Publications

Biomedicine and Health

• Neuronal Systems

  Principal Investigator: Claude Desplan 
  

  • Li, S. A., H. G. Li, N. Shoji, C. Desplan and Y. D. Chen (2023). "Protocol for replacing coding intronic MiMIC and CRIMIC lines with T2A-split-GAL4 lines in Drosophila using genetic crosses." STAR Protoc 4(4): 102706.
  • Chen, Y. D., Y. C. Chen, R. Rajesh, N. Shoji, M. Jacy, H. Lacin, T. Erclik and C. Desplan (2023). "Using single-cell RNA sequencing to generate predictive cell-type-specific split-GAL4 reagents throughout development." Proc Natl Acad Sci U S A 120(32): e2307451120.
  • El-Danaf, R. N., R. Rajesh and C. Desplan (2022). "Temporal regulation of neural diversity in Drosophila and vertebrates." Semin Cell Dev Biol.
  • Konstantinides, N., I. Holguera, A. M. Rossi, A. Escobar, L. Dudragne, Y.-C. Chen, T. N. Tran, A. M. Martínez Jaimes, M. N. Özel, F. Simon, Z. Shao, N. M. Tsankova, J. F. Fullard, U. Walldorf, P. Roussos and C. Desplan (2022). "A complete temporal transcription factor series in the fly visual system." Nature.
  • Malin, J. and C. Desplan (2021). "Neural specification, targeting, and circuit formation during visual system assembly." Proc Natl Acad Sci USA 118(28).
  • Özel, M. N., F. Simon, S. Jafari, I. Holguera, Y.-C. Chen, N. Benhra, R. N. El-Danaf, K. Kapuralin, J. A. Malin, N. Konstantinides and C. Desplan (2020). "Neuronal diversity and convergence in a visual system developmental atlas." Nature 589(7840): 88-95. 
    
  • Hazzouri, K. M., N. Sudalaimuthuasari, B. Kundu, D. Nelson, M. A. Al-Deeb, A. Le Mansour, J. J. Spencer, C. Desplan and K. M. A. Amiri (2020). "The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface." Commun Biol 3(1): 323.
    
  • Pinto-Teixeira, F., C. Koo, A. M. Rossi, N. Neriec, C. Bertet, X. Li, A. Del-Valle-Rodriguez and C. Desplan (2018). "Development of Concurrent Retinotopic Maps in the Fly Motion Detection Circuit." Cell 173(2): 485-498 e411.
  • Konstantinides, N., K. Kapuralin, C. Fadil, L. Barboza, R. Satija and C. Desplan (2018). "Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features." Cell 174(3): 622-635 e613.
  • Konstantinides N., S. Degabriel and C. Desplan (2018). "Neuro-evo-devo in the single cell sequencing era." Curr Opin Syst Biol 11: 32-40.
  • Holguera I. and C. Desplan (2018). "Neuronal specification in space and time." Science 362(6411): 176-180.
  • Rossi A. M., V. M. Fernandes and C. Desplan (2017). "Timing temporal transitions during brain development." Curr Opin Neurobiol 42: 84-92.
  • Perry, M., N. Konstantinides, F. Pinto-Teixeira and C. Desplan (2017). "Generation and Evolution of Neural Cell Types and Circuits: Insights from the Drosophila Visual System." Annu Rev Genet 51: 501-527.
  • Erclik, T., X. Li, M. Courgeon, C. Bertet, Z. Chen, R. Baumert, J. Ng, C. Koo, U. Arain, R. Behnia, A. del Valle Rodriguez, L. Senderowicz, N. Negre, K. P. White and C. Desplan (2017). "Integration of temporal and spatial patterning generates neural diversity." Nature 541(7637): 365-370.
    
  • Pinto-Teixeira, F., N. Konstantinides and C. Desplan (2016). "Programmed cell death acts at different stages of Drosophila neurodevelopment to shape the central nervous system." FEBS Lett 590(15): 2435-2453.
  • Pinto-Teixeira, F. and C. Desplan (2016). "Re-utilization of a transcription factor." Elife 5.
  • Perry, M., M. Kinoshita, G. Saldi, L. Huo, K. Arikawa and C. Desplan (2016). "Molecular logic behind the three-way stochastic choices that expand butterfly colour vision." Nature 535(7611): 280-284.
    
  • Neriec, N. and C. Desplan (2016). "From the Eye to the Brain: Development of the Drosophila Visual System." Curr Top Dev Biol 116: 247-271.
  • Chen, Z., A. Del Valle Rodriguez, X. Li, T. Erclik, V. M. Fernandes and C. Desplan (2016). "A Unique Class of Neural Progenitors in the Drosophila Optic Lobe Generates Both Migrating Neurons and Glia." Cell Rep 15(4): 774-786.
  • Wernet, M. F. and C. Desplan (2015). "Brain Wiring in the Fourth Dimension." Cell 162(1): 20-22.
  • Courgeon M., N. Konstantinides and C. Desplan (2015). "Cell competition: dying for communal interest." Curr Biol 25(8): R339-341.
  • Wernet, M. F., A. D. Huberman and C. Desplan (2014). "So many pieces, one puzzle: cell type specification and visual circuitry in flies and mice." Genes Dev 28(23): 2565-2584.
    
