Papers Acknowledging the TGC

 

 

  • Danielle Miller, Michael A Martin, Noam Harel, Talia Kustin, Omer Tirosh, Moran Meir, Nadav Sorek, Shiraz Gefen-Halevi, Sharon Amit, Olesya Vorontsov, Dana Wolf, Avi Peretz, Yonat Shemer-Avni, Diana Roif-Kaminsky, Na’ama Kopelman, Amit Huppert, Katia Koelle, Adi Stern. (2020) Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. medRxiv 2020.05.21.20104521;

 

  • Simaan, H., Shalaby, S., Hatoel, M. et al. The AP-1-like transcription factor ChAP1 balances tolerance and cell death in the response of the maize pathogen Cochliobolus heterostrophus to a plant phenolic. Curr Genet 66, 187–203 (2020).

 

  • Nitsan Fourier, Maya Zolty, Aviva Azriel, Donato Tedesco, Ben-Zion Levi, MafK Mediates Chromatin Remodeling to Silence IRF8 Expression in Non-immune Cells in a Cell Type-SpecificManner, Journal of Molecular Biology, Volume 432, Issue 16, (2020)

 

  • Kondratyeva, K., Salmon-Divon, M. & Navon-Venezia, S. Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations. Sci Rep 10, 36 (2020).

 

  • Esraa Saadi, Rapita Sood ,Ido Dromi ,Ranin Srouji,Ossama Abu Hatoum,Sharon Tal and Liza Barki-Harrington, Limited Proteolysis of Cyclooxygenase-2 Enhances Cell Proliferation, Int. J. Mol. Sci. 2020, 21(9), 3195

 

  • Karniely, S, Hamed, F, Gelman, B, et al. First isolation of foot and mouth disease virus from wild boars in the Middle East. Transbound Emerg Dis. 2020; 67: 1725– 1729.

 

  • Luria, N., Smith, E., Lachman, O. et al. Isolation and characterization of a novel cripavirus, the first Dicistroviridae family member infecting the cotton mealybug Phenacoccus solenopsis. Arch Virol 165, 1987–1994 (2020).

 

  • Kira, K., Salmon-Divon Mali, & Navon-Venezia Shiri. (2020). Meta-analysis of pandemic 0RW1S34RfeSDcfkexd09rT2escherichia coli1RW1S34RfeSDcfkexd09rT2 ST131 plasmidome proves restricted plasmid-clade associations. Scientific Reports (Nature Publisher Group), 10(1)

 

  • Maymon, M., Sela, N., Shpatz, U. et al. The origin and current situation of Fusarium oxysporum f. sp. cubense tropical race 4 in Israel and the Middle East. Sci Rep 10, 1590 (2020).

 

  • Kamer I, Steuerman Y, Daniel-Meshulam I, et al. Predicting brain metastasis in early stage non-small cell lung cancer patients by gene expression profiling. Transl Lung Cancer Res. 2020;9(3):682-692.

 

  • Michal Levin, Harel Zalts, Natalia Mostov, Tamar Hashimshony, Itai Yanai, Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms, Nucleic Acids Research, Volume 48, Issue 11, 19 June 2020, Pages 5926–5938

 

  • Panov, J.; Simchi, L.; Feuermann, Y.; Kaphzan, H. Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways. Int. J. Mol. Sci. 2020, 21, 4156.

 

  • Klap, C.; Luria, N.; Smith, E.; Hadad, L.; Bakelman, E.; Sela, N.; Belausov, E.; Lachman, O.; Leibman, D.; Dombrovsky, A. Tomato Brown Rugose Fruit Virus Contributes to Enhanced Pepino Mosaic Virus Titers in Tomato Plants. Viruses 2020, 12, 879.

 

  • Benyamini, Hadar et al. ‘Upregulation of Hallmark Muscle Genes Protects Gne M743T/M743T Mutated Knock-In Mice From Kidney and Muscle Phenotype’. 1 Jan. 2020 : 119 – 136.

 

  • Irina Langier Goncalves, Sharon Tal, Liza Barki-Harrington, Amir Sapir, Conserved statin-mediated activation of the p38-MAPK pathway protects Caenorhabditis elegans from the cholesterol-independent effects of statins, Molecular Metabolism (2020)

 

  • Talia Levitas-Djerbi, Dana Sagi, Ilana Lebenthal-Loinger, Tali Lerer-Goldshtein, Lior Appelbaum. Neurotensin Enhances Locomotor Activity and Arousal and Inhibits Melanin-Concentrating Hormone Signaling (2020)

 

  • Anavy, L., Vaknin, I., Atar, O. et al. Data storage in DNA with fewer synthesis cycles using composite DNA letters. Nat Biotechnol 37, 1229–1236 (2019).

