Academic literature on the topic 'Transcriptome size'
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Journal articles on the topic "Transcriptome size":
Mora-Márquez, Fernando, José Luis Vázquez-Poletti, Víctor Chano, Carmen Collada, Álvaro Soto, and Unai López de Heredia. "Hardware Performance Evaluation of De novo Transcriptome Assembly Software in Amazon Elastic Compute Cloud." Current Bioinformatics 15, no. 5 (October 14, 2020): 420–30. http://dx.doi.org/10.2174/1574893615666191219095817.
Ikeda, Hiroki, Shintaro Miyao, So Nagaoka, Tomoya Takashima, Sze-Ming Law, Takuya Yamamoto, and Kazuki Kurimoto. "High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis." Life Science Alliance 6, no. 11 (September 18, 2023): e202301929. http://dx.doi.org/10.26508/lsa.202301929.
Gonzalez-Ibeas, Daniel, Pedro J. Martinez-Garcia, Randi A. Famula, Annette Delfino-Mix, Kristian A. Stevens, Carol A. Loopstra, Charles H. Langley, David B. Neale, and Jill L. Wegrzyn. "Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)." G3 Genes|Genomes|Genetics 6, no. 12 (December 1, 2016): 3787–802. http://dx.doi.org/10.1534/g3.116.032805.
Stern, M. D., S. V. Anisimov, and K. R. Boheler. "Can transcriptome size be estimated from SAGE catalogs?" Bioinformatics 19, no. 4 (March 1, 2003): 443–48. http://dx.doi.org/10.1093/bioinformatics/btg018.
Beisser, Daniela, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, and Jens Boenigk. "Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes." PeerJ 5 (January 10, 2017): e2832. http://dx.doi.org/10.7717/peerj.2832.
Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (December 28, 2017): 16. http://dx.doi.org/10.12688/gatesopenres.12783.1.
Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae)." Gates Open Research 1 (February 13, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.2.
Sseruwagi, Peter, James Wainaina, Joseph Ndunguru, Robooni Tumuhimbise, Fred Tairo, Jian-Yang Guo, Alice Vrielink, et al. "The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition." Gates Open Research 1 (March 8, 2018): 16. http://dx.doi.org/10.12688/gatesopenres.12783.3.
Caurcel, Carlos, Dominik R. Laetsch, Richard Challis, Sujai Kumar, Karim Gharbi, and Mark Blaxter. "MolluscDB: a genome and transcriptome database for molluscs." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1825 (April 5, 2021): 20200157. http://dx.doi.org/10.1098/rstb.2020.0157.
Jensen, Michael Krogh, Josef Korbinian Vogt, Simon Bressendorff, Andaine Seguin-Orlando, Morten Petersen, Thomas Sicheritz-Pontén, and John Mundy. "Transcriptome and Genome Size Analysis of the Venus Flytrap." PLOS ONE 10, no. 4 (April 17, 2015): e0123887. http://dx.doi.org/10.1371/journal.pone.0123887.
Dissertations / Theses on the topic "Transcriptome size":
Schivre, Geoffrey. "Transcriptome augmentation, Polycomb-mediated chromatin dynamics and their links to metabolism during Arabidopsis thaliana photomorphogenesis." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASB014.