  • Pinto-Teixeira, F. and C. Desplan (2014). "Notch activity in neural progenitors coordinates cytokinesis and asymmetric differentiation." Sci Signal 7(348): pe26
    
  • Neriec, N. and C. Desplan (2014). "Different ways to make neurons: parallel evolution in the SoxB family." Genome Biol 15(5): 116.
  • Bertet C., X. Li, T. Erclik, M. Cavey, B. Wells and C. Desplan (2014). "Temporal Patterning of Neuroblasts Controls Notch-Mediated Cell Survival through Regulation of Hid or Reaper." Cell 158 (5): 1173-1186.
  • Wernet, M. F., M. W. Perry and C. Desplan (2015). "The evolutionary diversity of insect retinal mosaics: common design principles and emerging molecular logic." Trends Genet 31(6): 316-328.
    
  • Behnia, R., D. A. Clark, A. G. Carter, T. R. Clandinin and C. Desplan (2014). "Processing properties of ON and OFF pathways for Drosophila motion detection." Nature 512(7515): 427-430.
    
  • Perry, M. and C. Desplan (2013). "Opposing feedbacks on Ras tune receptor tyrosine kinase signaling." Sci Signal 6(300): pe35.

  Publications by Group Members

  • Nourreddine, S., G. Lavoie, J. Paradis, K. Ben El Kadhi, A. Meant, L. Aubert, B. Grondin, P. Gendron, B. Chabot, M. Bouvier, S. Carreno and P. P. Roux (2020). "NF45 and NF90 Regulate Mitotic Gene Expression by Competing with Staufen-Mediated mRNA Decay." Cell Rep 31(7): 107660.
  • Guttenplan, K. A., B. K. Stafford, R. N. El-Danaf, D. I. Adler, A. E. Munch, M. K. Weigel, A. D. Huberman and S. A. Liddelow (2020). "Neurotoxic Reactive Astrocytes Drive Neuronal Death after Retinal Injury." Cell Rep 31(12): 107776.
  • Del Valle Rodriguez, A., M. Cera and J. R. Portillo (2020). "A network approach to analyze neuronal lineage and layer innervation in the Drosophila optic lobes." PLoS One 15(2): e0227897.
  • Carim, S. C., K. Ben El Kadhi, G. Yan, S. T. Sweeney, G. R. Hickson, S. Carreno and M. Lowe (2019). "IPIP27 Coordinates PtdIns(4,5)P2 Homeostasis for Successful Cytokinesis." Curr Biol 29(5): 775-789 e777.
  • Gater, D. L., N. Widatalla, K. Islam, M. AlRaeesi, J. C. M. Teo and Y. E. Pearson (2017). "Quantification of sterol-specific response in human macrophages using automated imaged-based analysis." Lipids Health Dis 16(1): 242.
• Gene Expression in Circadian Neural Networks

  Principal Investigators: Justin Blau and Dipesh Chaudhury

  • Haniffa, S., P. Narain, M. A. Hughes, A. Petković, M. Šušić, V. Mlambo and D. Chaudhury (2023). "Chronic social stress blunts core body temperature and molecular rhythms of Rbm3 and Cirbp in mouse lateral habenula." Open Biol 13(7): 220380.
  • Hackley, C. R., E. O. Mazzoni and J. Blau (2018). "cAMPr: A single-wavelength fluorescent sensor for cyclic AMP." Sci Signal 11(520).
    
  • Lymer, S. and J. Blau (2016). "Do Flies Count Sheep or NMDA Receptors to Go to Sleep?" Cell 165(6): 1310-1311.
  • Cavey, M., B. Collins, C. Bertet and J. Blau (2016). "Circadian rhythms in neuronal activity propagate through output circuits." Nat Neurosci 19(4): 587-595.
  • Petsakou, A., T. P. Sapsis and J. Blau (2015). "Circadian Rhythms in Rho1 Activity Regulate Neuronal Plasticity and Network Hierarchy." Cell 162(4): 823-835.
    
  • Collins, B., H. S. Kaplan, M. Cavey, K. R. Lelito, A. H. Bahle, Z. Zhu, A. M. Macara, G. Roman, O. T. Shafer and J. Blau (2014). "Differentially timed extracellular signals synchronize pacemaker neuron clocks." PLoS Biol 12(9): e1001959.

