlan
  20. 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. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biology 2016 17(1):77.
  21. 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. The mid-developmental transition and the evolution of animal body plans. Nature 2016 531: 637–641.
  22. Hashimshony T, Feder M, Levin M, Hall BK, Yanai I. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature 2015 519: 219-22.
  23. 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. Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein. Nature 2015 522: 56-61.
  24. 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
  25. 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
  26. Schott D, Yanai I, Hunter CP. Natural RNA interference directs a heritable response to the environment. Scientific Reports 2014 4:1-10
  27. Grishkevich V, Yanai I. Gene length and expression level shape genomic novelties. Genome Research 2014 24: 1497-1503.
  28. Anavy L, Levin M, Khair S, Nakanishi N, Valverde SF, Degnan BM, Yanai I. BLIND ordering of large-scale transcriptomic developmental time-courses. Development 2014 141: 1161-6.
  29. Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I. ELOPER: Elongation of paired-end reads as a pre-processing tool to improve de novo genome assembly Bioinformatics 2013 29: 1455-7.
  30. Ben-Elazar S, Yakhini Z, Yanai I. Spatial localization of co-regulated genes exceeds genomic gene clustering in the S. cerevisiae genome. Nucleic Acids Research 2013 41: 2191-201.
  31. Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: Single cell RNA-Seq by multiplexed linear amplification. Cell Reports 2012 2: 666-673.
  32. Levin M, Hashimshony T, Wagner F, Yanai I. Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Developmental Cell 2012 22: 1101-8.
              News & Views by Michael Richardson
  33. Silver DH, Levin M, Yanai I. Identifying functional links between genes by evolutionary transcriptomics. Molecular Biosystems 2012 8: 2585-92.
  34. Grishkevich V, Ben-Elazar S, Hashimshony T, Schott D, Hunter CP, Yanai I. A genomic bias for genotype-environment interactions in C. elegans. Molecular Systems Biology 2012 8: 587.
  35. Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, 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.
  36. Grishkevich V, Hashimshony T, Yanai I. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Research 2011 21: 707-17.
  37. Yanai I*, Peshkin L*, Jorgensen P, Kirschner MW. Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility.  Developmental Cell 2011 20:483-96.
  38. Yanai I, Hunter CP. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Research 2009 8: 651-658.
  39. Yanai I*, Baugh LB*, Smith JJ, Roehrig C, Shen-Or SS, Claggett JM, Hill AA, Slonim DK, Hunter CP. Pairing competitive and topologically distinct regulatory modules enhances patterned gene expression. Molecular Systems Biology 2008 4: 163.
  40. Yanai I, Korbel J, Boue S, Bork P, Lercher M. Similar gene expression profiles do not imply similar tissue functions. Trends in Genetics 2006 22: 132-138.
  41. Feldmesser E, Olender T, Khen M, Yanai I, Ophir R, Lancet D. Widespread ectopic expression of olfactory receptor genes. BMC Genomics 2006 7:121.
  42. Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, Berman J, Barkai, N. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005 309:938-40.
  43. Cohen-Gihon I, Lancet D, Yanai I. Modular genes with metazoan-specific domains are enriched in tissue-specificity. Trends in Genetics 2005 21:210-213.
  44. 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, Shmueli O. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 2005 5:650-659.
  45. Yanai I, Yu Y, Yu X, Cantor CR, 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.
  46. Kopelman, N, Lancet D, Yanai I. Alternative splicing and gene duplication are inversely related evolutionary mechanisms. Nature Genetics 2005 37:588-589.
  47. Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D. GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics 2004 209:1457-8.
  48. Yanai I, Graur D, Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS 2004 8:15-24.
  49. Dassa B, Yanai I, Pietrokovski S. New type of polyubiquitin-like genes with intein-like autoprocessing domains. Trends in Genetics. 2004 Nov;20(11):538-42.
  50. Chalifa-Caspi V, Shmueli O, Benjamin-Rodrig H, Rosen N, Shmoish M, Yanai I, Ophir R, Kats P, Safran M, Lancet D. GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia. Briefings in Bioinformatics. 2003 4: 349-60.
  51. Yanai I, DeLisi C. The society of genes: networks of functional links between genes by comparative genomics. Genome Biology 2002 3:11.
  52. Yanai I, Wolf YI, Koonin EV. Evolution of gene fusions: horizontal transfer versus independent events. Genome Biology 2002 3:5.
  53. Yanai I, Mellor JC, DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends in Genetics 2002 18:176-179.
  54. Mellor JC*, Yanai I*, Clodfelter KH, Mintseris J, DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Research 2002 30:306-309.
  55. Yanai I, Derti A, 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.
  56. Glusman G, Yanai I, Rubin I, Lancet D. The complete human olfactory subgenome. Genome Research 2001 5:685-702.
  57. Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Phys Rev Lett. 2000 85:2641-2644.