Light fuels plant photosynthesis providing the energy source for growth. Light intensity and quality also convey essential information on the plant's immediate surroundings, which are integrated through multiple light sensors, the photoreceptors, enabling developmental and physiological adaptations. The photomorphogenic transition, or de-etiolation, occurs when a young germinating plantlet is exposed to light for the first time, and is one of the most spectacular plant developmental adaptations to light. Seedlings germinating underground, protected from light, undergo an etiolated development, or skotomorphogenesis, during which rapid hypocotyl elongation facilitates plant drilling through the soil, while cotyledon maturation is arrested and the plantlet remains non-photosynthetic. In the absence of photosynthesis, skotomorphogenic growth relies entirely on the plant metabolic reserves, predominantly stored in cotyledons. Upon reaching the soil surface, photoreceptor light sensing triggers the expansion and greening of cotyledons, independently from cell divisions. Inducing chloroplast biogenesis and the acquisition of photosynthesis, this developmental switch marks the transition toward photo-autotrophy. At the molecular scale, cotyledon de-etiolation associates with a specialization of the transcriptome and an intensification of RNA polymerase II (RNA Pol II) activity. At the cytological scale, chromatin rearrangements lead to nucleus enlargement and the condensation of pericentromeric regions in conspicuous heterochromatic foci. Considering that much of these metabolic, cellular, molecular and cytological controls are synchronously achieved during the transition, A. thaliana photomorphogenesis is a model of choice to characterize the interplays between light signaling, gene regulation and chromatin dynamics as well as their link to the plant energetic status. During my thesis, I first contributed to develop an RNA-seq normalization methodology to revisit transcriptome changes in light of the global increase in RNA Pol II activity. This identified a 2-fold increase in transcript abundance during cotyledon photomorphogenesis, which most likely results from the increase in RNA Pol II activity. I further explored the role played by the conserved metabolic sensor Target Of Rapamycin (TOR) in defining the transcriptional regime along with chromatin composition and organization during cotyledon photomorphogenesis. This notably shed a new light on the functional links between the TOR pathway and the homeostasis of a specific histone mark, trimethylation of histone H3 at lysine 27 (H3K27me3), mediated by Polycomb Repressive Complex 2 (PRC2). More precisely, this study revealed that H3K27me3 is less abundant at chromatin in etiolated cotyledons as compared to photomorphogenic ones, a global effect that was further shown here to be sensitive to sugar and TOR signaling. Hence, this work points towards unexpected roles of TOR signaling and the PRC2-regulated mark H3K27me3 in the global regulation of transcription and opens new perspectives on TOR-mediated gene regulation. Future studies aimed at deciphering the role of H3K27me3 homeostasis, especially at specific genes induced by light, should provide new insight on how metabolic signaling interplays with Polycomb-mediated chromatin dynamics and transcription with implications beyond plant photomorphogenesis
Díaz, Blanco Noelia 1975. "Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/380903.
A molts peixos gonocoristes, el sexe és plàstic donat que pot ésser alterat per la influència de factors ambientals. En aquesta tesi, utilitzant el llobarro (Dicentrarchus labrax) com a model, un peix teleosti amb un sistema poligènic de determinació del sexe influït per l'ambient, hem estudiat els efectes de diferents factors ambientals —incloent la disponibilitat d'aliment, temperatures elevades i presència d’estrògens— en el creixement, la diferenciació sexual i el desenvolupament gonadal dels juvenils. L'anàlisi global de l'expressió gènica s'ha realitzat mitjançant un xip d’ADN fet a mida. Hem trobat que, de la mateixa manera que ocorre en els mamífers, el sexe determina el creixement i que les primeres diferències en el creixement vinculades amb el sexe s'estableixen prèviament a l'aparició dels primers marcadors moleculars indicatius del sexe. A més, el transcriptoma de testicles juvenils està influït per un creixement pobre durant la diferenciació sexual, mentre que un subministrament adequat de menjar durant l’etapa juvenil és capaç de rescatar el transcriptoma testicular d’animals amb un pobre creixement previ. Hem trovat que la masculinització observada anteriorment com a resultat de les temperatures elevades està causada per efectes persistents a nivell transcriptòmic, afavorint l'expressió de gens relacionats amb el desenvolupament masculí i disminuint la dels gens relacionats amb el desenvolupament femení. Per contra, l'exposició a estrògens afecta negativament tant als gens relacionats amb el desenvolupament masculí com el femení. És destacable com els patrons d'expressió d'una sèrie de gens relacionats amb la regulació epigenètica de l’expressió gènica mostren graus diferents de dependència a factors genètics, període del desenvolupament i factors ambientals segons la seva categoria funcional.
Tang, Shiyuyun. "Improving algorithms of gene prediction in prokaryotic genomes, metagenomes, and eukaryotic transcriptomes." Diss., Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/54998.