  Publications by Group Members

  • Liu, H., A. Rastogi, P. Narain, Q. Xu, M. Sabanovic, A. D. Alhammadi, L. Guo, J. L. Cao, H. Zhang, H. Aqel, V. Mlambo, R. Rezgui, B. Radwan and D. Chaudhury (2021). "Blunted diurnal firing in lateral habenula projections to dorsal raphe nucleus and delayed photoentrainment in stress-susceptible mice." PLoS Biol 19(3): e3000709.
• Epigenetic Programming of Neuronal Identity

  Principal Investigators: Piergiorgio Percipalle and Mohammed Al-Sayegh

  • Venit, T., O. Sapkota, W. S. Abdrabou, P. Loganathan, R. Pasricha, S. R. Mahmood, N. H. El Said, S. Sherif, S. Thomas, S. Abdelrazig, S. Amin, D. Bedognetti, Y. Idaghdour, M. Magzoub and P. Percipalle (2023). "Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice." Nat Commun 14(1): 6328.
  • Gallardo-Dodd, C. J., C. Oertlin, J. Record, R. G. Galvani, C. Sommerauer, N. V. Kuznetsov, E. Doukoumopoulos, L. Ali, M. M. S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A. A. Sadova, S. M. Shulgina, V. A. Shmarov, O. V. Kutko, D. D. Vlasova, K. D. Orlova, M. P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S. A. Ponomarev and L. S. Westerberg (2023). "Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells." Sci Adv 9(34): eadg1610.
  • Mahmood, S. R., N. H. E. Said, K. C. Gunsalus and P. Percipalle (2023). "β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation." Genome Biology 24(1): 18.
    
  • Venit, T., O. Sapkota, W. S. Abdrabou, P. Loganathan, R. Pasricha, S. R. Mahmood, N. H. El Said, S. Thomas, Y. Idaghdour, M. Magzoub and P. Percipalle (2022). "Regulation of oxidative phosphorylation by Nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice." bioRxiv: 2022.2006.2030.498328.
  • Mahmood, S. R., N. H. El Said and P. Percipalle (2022). "The Role of Nuclear Actin in Genome Organization and Gene Expression Regulation During Differentiation." Results Probl Cell Differ 70: 607-624.
• Epigenetics of Cancer

  Principal Investigator: Kirsten Sadler Edepli

  • Ajouaou, Y., E. Magnani, B. Madakashira, E. Jenkins and K. C. Sadler (2023). "atm Mutation and Oxidative Stress Enhance the Pre-Cancerous Effects of UHRF1 Overexpression in Zebrafish Livers." Cancers 15(8): 2302.
• Chemical and Functional Genomics

  Principal Investigators: Kristin Gunsalus

  • Gjorgjieva, T., A. Chaloemtoem, T. Shahin, O. Bayaraa, M. M. Dieng, M. Alshaikh, M. Abdalbaqi, J. Del Monte, G. Begum, C. Leonor, V. Manikandan, N. Drou, M. Arshad, M. Arnoux, N. Kumar, A. Jabari, A. Abdulle, G. ElGhazali, R. Ali, S. Y. Shaheen, J. Abdalla, F. Piano, K. C. Gunsalus, H. Daggag, H. Al Nahdi, H. Abuzeid and Y. Idaghdour (2023). "Systems genetics identifies miRNA-mediated regulation of host response in COVID-19." Hum Genomics 17(1): 49.
  • Mahmood, S. R., N. H. E. Said, K. C. Gunsalus and P. Percipalle (2023). "β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation." Genome Biology 24(1): 18.
  • Pearson, Y. E., S. Kremb, G. L. Butterfoss, X. Xie, H. Fahs and K. C. Gunsalus (2022). "A statistical framework for high-content phenotypic profiling using cellular feature distributions." Commun Biol 5(1): 1409.
  • Marnik, E. A., M. V. Almeida, P. G. Cipriani, G. Chung, E. Caspani, E. Karaulanov, H. H. Gan, J. Zinno, I. J. Isolehto, F. Kielisch, F. Butter, C. S. Sharp, R. M. Flanagan, F. X. Bonnet, F. Piano, R. F. Ketting, K. C. Gunsalus and D. L. Updike (2022). "The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline." PLoS Genet 18(6): e1010245.
  • Gan, H. H., J. Zinno, F. Piano and K. C. Gunsalus (2022). "Omicron Spike protein has a positive electrostatic surface that promotes ACE2 recognition and antibody escape." bioRxiv: 2022.2002.2013.480261.[1]
  • Esposito, G., Y. Hunashal, M. Percipalle, T. Venit, M. M. Dieng, F. Fogolari, G. Hassanzadeh, F. Piano, K. C. Gunsalus, Y. Idaghdour and P. Percipalle (2021). "NMR-Based Analysis of Nanobodies to SARS-CoV-2 Nsp9 Reveals a Possible Antiviral Strategy Against COVID-19." Adv Biol (Weinh): e2101113.
  • Murade C. U., S. Chaudhuri, I. Nabti, H. Fahs, F. Refai, X. Xie, Y. E. Pearson, K. C Gunsalus  and G. T Shubeita. (2021). "FRET-Based Probe for High-Throughput DNA Intercalator Drug Discovery and In Vivo Imaging." ACS Sens 6(6): 2233-2240.
    