 

  • Neta Luria, Elisheva Smith, Noa Sela, Amnon Koren, Oded Lachman, and Aviv Dombrovsky, Insights Into a Watermelon Virome Contribute to Monitoring Distribution of Whitefly-Borne Viruses, Phytobiomes Journal 2019 3:1, 61-70

 

  • Anastasya Birger, Israel Ben-Dor, Miri Ottolenghi et al. Human iPSC-derived astrocytes from ALS patients with mutated C9ORF72 show increased oxidative stress and neurotoxicity, EBioMedicine, Volume 50, 2019, Pages 274-289, ISSN 2352-3964,

 

  • Feldman, A., Saleh, A., Pnueli, L., Qiao, S., Shlomi, T., Boehm, U. and Melamed, P. (2019), Sensitivity of pituitary gonadotropes to hyperglycemia leads to epigenetic aberrations and reduced follicle‐stimulating hormone levels. The FASEB Journal, 33: 1020-1032.

 

  • Nitzan Tali, Kokou Fotini, Doron-Faigenboim Adi et al. Transcriptome Analysis Reveals Common and Differential Response to Low Temperature Exposure Between Tolerant and Sensitive Blue Tilapia (Oreochromis aureus) Frontiers in Genetics, VOLUME 10 , YEAR 2019

 

  • Yanai I., Hashimshony T. (2019) CEL-Seq2—Single-Cell RNA Sequencing by Multiplexed Linear Amplification. In: Proserpio V. (eds) Single Cell Methods. Methods in Molecular Biology, vol 1979. Humana, New York, NY.

 

  • Shaar‐Moshe, L, Hayouka, R, Roessner, U, Peleg, Z. Phenotypic and metabolic plasticity shapes life‐history strategies under combinations of abiotic stresses. Plant Direct. 2019; 3: 1-13

 

  • Hadad L, Luria N, Smith E, Sela N, Lachman O, Dombrovsky A. Lettuce Chlorosis Virus Disease: A New Threat to Cannabis Production. Viruses. 2019; 11(9):802.

 

  • Beate Kaufmann, Or Willinger, Noa Eden, Lisa Kermas, Leon Anavy, Oz Solomon, Orna Atar, Zohar Yakhini, Sarah Goldberg, Roee Amit. Identifying triplex binding rules in vitro leads to creation of a new synthetic regulatory tool in vivo. bioRxiv (2019).12.25.888362;

 

  • Michal Werbner, Yiftah Barsheshet, Nir Werbner, Mor Zigdon, Itamar Averbuch, Oren Ziv, Boris Brant, Evan Elliott, Shachaf Gelberg, Moran Titelbaum, Omry Koren, Orly Avni. Social-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper Cells. mSystems May 2019, 4 (4) e00292-18;

 

  • Glaich, O., Parikh, S., Bell, R.E. et al. DNA methylation directs microRNA biogenesis in mammalian cells. Nat Commun 10, 5657 (2019

 

  • Levin, S.; Sela, N.; Erez, T.; Nestel, D.; Pettis, J.; Neumann, P.; Chejanovsky, N. New Viruses from the Ectoparasite Mite Varroa destructor Infesting Apis mellifera and Apis cerana. Viruses 2019, 11, 94.

 

  • Ofri Levi,Yoav Arava, mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels, May 17, 2019

 

  • Lukić, I., Getselter, D., Ziv, O. et al. Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior. Transl Psychiatry 9, 133 (2019).

 

  • Akiva Shalit-Kaneh, Tamar Eviatar-Ribak, Guy Horev, Naomi Suss, Roni Aloni, Yuval Eshed, Eliezer Lifschitz. The flowering hormone florigen accelerates secondary cell wall biogenesis to harmonize vascular maturation with reproductive development. Proceedings of the National Academy of Sciences Aug 2019, 116 (32) 16127-16136;

 

  • Haas Roni, Horev Guy, Lipkin Ehud, Kesten Inbar, Portnoy Maya, Buhnik-Rosenblau Keren, Soller Morris, Kashi Yechezkel. Mapping Ethanol Tolerance in Budding Yeast Reveals High Genetic Variation in a Wild Isolate(2019) Frontiers in Genetics

 