Raborn, R. Taylor. "Genome-wide analysis of transcription initiation and promoter architecture in eukaryotes." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4728.
Colman, Hélène. "Régulations traductionnelles lors de l'infection par le virus de l'hépatite C (VHC)." Nantes, 2010. https://archive.bu.univ-nantes.fr/pollux/show/show?id=867ac444-7efa-4ea8-a33f-89bd65a8dc7d.
The hepatitis C virus (HCV) infection is a major world health problem, since 3% of the world’s population is chronically infected and it can lead to cirrhosis and hepatocellular carcinoma. There is currently no vaccine against this virus and the treatment is inactive for about half of the patients. HCV is a positive sense single strand RNA virus with highly sequence variability. Its translation initiation occurs through an internal ribosome entry site (IRES) in its 5’untranslated region, allowing the ribosome recruitment without the need of all the canonical translation initiation factors. This region is highly structured and is well conserved amongst the viral genotypes. That makes the IRES an attractive target for future therapies. The IRES function is modulated by viral and cellular factors, but the mecanisms of this regulation are not well understood. With the study of natural IRES variants harboring different translationnal efficiencies and cellular tropisms, we have tried to understand some factors (the viral sequence and the cellular proteins acting in trans (ITAFs, IRES Trans Acting Factors)) conditionning the efficiency of HCV translation in hepatocytes. We have also studied the translational modifications of the cellular genes during HCV infection in Huh7 cells harbouring replication of the JHF-1 strain, by comparing the translated transriptome, bound to the ribosomes (polysome) and the free transcriptome. We have shown that the viral infection modulates the translation of genes belonging to specific functional categories (cytoskeleton, translation, mitochondrial metabolism, cell cycle regulation). Some of this regulations could occur via microRNA modulation
Konishi, Atsushi. "Studies on the thermostabilization of reverse transcriptases from Moloney murine leukemia virus and avian myeloblastosis virus." Kyoto University, 2015. http://hdl.handle.net/2433/199340.
0048
新制・課程博士
博士(農学)
甲第19016号
農博第2094号
新制||農||1029(附属図書館)
学位論文||H27||N4898(農学部図書室)
31967
京都大学大学院農学研究科食品生物科学専攻
(主査)教授 保川 清, 教授 河田 照雄, 教授 谷 史人
学位規則第4条第1項該当
Dufour, Emmanuelle. "Interaction de la transcriptase inverse de HIV-1 avec son tRNA amorce : études biochimiques et détermination du site de liaison de l'enzyme à l'extrémité 3' du tRNA-Lys3." Bordeaux 2, 1997. http://www.theses.fr/1997BOR28523.
Borcier, Elodie. "Vulnérabilité de populations de poissons (Platichthys flesus) face aux multi-stress en estuaires : une approche intégrative Bioenergetic transcriptomic responses of European flounder (Platichthys flesus) populations in contrasted environments: impacts of pollution and global warming, in Journal of Xenobiotics 6(6586), 2016." Thesis, Brest, 2019. http://www.theses.fr/2019BRES0020.
The vulnerability level of natural flounder populations was assessed, integrating responses at the molecular, individual and population levels. A multi-estuary approach was carried out on the fish responses in contrasted environments (thermal stress: Mondego estuary; chemical stress: Seine estuary; moderately stressed systems: Bay of Douarnenez, Vilaine and Canche estuaries).A demo-genetic approach, considering the variability of microsatellites, underlined a reduced effective size for the southern peripheral population of the Mondego estuary, thus characterized by a high ecological risk.In the Seine population, a reduced interindividual variability was observed considering the expression levels of genes involved in bioenergetics (COII, 12S); this pattern could explain the reduced ability of this population to cope with another stress (ie thermal stress).Signatures of adaptation to pollutants (high level of energetic metabolism, management of oxidative stress, modification of membrane phopholipids) were observed in the Seine, but could be very costly (reduced muscle energetic reserve). Thus, we consider that the Seine population is displaying a high ecological risk.A one month fish caging experiment was conducted in the Seine estuary. Fish responses were analyzed by proteomic; they underlined a decreasing pollution gradient from upstream to downstream, and thus allowed to characterize the ecological status of the estuary atmicroscale.This study highlighted pertinent tools for the assessment of flounder population vulnerability and for the exploration of the ecological status of estuarine systems
Noiret, Maud. "Étude des protéines de liaison à l'ARN des familles PTB et ARE-BP au cours du développement chez le xénope." Phd thesis, Rennes 1, 2012. https://ecm.univ-rennes1.fr/nuxeo/site/esupversions/a420494c-0828-469e-bd2f-60a70118ef9f.