  • Mahmood, S. R., X. Xie, N. Hosny El Said, T. Venit, K. C. Gunsalus and P. Percipalle (2021). "β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture." Nature Communications 12(1): 5240.
  • Khoury, E., A. Abou Fayad, D. Karam Sarkis, H. Fahs, K. C. Gunsalus and M. Kallassy Awad (2021). "The Microbiome of the Lebanese Wild Apple, Malus trilobata, is a Rich Source of Potential Biocontrol Agents for Fungal Post-harvest Pathogens of Apples." Curr Microbiol 1432-0991.
    
  • Hark H. G., A. Twaddle , B. Marchand , K. C. Gunsalus (2021). "Structural modeling of the SARS-CoV-2 Spike/human ACE2 complex interface can identify high-affinity variants associated with increased transmissibility." jmb 2021.167051.
  • Cipriani, P. G., O. Bay, J. Zinno, M. Gutwein, H. H. Gan, V. K. Mayya, G. Chung, J. X. Chen, H. Fahs, Y. Guan, T. F. Duchaine, M. Selbach, F. Piano and K. C. Gunsalus (2021). "Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules." eLife 10.7554.
  • Xie, X., T. Gjorgjieva, Z. Attieh, M. Dieng, M. Arnoux, M. Khair, Y. Moussa, F. Al Jallaf, N. Rahiman, C. Jackson, L.E. Messery, K. Pamplona, Z. Victoria, M. Zafar, R. Ali, F. Piano, K. C. Gunsalus, and Y. Idaghdour. 2020. "Microfluidic Nano-Scale qPCR enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2." Processes 8, no. 11: 1425.
    
  • Murade C. U., S. Chadhuri, I. Nabita, H. Fahs, F. Refai, K. Gunsalus and G. Shubeita (2020). "A FRET-based Probe for High Throughput DNA Intercalator Drug Discovery and In Vivo Imaging." Biophysical Journal 118(3, Supplement 1): 315a.

  • Gjorgjieva, T., X. Xie, P. Commins, R. Pasricha, S. R. Mahmood, K. C. Gunsalus, P. Naumov and P. Percipalle "Loss of β-Actin Leads to Accelerated Mineralization and Dysregulation of Osteoblast-Differentiation Genes during Osteogenic Reprogramming." Advanced Science 2002261.
  • Solntsev, K. M., S. Schramm, S. Kremb, K. C. Gunsalus and S. A. Amin (2019). "Isolation of biologically active compounds from mangrove sediments." Anal Bioanal Chem 411(25): 6521-6529.
  • Sofela, S., S. Sahloul, C. Stubbs, A. Orozaliev, F. S. Refai, A. M. Esmaeel, H. Fahs, M. O. Abdelgawad, K. C. Gunsalus and Y. A. Song (2019). "Phenotyping of the thrashing forces exerted by partially immobilized C. elegans using elastomeric micropillar arrays." Lab Chip 19(21): 3685-3696.
  • Gan, H. H. and K. C. Gunsalus (2019). "The Role of Tertiary Structure in MicroRNA Target Recognition." Methods Mol Biol 1970: 43-64.
  • Chahal J., L. F. R. Gebert, H. H. Gan, E. Camacho, K. C Gunsalus, I. J MacRae, S. M. Saganet al. (2019). "miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5' terminus." Nucleic Acids Res 47(10): 5307-5324.
  • Bezler A., F. Braukmann, S. M. West, A. Duplan, R. Conconi, F. Schütz, P. Gönczy, F. Piano, K. C. Gunsalus, E. A. Miska, L. Keller. (2019). "Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment." PLoS Genet 15(2): e1007905.
  • Beltran T., C. Barroso, T. Y. Birkle, L. Stevens, H. T. Schwartz, P. W. Sternberg, H. Fradin, K. C. Gunsalus, F. Piano, G. Sharma, C. Cerrato, J. Ahringer, E. Martínez-Pérez, M. Blaxter and P. Sarkies. (2019). "Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis." Dev Cell 48(6): 793-810.e796.
  • Xie, X., B. Almuzzaini, N. Drou, S. Kremb, A. Yousif, A. O. Farrants, K. Gunsalus and P. Percipalle (2018). "beta-Actin-dependent global chromatin organization and gene expression programs control cellular identity." FASEB J 32(3): 1296-1314.
  • West, S. M., D. Mecenas , M. Gutwein, D. Aristizábal-Corrales, F. Piano  and K. C. Gunsalus. (2018). "Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline." Genome Biol 19(1): 8.
  • Nelson, D. R., B. Khraiwesh, W. Fu, S. Alseekh, A. Jaiswal, A. Chaiboonchoe, K. M. Hazzouri, M. J. O'Connor, G. L. Butterfoss, N. Drou, J. D. Rowe, J. Harb, A. R. Fernie, K. C. Gunsalus and K. Salehi-Ashtiani (2017). "The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization." eLife 6.
  • Fradin, H., K. Kiontke , C. Zegar , M. Gutwein , J. Lucas, M. Kovtun, D. L. Corcoran, L.  R. Baugh, D. H. A. Fitch, F. Piano and K. C. Gunsalus. (2017). "Genome Architecture and Evolution of a Unichromosomal Asexual Nematode." Curr Biol 27(19): 2928-2939 e2926.
  • Flamand, M. N., H. K. Gan , V. K. Mayya , K. C. Gunsalus and T. F. Duchaine. (2017). "A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing." Nucleic Acids Res 45(12): 7212-7225.
  • Desta, I. T., A. Al-Sharif, N. AlGharibeh, N. Mustafa, A. Orozaliev, N. Giakoumidis, K. C. Gunsalus and Y. A. Song (2017). "Detecting and Trapping of a Single C. elegans Worm in a Microfluidic Chip for Automated Microplate Dispensing." SLAS Technol 22(4): 431-436.
    