  • Hadar Reichman, Michal Itan, Perri Rozenberg, Tal Yarmolovski, Eli Brazowski, Chen Varol, Nathan Gluck, Shiran Shapira, Nadir Arber, Udi Qimron, Danielle Karo-Atar, James J. Lee and Ariel Munitz. Activated Eosinophils Exert Antitumorigenic Activities in Colorectal Cancer Cancer Immunol Res March 1 2019 (7) (3) 388-400;

 

  • Leron Katsir, Ruan Zhepu, Alon Piasezky, Jiandong Jiang, Noa Sela, Shiri Freilich, Ofir Bahar. Genome Sequence of “Candidatus Carsonella ruddii” Strain BT from the Psyllid Bactericera trigonica Genome Announcements Jan 2018, 6 (4) e01466-17;

 

  • Segal, T.; Salmon-Divon, M.; Gerlitz, G. The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations. Cells 2018, 7, 205.

 

  • Katsir Leron, Zhepu Ruan, Santos Garcia Diego, Piasezky Alon, Jiang Jiandong, Sela Noa, Freilich Shiri, Bahar Ofir (2018) Genome Analysis of Haplotype D of Candidatus Liberibacter Solanacearum, Frontiers in Microbiology.

 

  • Leon Anavy, Inbal Vaknin, Orna Atar, Roee Amit, Zohar Yakhini. (2018) Improved DNA based storage capacity and fidelity using composite DNA letters. bioRxiv 433524;

 

  • Shammai, A., Petreikov, M., Yeselson, Y., Faigenboim, A., Moy‐Komemi, M., Cohen, S., Cohen, D., Besaulov, E., Efrati, A., Houminer, N., Bar, M., Ast, T., Schuldiner, M., Klemens, P., Neuhaus, E., Baxter, C.J., Rickett, D., Bonnet, J., White, R., Giovannoni, J.J., Levin, I. and Schaffer, A. (2018), Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit. Plant J, 96: 343-357.

 

  • Tamar Segal, Mali Salmon-Divon, Gabi Gerlitz. (2018) The heterochromatin landscape in migrating cells and the importance of H3K27me3 for migration-associated transcriptional changes bioRxiv 344887

 

  • Arafat, H., Alamaru, A., Gissi, C. et al. Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida. BMC Evol Biol 18, 65 (2018).

 

  • Khateb, S., Kowalewski, B., Bedoni, N. et al. A homozygous founder missense variant in arylsulfatase G abolishes its enzymatic activity causing atypical Usher syndrome in humans. Genet Med 20, 1004–1012 (2018).

 

  • Shenkar, N., Shmuel, Y. & Huchon, D. The invasive ascidian Ciona robusta recorded from a Red Sea marina. Mar Biodiv 48, 2211–2214 (2018

 

  • Dalal, V., Dagan, S., Friedlander, G. et al. Transcriptome analysis highlights nuclear control of chloroplast development in the shoot apex. Sci Rep 8, 8881 (2018).

 

  • Arie Ryvkin, Haim Ashkenazy, Yael Weiss-Ottolenghi, Chen Piller, Tal Pupko, Jonathan M Gershoni, Phage display peptide libraries: deviations from randomness and correctives, Nucleic Acids Research, Volume 46, Issue 9, 18 May 2018, Page e52

 

  • Enav, H., Kirzner, S., Lindell, D. et al. Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nat Commun 9, 4698 (2018

 

  • Reizel, Y., Sabag, O., Skversky, Y. et al. Postnatal DNA demethylation and its role in tissue maturation. Nat Commun 9, 2040 (2018).

 

  • Amar Pal Singh, Yulia Fridman, Neta Holland, Michal Ackerman-Lavert, Rani Zananiri, Yvon Jaillais, Arnon Henn, Sigal Savaldi-Goldstein, Interdependent Nutrient Availability and Steroid Hormone Signals Facilitate Root Growth Plasticity, Developmental Cell,

 

  • Philipp H. Schiffer, Avital L. Polsky, Alison G. Cole, Julia I. R. Camps, Michael Kroiher, David H. Silver, Vladislav Grishkevich, Leon Anavy, Georgios Koutsovoulos, Tamar Hashimshony, Itai Yanai (2018) The gene regulatory program of Acrobeloides nanus reveals conservation of phylum-specific expression. Proceedings of the National Academy of Sciences Apr 2018, 115 (17) 4459-4464;

 

  • Ushakov, K., Koffler-Brill, T., Rom, A. et al. Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems. Sci Rep 7, 8637 (2017).

 

  • Ginzburg, N, Cohen, M, Chipman, AD. Factors involved in early polarization of the anterior‐posterior axis in the milkweed bug Oncopeltus fasciatus. Genesis. 2017; 55:e23027.

