Itai Yanai, Ph.D. - Publications

Affiliations: 
2002 Boston University, Boston, MA, United States 
Area:
Genetics, Microbiology Biology

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Cole AG, Hashimshony T, Du Z, Yanai I. Gene regulatory patterning codes in early cell fate specification of the embryo. Elife. 12. PMID 38284404 DOI: 10.7554/eLife.87099  0.641
2024 Pountain AW, Jiang P, Yao T, Homaee E, Guan Y, McDonald KJC, Podkowik M, Shopsin B, Torres VJ, Golding I, Yanai I. Transcription-replication interactions reveal bacterial genome regulation. Nature. PMID 38267581 DOI: 10.1038/s41586-023-06974-w  0.442
2023 Yanai I, Pountain A, Jiang P, Yao T, Homaee E, Guan Y, Podkowik M, Shopsin B, Torres V, Golding I. Transcription-replication interactions reveal principles of bacterial genome regulation. Research Square. PMID 37034646 DOI: 10.21203/rs.3.rs-2724389/v1  0.413
2022 Yanai I. Quantifying gene duplication. Nature Reviews. Genetics. 23: 196-197. PMID 35132201 DOI: 10.1038/s41576-022-00457-w  0.386
2021 Xia B, Yanai I. Gene expression levels modulate germline mutation rates through the compound effects of transcription-coupled repair and damage. Human Genetics. PMID 34482438 DOI: 10.1007/s00439-021-02355-3  0.419
2020 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. PMID 32910905 DOI: 10.1016/J.Cels.2020.08.018  0.33
2020 Levin M, Zalts H, Mostov N, Hashimshony T, Yanai I. Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms. Nucleic Acids Research. PMID 32421815 DOI: 10.1093/Nar/Gkaa359  0.429
2020 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. 180: 248-262.e21. PMID 31978344 DOI: 10.1016/J.Cell.2019.12.015  0.468
2020 Moncada R, Barkley D, Wagner F, Chiodin M, Devlin JC, Baron M, Hajdu CH, Simeone DM, Yanai I. Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nature Biotechnology. PMID 31932730 DOI: 10.1038/S41587-019-0392-8  0.365
2019 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. PMID 31745563 DOI: 10.1093/Nar/Gkz1098  0.307
2019 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, ... ... Yanai I, et al. Author Correction: The mid-developmental transition and the evolution of animal body plans. Nature. PMID 31673121 DOI: 10.1038/S41586-019-1698-X  0.56
2018 Tzur YB, Winter E, Gao J, Hashimshony T, Yanai I, Colaiácovo MP. Spatiotemporal Gene Expression Analysis of the Germline Uncovers a Syncytial Expression Switch. Genetics. PMID 30093412 DOI: 10.1534/Genetics.118.301315  0.499
2018 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 reveals conservation of phylum-specific expression. Proceedings of the National Academy of Sciences of the United States of America. PMID 29626130 DOI: 10.1073/Pnas.1720817115  0.698
2017 Yanai I. Development and Evolution through the Lens of Global Gene Regulation. Trends in Genetics : Tig. PMID 29061469 DOI: 10.1016/J.Tig.2017.09.011  0.434
2017 Baron M, Yanai I. New skin for the old RNA-Seq ceremony: the age of single-cell multi-omics. Genome Biology. 18: 159. PMID 28837001 DOI: 10.1186/S13059-017-1300-5  0.341
2017 Zalts H, Yanai I. Developmental constraints shape the evolution of the nematode mid-developmental transition. Nature Ecology & Evolution. 1: 113. PMID 28812710 DOI: 10.1038/S41559-017-0113  0.464
2017 Baron M, Yanai I. It's about time: studying gene regulatory programs across serial organs. Genome Biology. 18: 30. PMID 28209204 DOI: 10.1186/S13059-017-1166-6  0.367
2017 Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, Nyman J, Sakuishi K, Kurtulus S, Gennert D, Xia J, Kwon JY, Nevin J, Herbst RH, Yanai I, et al. Abstract A10: A distinct gene module for T cell dysfunction uncoupled from T cell activation and controlled by metallothioneins Cancer Immunology Research. 5. DOI: 10.1158/2326-6074.Tumimm16-A10  0.309
2016 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. PMID 27667365 DOI: 10.1016/J.Cels.2016.08.011  0.374
2016 Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, Nyman J, Sakuishi K, Kurtulus S, Gennert D, Xia J, Kwon JY, Nevin J, Herbst RH, Yanai I, et al. A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Cell. 166: 1500-1511.e9. PMID 27610572 DOI: 10.1016/J.Cell.2016.08.052  0.322