  • Benyettou, F., H. Fahs, R. Elkharrag, R. A. Bilbeisi, B. Asma, R. Rezgui, L. Motte, M., Magzoub, J., Brandel, Olsen, J., F., Piano, K. C., Gunsalus, C. Platas-Iglesias, and A., Trabolsi (2017). "Selective growth inhibition of cancer cells with doxorubicin-loaded CB[7]-modified iron-oxide nanoparticles." RSC Advances 7(38): 23827-23834.
  • Weicksel, S. E., A. Mahadav, M. Moyle, P. G. Cipriani, M. Kudron, Z. Pincus, S. Bahmanyar, L. Abriola, J. Merkel, M. Gutwein, A. G. Fernandez, F. Piano, K. C. Gunsalus and V. Reinke (2016). "A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans." Development 143(19): 3540-3548.
  • Chen, J. X., P. G. Cipriani, D. Mecenas, J. Polanowska, F. Piano, K. C. Gunsalus and M. Selbach (2016). "In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics." Mol Cell Proteomics 15(5): 1642-1657.
  • Gan, H. H. and K. C. Gunsalus (2015). "Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition." Nucleic Acids Res 43(20): 9613-9625.
  • Gan, H. H. and K. C. Gunsalus (2013). "Tertiary structure-based analysis of microRNA-target interactions." RNA 19(4): 539-551.
  • Mizrak, D., M. Ruben, G. N.Myers, K. Rhrissorrakrai, K. C. Gunsalus and J. Blau. (2012). "Electrical Activity Can Impose Time of Day on the Circadian Transcriptome of Pacemaker Neurons." Current Biology 22(20): 1871-1880.
  • Green, R. A., H.L Kao, A. Audhya, S. Arur, J. R. Mayers, H. N. Fridolfsson, M. Schulman, S. Schloissnig, S. Niessen, K. Laband, S. Wang, D. A. Starr, A. A. Hyman, T. Schedl, A. Desai, F. Piano, K. C. Gunsalus and K. Oegema. (2011). "A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue." Cell 145(3): 470-482.
  • Mangone, M., A. P Manoharan, D.Thierry-Mieg, J. Thierry-Mieg, T. Han, S. D. Mackowiak, E. Mis, C. Zegar, M. R. Gutwein, V. Khivansara, O. Attie, K. Chen, K. Salehi-Ashtiani, M. Vidal, T. T. Harkins, P. Bouffard, Y. Suzuki, S. Sugano, Y. Kohara, N. Rajewsky, F. Piano, K. C. Gunsalus and J. K. Kim . (2010). "The landscape of C. elegans 3'UTRs." Science 329(5990): 432-435.
  • Gerstein M.B., Z. J. Lu, E. L. V. Nostrand, C. Cheng, B. I. Arshinoff, T. Liu, K. Y. Yip, R. Robilotto, A. Rechtsteiner, K. Ikegami, P. Alves, A. Chateigner, M. Perry, M. Morris, R. K. Auerbach, X. Feng, J. Leng, A. Vielle, W. Niu, K. Rhrissorrakrai, A. Agarwal, R. P. Alexander, G. Barber, C. M. Brdlik, J. Brennan, J. J. Brouillet, A. Carr, M.S. Cheung, H. Clawson, S. Contrino, L. O. Dannenberg, A. F. Dernburg, A. Desai, L. Dick, A. C. Dosé, J. Du, T. Egelhofer, S. Ercan, G. Euskirchen, Brent Ewing, E. A. Feingold, R. Gassmann, P. J. Good, P. Green, F. Gullier, M. Gutwein, M. S. Guyer, L. Habegger, T. Han, J. G. Henikoff, S. R. Henz, A. Hinrichs, H. Holster, T. Hyman, A. L. Iniguez, J. Janette, M. Jensen, M. Kato, W. J. Kent, E. Kephart, V. Khivansara, E. Khurana, J. K. Kim, P. Kolasinska-Zwierz, E C. Lai, I. Latorre, A. Leahey, S. Lewis, P. Lloyd, L. Lochovsky, R. F. Lowdon, Y. Lubling, R. Lyne, M. MacCoss, S. D. Mackowiak, M. Mangone, S. McKay, D. Mecenas, G. Merrihew, D. M. Miller III, A. Muroyama,  J. I. Murray, S.L Ooi, Hoang. Pham, T. Phippen, E. A. Preston, N. Rajewsky, G. Rätsch, H. Rosenbaum,J. Rozowsky, K. Rutherford, P. Ruzanov, M. Sarov, R. Sasidharan, A. Sboner, P. Scheid, E. Segal, H. Shin,  C. Shou, F. J. Slack, C. Slightam, R. Smith, W. C. Spencer, E. O. Stinson, S. Taing, T. Takasaki, D. Vafeados, K. Voronina, G. Wang, N. L. Washington, C. M. Whittle, B. Wu, K.K Yan, G. Zeller, Z. Zha, M. Zhong, X. Zhou, modENCODE Consortium, J. Ahringer, S. Strome, K. C. Gunsalus, G. Micklem,  X. S. Liu, V. Reinke, S. K. Kim, L. W. Hillier, S. Henikoff, F. Piano, M. Snyder,  L. Stein, J. D. Lieb and R. H. Waterston. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project." Science 330(6012): 1775-1787.