My work has focused on the function of RNA binding-proteins during early development in Xenopus. I first documented the expression pattern of members of the AU-rich element binding protein (ARE-BP) and of the polypyrimidin tract binding protein (PTB) families during development. Study of the expression patterns of five members of the ARE-BP family (AUF1, KSRP, HuR, TIA1 and TTP) has underlined the broad role and the redundancy of expression of four of these proteins. Conversely, the highly specific expression pattern of TTP in macrophages suggests a potential function for this ARE-BP in hematopoietic development. My study of the PTB family (PTBP1, PTBP2 and PTBP3), has showed that each paralog presents a unique pattern of expression emphasizing their diverse functions during development. From previous work in the lab we knew that morpholino mediated knockdown of both PTBP1 and EXOSC9, a component of the RNA exosome, generated similar defects in the dorsal fin morphology. To identify the molecular origin of these defects we realized the transcriptome analysis by high throughput sequencing (RNA-Seq) of both morphants embryos. I produced cDNA libraries of control and morphant embryos and the sequencing was performed at the Genoscope. Analysis of a known PTBP1 target showed that even modest modifications of alternative splicing could be detected in our data sets. In addition, because these defects are not found in the EXOSC9 morphants it validated its use as an additional screen to exclude splicing events not involved in the epidermal defects. Identification of RNA whose deregulation may be involved in the fin phenotype is currently under study for a set of candidate genes
Boukharta, Lars. "Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212103.
Books on the topic "Transcriptome size":
Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima, and Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.
Grant, Warren, and Martin Scott-Brown. Principles of oncogenesis. Edited by Patrick Davey and David Sprigings. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199568741.003.0322.
Book chapters on the topic "Transcriptome size":
Feldman, Moshe, and Avraham A. Levy. "Genome Structure of Triticeae Species." In Wheat Evolution and Domestication, 43–70. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-30175-9_3.
Rungrotmongkol, Thanyada, Nadtanet Nunthaboot, Ornjira Aruksakunwong, and Supot Hannongbua. "HIV-1 Reverse Transcriptase – Computational Studies on the Polymerase Active Site." In Encyclopedia of Biophysics, 989–92. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_240.
de Souza Moreira, Leonora Rios, Camila Louly Corrêa, Helder Andrey Rocha Gomes, Glaucia Emy Okida Midorikawa, Robert Neil Gerard Miller, and Edivaldo Ximenes Ferreira Filho. "The Role of Fungal Transcriptome Analysis and Side-Chain Hydrolyzing Enzymes in Sugarcane Bagasse Breakdown." In Advances of Basic Science for Second Generation Bioethanol from Sugarcane, 81–106. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-49826-3_6.
Swaminathan, Angavai, Paul F. Harrison, Thomas Preiss, and Traude H. Beilharz. "PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes." In Methods in Molecular Biology, 141–64. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9736-7_9.
R. Sripathi, Venkateswara, Varsha C. Anche, Zachary B. Gossett, and Lloyd T. Walker. "Recent Applications of RNA Sequencing in Food and Agriculture." In Applications of RNA-Seq in Biology and Medicine [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97500.
Lata, Suman, Ramesh Kumar Yadav, and B. S. Tomar. "Genomic Tools to Accelerate Improvement in Okra (Abelmoschus esculentus)." In Landraces - Traditional Variety and Natural Breed. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97005.