2016 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. 17: 77. PMID 27121950 DOI: 10.1186/S13059-016-0938-8  0.334
2016 Yanai I, Lercher MJ. Forty years of The Selfish Gene are not enough. Genome Biology. 17: 39. PMID 26936472 DOI: 10.1186/S13059-016-0910-7  0.547
2016 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, ... ... Yanai I, et al. The mid-developmental transition and the evolution of animal body plans. Nature. PMID 26886793 DOI: 10.1038/Nature16994  0.629
2015 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, et al. Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856. Genetics. 200: 975-89. PMID 25995208 DOI: 10.1534/Genetics.115.175950  0.371
2015 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. 32: 2367-82. PMID 25976353 DOI: 10.1093/Molbev/Msv117  0.362
2015 Hashimshony T, Feder M, Levin M, Hall BK, Yanai I. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature. 519: 219-22. PMID 25487147 DOI: 10.1038/Nature13996  0.394
2014 Schott D, Yanai I, Hunter CP. Natural RNA interference directs a heritable response to the environment. Scientific Reports. 4: 7387. PMID 25552271 DOI: 10.1038/Srep07387  0.328
2014 Grishkevich V, Yanai I. Gene length and expression level shape genomic novelties. Genome Research. 24: 1497-503. PMID 25015383 DOI: 10.1101/Gr.169722.113  0.534
2014 Anavy L, Levin M, Khair S, Nakanishi N, Fernandez-Valverde SL, Degnan BM, Yanai I. BLIND ordering of large-scale transcriptomic developmental timecourses. Development (Cambridge, England). 141: 1161-6. PMID 24504336 DOI: 10.1242/Dev.105288  0.331
2013 Grishkevich V, Yanai I. The genomic determinants of genotype × environment interactions in gene expression. Trends in Genetics : Tig. 29: 479-87. PMID 23769209 DOI: 10.1016/J.Tig.2013.05.006  0.374
2013 Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I. ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly. Bioinformatics (Oxford, England). 29: 1455-7. PMID 23603334 DOI: 10.1093/Bioinformatics/Btt169  0.307
2013 Ben-Elazar S, Yakhini Z, Yanai I. Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome. Nucleic Acids Research. 41: 2191-201. PMID 23303780 DOI: 10.1093/Nar/Gks1360  0.493
2012 Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Reports. 2: 666-73. PMID 22939981 DOI: 10.1016/J.Celrep.2012.08.003  0.38
2012 Silver DH, Levin M, Yanai I. Identifying functional links between genes by evolutionary transcriptomics. Molecular Biosystems. 8: 2585-92. PMID 22772133 DOI: 10.1039/C2Mb25054C  0.519
2012 Grishkevich V, Ben-Elazar S, Hashimshony T, Schott DH, Hunter CP, Yanai I. A genomic bias for genotype-environment interactions in C. elegans. Molecular Systems Biology. 8: 587. PMID 22669615 DOI: 10.1038/Msb.2012.19  0.424
2012 Levin M, Hashimshony T, Wagner F, Yanai I. Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Developmental Cell. 22: 1101-8. PMID 22560298 DOI: 10.1016/J.Devcel.2012.04.004  0.377
2012 Sabehi G, Shaulov L, Silver DH, Yanai I, Harel A, Lindell D. A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proceedings of the National Academy of Sciences of the United States of America. 109: 2037-42. PMID 22308387 DOI: 10.1073/Pnas.1115467109  0.479
2012 Beer R, Wagner F, Grishkevich V, Peshkin L, Yanai I. Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks Genesis. 50: 186-191. PMID 21956895 DOI: 10.1002/Dvg.20811  0.553
2011 Yanai I, Peshkin L, Jorgensen P, Kirschner MW. Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. Developmental Cell. 20: 483-96. PMID 21497761 DOI: 10.1016/J.Devcel.2011.03.015  0.45
2011 Grishkevich V, Hashimshony T, Yanai I. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Research. 21: 707-17. PMID 21367940 DOI: 10.1101/Gr.113381.110  0.386
2010 Hashimshony T, Yanai I. Revealing developmental networks by comparative transcriptomics. Transcription. 1: 154-158. PMID 21326891 DOI: 10.4161/trns.1.3.13190  0.343
2009 Slonim DK, Yanai I. Getting started in gene expression microarray analysis. Plos Computational Biology. 5: e1000543. PMID 19876380 DOI: 10.1371/Journal.Pcbi.1000543  0.475