  Publications by Group Members

  • Venit, T., N. H. El Said, S. R. Mahmood and P. Percipalle (2021). "A dynamic actin-dependent nucleoskeleton and cell identity." J Biochem 169(3): 243-257.
  • Guo, Y., Y. Q. Xie, M. Gao, Y. Zhao, F. Franco, M. Wenes, I. Siddiqui, A. Bevilacqua, H. Wang,H. Yang, B. Feng, X. Xie, C. M. Sabatel, B. Tschumi,A. Chaiboonchoe, Y. Wang, W. Li, W. Xiao, W. Held, P. Romero, P. C. Ho and L. Tang . (2021). "Metabolic reprogramming of terminally exhausted CD8+ T cells by IL-10 enhances anti-tumor immunity." Nature Immunology 22(6): 746-756.
  • Xie, X., S. R. Mahmood, T. Gjorgjieva and P. Percipalle (2020). "Emerging roles of cytoskeletal proteins in regulating gene expression and genome organization during differentiation." Nucleus 11(1): 53-65.
  • Wang, H., F. Franco, Y. C. Tsui, X. Xie, M. P. Trefny, R. Zappasodi, S. R. Mohmood, J. Fernandez-Garcia, C. H. Tsai, I. Schulze, F. Picard, E. Meylan, R. Silverstein, I. Goldberg, S. M. Fendt, J. D. Wolchok, T. Merghoub, C. Jandus, A. Zippelius and P. C. Ho (2020). "CD36-mediated metabolic adaptation supports regulatory T cell survival and function in tumors." Nat Immunol 21(3): 298-308.
  • Venit, T., S. R. Mahmood, M. Endara-Coll and P. Percipalle (2020). "Nuclear actin and myosin in chromatin regulation and maintenance of genome integrity." Int Rev Cell Mol Biol 355: 67-108.
  • Venit, T., M. Dowaidar, M. Gestin, S. R. Mahmood, Ü. Langel and P. Percipalle (2020). "Transcriptional Profiling Reveals Ribosome Biogenesis, Microtubule Dynamics and Expression of Specific lncRNAs to be Part of a Common Response to Cell-Penetrating Peptides." Biomolecules 10(11).
  • Mueller, C., S. Kremb, M. Gonsior, R. Brack-Werner, C. R. Voolstra and P. Schmitt-Kopplin (2020). "Advanced identification of global bioactivity hotspots via screening of the metabolic fingerprint of entire ecosystems." Sci Rep 10(1): 1319.
  • Al-Sayegh, M. A., S. R. Mahmood, S. B. A. Khair, X. Xie, M. El Gindi, T. Kim, A. Almansoori and P. Percipalle (2020). "β-actin contributes to open chromatin for activation of the adipogenic pioneer factor CEBPA during transcriptional reprograming." Mol Biol Cell 31(23): 2511-2521.
  • Xie, X., M. Endara-Coll, R. Mahmood, R. Jankauskas, T. Gjorgjieva and P. Percipalle (2019). "Mitochondria-localized beta-actin is essential for priming innate antiviral immune signaling by regulating IRF3 protein stability." Cell Mol Immunol 16(10): 837-840.
  • Wijaya, A. W., A. I. Nguyen, L. T. Roe, G. L. Butterfoss, R. K. Spencer, N. K. Li and R. N. Zuckermann (2019). "Cooperative Intramolecular Hydrogen Bonding Strongly Enforces cis-Peptoid Folding." J Am Chem Soc 141(49): 19436-19447.
  • Spencer, R. K., G. L. Butterfoss, J. R. Edison, J. R. Eastwood, S. Whitelam, K. Kirshenbaum and R. N. Zuckermann (2019). "Stereochemistry of polypeptoid chain configurations." Biopolymers 110(6): e23266.
  • Roe, L. T., J. G. Pelton, J. R. Edison, G. L. Butterfoss, B. W. Tresca, B. A. LaFaye, S. Whitelam, D. E. Wemmer and R. N. Zuckermann (2019). "Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution." Biopolymers 110(6): e23267.
  • Shirke, A. N., C. White, J. A. Englaender, A. Zwarycz, G. L. Butterfoss, R. J. Linhardt and R. A. Gross (2018). "Stabilizing Leaf and Branch Compost Cutinase (LCC) with Glycosylation: Mechanism and Effect on PET Hydrolysis." Biochemistry 57(7): 1190-1200.
  • Jiang, T., P. D. Renfrew, K. Drew, N. Youngs, G. L. Butterfoss, R. Bonneau and D. N. Shasha (2018). "An adaptive geometric search algorithm for macromolecular scaffold selection." Protein Eng Des Sel 31(9): 345-354.
  • Edison, J. R., R. K. Spencer, G. L. Butterfoss, B. C. Hudson, A. I. Hochbaum, A. K. Paravastu, R. N. Zuckermann and S. Whitelam (2018). "Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions." Proc Natl Acad Sci USA 115(22): 5647-5651.
  • Shirke, A. N., A. Su, J. A. Jones, G. L. Butterfoss, M. A. Koffas, J. R. Kim and R. A. Gross (2017). "Comparative thermal inactivation analysis of Aspergillus oryzae and Thiellavia terrestris cutinase: Role of glycosylation." Biotechnol Bioeng 114(1): 63-73.
  • Shirke, A. N., G. L. Butterfoss, R. Saikia, A. Basu, L. de Maria, A. Svendsen and R. A. Gross (2017). "Engineered Humicola insolens cutinase for efficient cellulose acetate deacetylation." Biotechnol J 12(8).
  • Gater, D. L., N. Widatalla, K. Islam, M. AlRaeesi, J. C. M. Teo and Y. E. Pearson (2017). "Quantification of sterol-specific response in human macrophages using automated imaged-based analysis." Lipids Health Dis 16(1): 242.
  • Shirke, A. N., D. Basore, S. Holton, A. Su, E. Baugh, G. L. Butterfoss, G. Makhatadze, C. Bystroff and R. A. Gross (2016). "Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics." Appl Microbiol Biotechnol 100(10): 4435-4446.
    