Preprints on bioRxiv

  1. Cole AG, Hashimshony T, Yanai I. Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo. bioRxiv 2023.02.05.527193v1.
  2. Pountain A, Jiang P, Podkowik M, Shopsin B, Torres VJ, Yanai I. A quantitative model for the transcriptional landscape of the bacterial cell cycle. bioRxiv 2022.10.22.513359v1.
  3. França GS, Baron M, Pour M, King BR, Rao A, Misirlioglu S, Barkley D, Dolgalev I, Ho-Tang K, Avital G, Kuperwaser F, Patel A, Levine DA,
    Lionnet T, Yanai I. Drug-induced adaptation along a resistance continuum in cancer cells. bioRxiv 2022.06.21.496830v1.
  4. Xia B, Zhang W, Wudzinska A, Huang E, Brosh R, Pour M, Miller A, Dasen JS, Maurano MT, Kim SY, Boeke JD, Yanai I. The genetic basis of tail-loss evolution in humans and apes. bioRxiv 2021.09.14.460388. New York Times piece. Science news story.
  5. Florian Wagner, Dalia Barkley, Itai Yanai. Accurate denoising of single-cell RNA-Seq data using unbiased principal component analysis.
  6. Florian Wagner & Itai Yanai. Moana: A robust and scalable cell type classification framework for single-cell RNA-Seq data.
  7. Florian Wagner, Yun Yan, Itai Yanai. K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data.

Reviews

  1. Pour M, Yanai I. New adventures in spatial transcriptomics. Developmental Cell 2022, 57: 1209-1210.
  2. Yanai I. Quantifying gene duplication. Nature Review Genetics (2022).
  3. Yanai I, Lercher MJ. Iterations of evolution. Science 2021 374(6569) pp. 828.
  4. Barkley D*, Rao A*, Pour M*, Franca GS*, Yanai I. Cancer cell states and emergent properties of the dynamic tumor system. Genome Research 2021 31: 1719-1727.
  5. Rao A*, Barkley D*, Franca GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature 2021 596: 211-220. Watch a session on this review! https://vimeo.com/605706347
  6. Kuperwaser F, Yanai I. Developmental biology: A molecular handbook for human development. Nature (2021).
  7. Yanai I, Lercher MJ. Science’s irrational origins. Science 2021 371(6524) pp. 37.
  8. Xia B, Yanai I. A periodic table of cell types. Development 2019 146 (12).
  9. Barkley D, Yanai I. Plasticity and Clonality of Cancer Cell States. Trends in Cancer. 2019 5(11):655-656.
  10. Baron M, Yanai I. New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics. Genome Biology 2017 Aug 24;18(1):159. 
  11. Yanai I. Development and Evolution through the Lens of Global Gene Regulation. Trends in Genetics. 2017.
  12. Baron M, Yanai I. It’s about time: studying gene regulatory programs across serial organs. Genome Biology 2017 Feb 16;18(1):30.
  13. Yanai I and Lercher MJ. Forty years of The Selfish Gene are not enough. Genome Biology 2016 17:39. Comment
  14. Avital G, Hashimshony T, Yanai I. Seeing is believing: new methods for in situ single-cell transcriptomics. Genome Biology 2014 15:110 Research highlight
  15. Grishkevich V and Yanai I. The genomic determinants of genotype-environment interactions on gene expression. Trends in Genetics 2013 29:479-87.
  16. 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.
  17. Hashimshony T and Yanai I. Revealing developmental networks by comparative transcriptomics. Transcription 2010 Volume 1 Issue 3.
  18. Slonim DK, Yanai I. Getting started in gene expression microarray analysis. PLoS Computational Biology 2009 5: e1000543.

Book chapters and other publications

  1. Yanai I, Hashimshony T. CEL-Seq2-Single-Cell RNA Sequencing by Multiplexed Linear Amplification. Methods in Molecular Biology. 2019;1979:45-56.
  2. Yanai I, Chmielnicki E. Computational biologists: moving to the driver’s seat. Genome Biology 2017 Nov 23;18(1):223. doi: 10.1186/s13059-017-1357-1.
  3. Yanai I. The Edge 2017 Annual Question. Somatic Evolution.What scientific term or concept ought to be more widely known? 
  4. I Yanai, M Lercher. Is our genome full of junk DNA? Aeon Magazine. Aug 25, 2014 .
  5. Normand R, Yanai I. An introduction to high-throughput sequencing experiments: design and bioinformatics analysis. Deep Sequencing Data Analysis, edited by Noam Shomron. Springer, 2012.
  6. Yanai I, Tzezana R. Science’s white lie. Odyssey 2012 (in Hebrew) השקר הלבן של המדע PDF
  7. Yanai I. Neutrality and selection in the evolution of gene family sizes. Power Laws, Scale-free Networks and Genome Biology. Editor: Eugene Koonin 2005.
  8. 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.
  9. Yanai I. Meeting report: The integrated world of functional genomics. Genome Biology 2002;4 (301).
  10. Yanai I, Derti, A, and DeLisi, C. Beyond sequence similarity, or sequence analysis in the age of the genome. Functional Genomics, Editors: Galas DJ and McCormack SJ 2002.
  11. Yanai I. Brave New Patents: The Law of DNA Worship. Journal of BioLaw & Business, 2001 Vol. 4, No. 2.
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