2009 Yanai I, Hunter CP. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Research. 19: 2214-20. PMID 19745112 DOI: 10.1101/Gr.093815.109  0.555
2008 Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP. Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. Molecular Systems Biology. 4: 163. PMID 18277379 DOI: 10.1038/Msb.2008.6  0.455
2008 Yanai I, Hunter CP. Widespread gene expression divergence between organisms with near-identical embryonic development Developmental Biology. 319: 469. DOI: 10.1016/J.Ydbio.2008.05.470  0.45
2006 Feldmesser E, Olender T, Khen M, Yanai I, Ophir R, Lancet D. Widespread ectopic expression of olfactory receptor genes. Bmc Genomics. 7: 121. PMID 16716209 DOI: 10.1186/1471-2164-7-121  0.421
2006 Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ. Similar gene expression profiles do not imply similar tissue functions. Trends in Genetics : Tig. 22: 132-8. PMID 16480787 DOI: 10.1016/J.Tig.2006.01.006  0.468
2005 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 (New York, N.Y.). 309: 938-40. PMID 16081737 DOI: 10.1126/Science.1113833  0.459
2005 Kopelman NM, Lancet D, Yanai I. Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nature Genetics. 37: 588-9. PMID 15895079 DOI: 10.1038/Ng1575  0.495
2005 Cohen-Gihon I, Lancet D, Yanai I. Modular genes with metazoan-specific domains have increased tissue specificity. Trends in Genetics : Tig. 21: 210-3. PMID 15797615 DOI: 10.1016/J.Tig.2005.02.008  0.382
2005 Yanai I, Yu Y, Zhu 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 : a Publication of the Protein Society. 14: 417-23. PMID 15659374 DOI: 10.1110/Ps.04898705  0.473
2005 Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, 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 (Oxford, England). 21: 650-9. PMID 15388519 DOI: 10.1093/Bioinformatics/Bti042  0.475
2004 Dassa B, Yanai I, Pietrokovski S. New type of polyubiquitin-like genes with intein-like autoprocessing domains. Trends in Genetics : Tig. 20: 538-42. PMID 15475112 DOI: 10.1016/J.Tig.2004.08.010  0.395
2004 Yanai I, Graur D, Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. Omics : a Journal of Integrative Biology. 8: 15-24. PMID 15107234 DOI: 10.1089/153623104773547462  0.458
2004 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 (Oxford, England). 20: 1457-8. PMID 14962929 DOI: 10.1093/Bioinformatics/Bth081  0.48
2003 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. 4: 349-60. PMID 14725348 DOI: 10.1093/Bib/4.4.349  0.469
2003 Yanai I. The integrated world of functional genomics. Genome Biology. 4: 301. PMID 12537543 DOI: 10.1186/Gb-2002-4-1-301  0.367
2002 Yanai I, DeLisi C. The society of genes: networks of functional links between genes from comparative genomics. Genome Biology. 3: research0064. PMID 12429063 DOI: 10.1186/Gb-2002-3-11-Research0064  0.672
2002 Yanai I, Wolf YI, Koonin EV. Evolution of gene fusions: horizontal transfer versus independent events. Genome Biology. 3: research0024. PMID 12049665 DOI: 10.1186/Gb-2002-3-5-Research0024  0.469
2002 Yanai I, Mellor JC, DeLisi C. Identifying functional links between genes using conserved chromosomal proximity. Trends in Genetics : Tig. 18: 176-9. PMID 11932011 DOI: 10.1016/S0168-9525(01)02621-X  0.734
2002 Mellor JC, Yanai I, Clodfelter KH, Mintseris J, DeLisi C. Predictome: a database of putative functional links between proteins. Nucleic Acids Research. 30: 306-9. PMID 11752322 DOI: 10.1093/Nar/30.1.306  0.683
2001 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 Proceedings of the National Academy of Sciences of the United States of America. 98: 7940-7945. PMID 11438739 DOI: 10.1073/Pnas.141236298  0.759
2001 Glusman G, Yanai I, Rubin I, Lancet D. The complete human olfactory subgenome. Genome Research. 11: 685-702. PMID 11337468 DOI: 10.1101/Gr.171001  0.402
2000 Yanai I, Camacho CJ, DeLisi C. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. Physical Review Letters. 85: 2641-4. PMID 10978127 DOI: 10.1103/Physrevlett.85.2641  0.732
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