  • Shirke, A. N., D. Basore, G. L. Butterfoss, R. Bonneau, C. Bystroff and R. A. Gross (2016). "Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability." Proteins 84(1): 60-72.
  • Mannige, R. V., T. K. Haxton, C. Proulx, E. J. Robertson, A. Battigelli, G. L. Butterfoss, R. N. Zuckermann and S. Whitelam (2015). "Peptoid nanosheets exhibit a new secondary-structure motif." Nature 526(7573): 415-420.
  • Butterfoss, G. L., K. Drew, P. D. Renfrew, K. Kirshenbaum and R. Bonneau (2014). "Conformational preferences of peptide-peptoid hybrid oligomers." Biopolymers 102(5): 369-378.

Environmental Adaptation and Sustainability

• Date Palm Evolutionary Genomics

  Principal Investigator: Michael Purugganan

  • Castanera, R., N. Morales-Díaz, S. Gupta, M. Purugganan and J. M. Casacuberta (2023). "Transposons are important contributors to gene expression variability under selection in rice populations." Elife 12.
  • He, Q., S. Tang, H. Zhi, J. Chen, J. Zhang, H. Liang, O. Alam, H. Li, H. Zhang, L. Xing, X. Li, W. Zhang, H. Wang, J. Shi, H. Du, H. Wu, L. Wang, P. Yang, H. Yan, Z. Song, J. Liu, X. Tian, Z. Qiao, G. Feng, R. Guo, W. Zhu, Y. Ren, H. Hao, M. Li, A. Zhang, E. Guo, F. Yan, Q. Li, Y. Liu, B. Tian, X. Zhao, R. Jia, B. Feng, J. Wei, J. Lai, G. Jia, M. Purugganan and X. Diao (2023). "A graph-based genome and pan-genome variation of the model plant Setaria." Nat Genet.
  • Purugganan, M. (2022). "Control as a unique attribute of domestication (a reply to Clement)." Trends Ecol Evol 37(10): 825.
  • Sudalaimuthuasari, N., R. Ali, M. Kottackal, M. Rafi, M. Al Nuaimi, B. Kundu, R. S. Al-Maskari, X. Wang, A. K. Mishra, J. Balan, S. R. Chaluvadi, F. Al Ansari, J. L. Bennetzen, M. D. Purugganan, K. M. Hazzouri and K. M. A. Amiri (2022). "The Genome of the Mimosoid Legume." Int J Mol Sci 23(15).
  • Andersson, L. and M. Purugganan (2022). "Molecular genetic variation of animals and plants under domestication." Proc Natl Acad Sci U S A 119(30): e2122150119.
  • Hazzouri, K. M., N. Sudalaimuthuasari, E. E. Saeed, B. Kundu, R. S. Al-Maskari, D. Nelson, A. A. AlShehhi, M. A. Aldhuhoori, D. S. Almutawa, F. R. Alshehhi, J. Balan, S. Mundra, M. Alam, K. Salehi-Ashtiani, M. Purugganan and K. M. A. Amiri (2022). "Salt flat microbial diversity and dynamics across salinity gradient." Sci Rep 12(1): 11293.
    