 

  • Schatz, D., Rosenwasser, S., Malitsky, S. et al. Communication via extracellular vesicles enhances viral infection of a cosmopolitan alga. Nat Microbiol 2, 1485–1492 (2017).

 

  • Haramati, O., Brodov, A., Yelin, I. et al. Identification and characterization of roles for Puf1 and Puf2 proteins in the yeast response to high calcium. Sci Rep 7, 3037 (2017).

 

  • Sarit Avrani, Evgeni Bolotin, Sophia Katz, Ruth Hershberg, Rapid Genetic Adaptation during the First Four Months of Survival under Resource Exhaustion, Molecular Biology and Evolution, Volume 34, Issue 7, July 2017, Pages 1758–1769

 

  • Zalts, H., Yanai, I. Developmental constraints shape the evolution of the nematode mid-developmental transition. Nat Ecol Evol 1, 0113 (2017).

 

  • Schwartz, D., Lindell, D. Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them. ISME J 11, 1836–1851 (2017).

 

  • Eliash, N., Singh, N.K., Thangarajan, S. et al. Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis. Sci Rep 7, 13091 (2017).

 

  • Liran Dray, Moran Neuhof, Arik Diamant & Dorothée Huchon (2016) The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae), Mitochondrial DNA Part A, 27:1, 781-782

 

  • Trainin, T., Zohar, M., Shimoni-Shor, E. et al. A Unique haplotype found in apple accessions exhibiting early bud-break could serve as a marker for breeding apples with low chilling requirements. Mol Breeding 36, 158 (2016).

 

  • Levin, M., Anavy, L., Cole, A. et al. The mid-developmental transition and the evolution of animal body plans. Nature 531, 637–641 (2016).

 

  • Liran Dray, Moran Neuhof, Arik Diamant & Dorothée Huchon (2016) The complete mitochondrial genome of the devil firefish Pterois miles (Bennett, 1828) (Scorpaenidae), Mitochondrial DNA Part A, 27:1, 783-784

 

  • Yoram Keness, Naiel Bisharat. Draft Genome Sequences of Streptococcus pneumoniae with High-Level Resistance to Respiratory Fluoroquinolones Genome Announcements Mar 2016, 4 (2) e00181-16

 

  • Eran Carasso, Mali Salmon-Divon, Yehuda Carmeli, Ehud Banin, Shiri Navon-Venezia. Draft Genome Sequences of Two Multidrug-Resistant Extended-Spectrum-β-Lactamase-Producing Klebsiella pneumoniae Strains Causing Bloodstream Infections Genome Announcements Jan 2016, 4 (1) e01533-15

 

  • Hashimshony, T., Senderovich, N., Avital, G. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol 17, 77 (2016).

 

  • Levin, S., Sela, N. & Chejanovsky, N. Two novel viruses associated with the Apis mellifera pathogenic mite Varroa destructor. Sci Rep 6, 37710 (2016).

 

  • Shomer Inna, Avisar Alon, Desai Prerak, Azriel Shalhevet et al. Genetic and Phenotypic Characterization of a Salmonella enterica serovar Enteritidis Emerging Strain with Superior Intra-macrophage Replication Phenotype. Frontiers in Microbiology, VOLUME=7 (2016)

 

  • Golan Yelena, Shirron Natali, Avni Avishi, Shmoish Michael, Gepstein Shimon. Cytokinins Induce Transcriptional Reprograming and Improve Arabidopsis Plant Performance under Drought and Salt Stress Conditions.Frontiers in Environmental Science (2016)

 

  • Bracha Shraibman, Dganit Melamed Kadosh, Eilon Barnea, Arie Admon. Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy. Molecular & Cellular Proteomics September 1, 2016, First published on July 13, 2016, 15 (9) 3058-3070

 

  • Bracha Shraibman, Dganit Melamed Kadosh, Eilon Barnea, Arie Admon. HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy. Molecular & Cellular Proteomics July 13, 2016, mcp.M116.060350

 

  • Noa Shenkar, Gil Koplovitz, Liran Dray, Carmela Gissi, Dorothée Huchon, Back to solitude: Solving the phylogenetic position of the Diazonidae using molecular and developmental characters, Molecular Phylogenetics and Evolution, 2016

 

  • Gili Aviv, Galia Rahav, Ohad Gal-Mor (2016) Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm-Blooded Hosts. mBio Sep 2016, 7 (5) e01395-16

 

  • Shahi, P., Trebicz-Geffen, M., Nagaraja, S. et al. N-acetyl ornithine deacetylase is a moonlighting protein and is involved in the adaptation of Entamoeba histolytica to nitrosative stress. Sci Rep 6, 36323 (2016).