"Non-nucleoside reverse transcriptase inhibitors (NNRTIs)." In Meyler's Side Effects of Drugs, 234–35. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-444-53717-1.01164-1.
"Nucleoside analogue reverse transcriptase inhibitors (NRTIs)." In Meyler's Side Effects of Drugs, 280–86. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-444-53717-1.01173-2.
Pervaiz, Saima, and Shehryar Awan. "Molecular Mechanisms of Human Immunodeficiency Virus Resistance to Antiretroviral." In Fundamentals of Cellular and Molecular Biology, 225–41. BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/9789815238037124010020.
"Non-nucleoside reverse transcriptase inhibitors (NNRTIs)." In Meyler's Side Effects of Drugs: The International Encyclopedia of Adverse Drug Reactions and Interactions, 2553–55. Elsevier, 2006. http://dx.doi.org/10.1016/b0-44-451005-2/00768-3.
Conference papers on the topic "Transcriptome size":
BIROL, INANÇ, ANTHONY RAYMOND, READMAN CHIU, KA MING NIP, SHAUN D. JACKMAN, MAAYAN KREITZMAN, T. RODERICK DOCKING, CATHERINE A. ENNIS, A. GORDON ROBERTSON, and ALY KARSAN. "KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2014. http://dx.doi.org/10.1142/9789814644730_0034.
Gebim, Anna Beatriz Silva, RENATO MASSAHARU HASSUNUMA, and PATRÍCIA CARVALHO GARCIA. "AÇÃO DA TELOMERASE NA REPLICAÇÃO DO DNA TELOMÉRICO." In III Congresso Brasileiro de Ciências Biologicas. Revista Multidisciplinar de Educação e Meio Ambiente, 2022. http://dx.doi.org/10.51189/iii-conbracib/6602.
Garcia, Luan Ednelson Soares, Fábio Aparecido Da Silva, Renato Massaharu Hassunuma, and Patrícia Carvalho Garcia. "TELOMERASE: UMA SOLUÇÃO BIOQUÍMICA PARA O ENVELHECIMENTO?" In II Congresso Brasileiro de Bioquímica Humana On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/conbraqui/19.
Raghunathan, Megha, Elliot Imler, Christy Trejo, Peter Shepard, and Bruce Seligmann. "Abstract LB-097: Whole transcriptome dose response profiling enables characterization of efficacy, metabolism, side effects and cytotoxicity in a single comprehensive assay." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-lb-097.
Raghunathan, Megha, Elliot Imler, Christy Trejo, Peter Shepard, and Bruce Seligmann. "Abstract LB-097: Whole transcriptome dose response profiling enables characterization of efficacy, metabolism, side effects and cytotoxicity in a single comprehensive assay." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-lb-097.
Reports on the topic "Transcriptome size":
Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.
Sherman, A., D. N. Kuhn, Y. Cohen, R. Ophir, and R. Goenaga. Exploring the polyembryonic seed trait in mango as a basis for a biotechnology platform for fruit tree crops. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134176.bard.
Wisniewski, Michael, Samir Droby, John Norelli, Dov Prusky, and Vera Hershkovitz. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the identification of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597928.bard.
Crowley, David E., Dror Minz, and Yitzhak Hadar. Shaping Plant Beneficial Rhizosphere Communities. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7594387.bard.
Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.
Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.
Eshed-Williams, Leor, and Daniel Zilberman. Genetic and cellular networks regulating cell fate at the shoot apical meristem. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699862.bard.
Bloch, G., and H. S. Woodard. regulation of size related division of labor in a key pollinator and its impact on crop pollination efficacy. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134168.bard.
Fluhr, Robert, and Maor Bar-Peled. Novel Lectin Controls Wound-responses in Arabidopsis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697123.bard.
Iudicone, Daniele, and Marina Montresor. Omics community protocols. EuroSea, 2023. http://dx.doi.org/10.3289/eurosea_d3.19.