 

  • Joao Gatica, Vijay Tripathi, Stefan Green, Celia M. Manaia, Thomas Berendonk, Damiano Cacace, Christophe Merlin, Norbert Kreuzinger, Thomas Schwartz, Despo Fatta-Kassinos, Luigi Rizzo, Carsten U. Schwermer, Hemda Garelick, Edouard Jurkevitch, and Eddie Cytryn. High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments Environmental Science & Technology 2016 50 (21), 11825-11836

 

  • Itay Valenci, Lital Yonai, Dan Bar-Yaacov, Dan Mishmar, Anat Ben-Zvi, Parkin modulates heteroplasmy of truncated mtDNA in Caenorhabditis elegans, Mitochondrion, volume 20, 2015, Pages 64-70, ISSN 1567-7249

 

  • Weinberg-Shukron A, Abu-Libdeh A, Zhadeh F, et alCombined mineralocorticoid and glucocorticoid deficiency is caused by a novel founder nicotinamide nucleotide transhydrogenase mutation that alters mitochondrial morphology and increases oxidative stressJournal of Medical Genetics 2015;52:636-641.

 

  • Hashimshony, T., Feder, M., Levin, M. et al. Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature 519, 219–222 (2015).

 

  • Sarit Avrani and Debbie Lindell. Convergent evolution toward an improved growth rate and a reduced resistance range in Prochlorococcus strains resistant to phage. PNAS April 28, 2015 112 (17) E2191-E2200; first published April 14, 2015

 

  • Sally Chang, Moran Neuhof, Nimrod D. Rubinstein, Arik Diamant, Hervé Philippe, Dorothée Huchon, Paulyn Cartwright. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. PNAS December 1, 2015 112 (48) 14912-14917; first published November 16, 2015

 

  • Koton Yael, Gordon Michal, Chalifa-Caspi Vered, Bisharat Naiel. Comparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships (2015) Frontiers in Microbiology.

 

  • Yael Koton, Saleh Eghbaria, Michal Gordon, Vered Chalifa-Caspi, Naiel Bisharat. Draft Genome Sequence of Fish Pathogenic Vibrio vulnificus Biotype 2, Genome Announcements Nov 2014, 2 (6) e01224-14

 

  • Leon Anavy, Michal Levin, Sally Khair et al. BLIND ordering of large-scale transcriptomic developmental timecourses. Development 2014 141: 1161-1166;

 

  • Normand R., Yanai I. (2013) An Introduction to High-Throughput Sequencing Experiments: Design and Bioinformatics Analysis. In: Shomron N. (eds) Deep Sequencing Data Analysis. Methods in Molecular Biology (Methods and Protocols), vol 1038. Humana Press, Totowa, NJ.

 

  • Levin L, Bar-Yaacov D, Bouskila A, Chorev M, Carmel L, Mishmar D. LEMONS–A tool for the identification of splice junctions in transcriptomes of organisms lacking reference genomes. PLoS one. 10(11), e0143329 (November 2015)

 

  • Zou H, Tzarfati R, Hübner S, Krugman T, Fahima T, Abbo S, Saranga Y, Korol AB. Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars. BMC Genomics. 16, 777 (October 2015)

 

  • Kravchik M, Damodharan S, Stav R, Arazi T. Generation and characterization of a tomato DCL3-silencing mutant. Plant Science. 221-222, 81-89 (May 2014)

 

  • Mandel T, Moreau F, Kutsher Y, Fletcher JC, Carles CC, Eshed Williams L. The ERECTA receptor kinase regulates Arapidopsis shoot apical meristem size, phyllotaxy and floral meristem identity. Development. 141(4), 830-841 (February 2014)

 

  • 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. 29(11), 1455-7 (June 2013)

 

  • Bar-Yaacov D, Avital G, Levin L, Richards AL, Hachen N, Rebolledo Jaramillo B, Nekrutenko A, Zarivach R, Mishmar D. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA. Genome Res. 23(11), 1789-96 (November 2013)

 

  • 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. 8, 587 (June 2012)

 

  • 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. 109(6), 2037-42 (February 2012)

 

  • Hashimshony T, Wagner F, Sher N, and Yanai I. CEL-Seq: Single cell RNA-Seq by multiplexed linear amplification. Cell Reports. 2(3), 666-673 (September 2012)