  • Ćalić, I., S. C. Groen, J. Y. Choi, Z. Joly-Lopez, E. Hamann, M. A. Natividad, K. Dorph, C. L. U. Cabral, R. O. Torres, G. V. Vergara, A. Henry, M. D. Purugganan and S. J. Franks (2022). "The influence of genetic architecture on responses to selection under drought in rice." Evolutionary Applications.
  • Purugganan, M. D. (2022). "What is domestication?" Trends Ecol Evol.
  • Flowers, J. M., K. M. Hazzouri, A. Lemansour, T. Capote, M. Gros-Balthazard, S. Ferrand, M. Lebrun, K. M. A. Amiri and M. D. Purugganan (2022). "Patterns of Volatile Diversity Yield Insights Into the Genetics and Biochemistry of the Date Palm Fruit Volatilome." Frontiers in Plant Science 13.
  • Purugganan, M. D. (2022). "Vavilov's law and phenotypes across species." Nat Rev Genet.
  • Groen, S. C., Z. Joly-Lopez, A. E. Platts, M. Natividad, Z. Fresquez, W. M. Mauck, M. R. Quintana, C. L. U. Cabral, R. O. Torres, R. Satija, M. D. Purugganan and A. Henry (2022). "Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems." Plant Cell 34(2): 759-783.
  • Purugganan M. D. and S. A. Jackson (2021). "Advancing crop genomics from lab to field." Nat Genet 53(5): 595-601.
  • Perez-Escobar O. A., S. Bellot, N. A. S. Przelomska, J. M Flowers, M. Nesbitt, P. Ryan, R. M. Gutaker, M. Gros-Balthazard, T. Wells, B. G. Kuhnhäuser, R. Schley, D. Bogarín, S. Dodsworth, R. Diaz, M. Lehmann, P. Petoe, W. L. Eiserhardt, M. Preick, M. Hofreiter, I. Hajdas, M. Purugganan, A. Antonelli, B. Gravendeel, I. J. Leitch, M. F. T. Jimenez, A. S. T. Papadopulos, G. Chomicki, S. S. Renner and W. J. Baker. (2021). "Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication." Mol Biol Evol.
  • Kurbidaeva, A. and M. Purugganan (2021). "Insulators in Plants: Progress and Open Questions." Genes 12(9): 1422.
  • Gros-Balthazard, M., J. M. Flowers, K. M. Hazzouri, S. Ferrand, F. Aberlenc, S. Sallon and M. D. Purugganan, (2021) “The genomes of ancient date palms germinated from 2,000-year-old seeds”. Proceedings of the National Academy of Sciences 118(19): e2025337118.
    
  • Capote, T. C., J. Flowers, K. M. Hazzouri, M.D. Purugganan and K.A. Amiri, (2021). “The genomics of date palms: current perspectives.” In Annual Plant Reviews online, J.A. Roberts (Ed.). 4: 57 – 86.
  • Read, A. C., M. J. Moscou, A. V. Zimin, G. Pertea, R. S. Meyer, M. D. Purugganan, J. E. Leach, L. R. Triplett, S. L. Salzberg and A. J. Bogdanove (2020). "Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing." PLoS Genet 16(1): e1008571.
  • Perez Escobar, O., S. Bellot, M. Gros-Balthazard, J. Flowers, M. Nesbitt, P. Ryan, R. Gutaker, T. Wells, R. Schley, D. Bogarín, N. Przelomska, S. Dodsworth, R. Diaz, M. Lehmann, P. Petoe, M. Preick, M. Hofreiter, I. Hajdas, A. Antonelli, Ilia J. Leitch, B. Gravendeel, M. Torres, G. Chomicki, S. Renner, A. Papadopulos, and M. D. Purugganan, W. Baker (2020) “Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication.” bioRxiv 2020.11.26.400408.
  • Joly-Lopez, Z., A. E. Platts, B. Gulko, J. Y. Choi, S. C. Groen, X. Zhong, A. Siepel and M. D. Purugganan (2020). "An inferred fitness consequence map of the rice genome." Nat Plants 6(2): 119-130.
  • Hinojosa-Alvarez, S., S. Arias, S. Ferrand, M. D. Purugganan, J. Rozas, U. Rosas, and A. Wegier (2020). “The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-angelensis, a Mexican endangered species.” Mitochondrial DNA Part B, 5:3, 2038-2039.
  • Groen, S. C., I. Calic, Z. Joly-Lopez, A. E. Platts, J. Y. Choi, M. Natividad, K. Dorph, W. M. Mauck, 3rd, B. Bracken, C. L. U. Cabral, A. Kumar, R. O. Torres, R. Satija, G. Vergara, A. Henry, S. J. Franks and M. D. Purugganan (2020). "The strength and pattern of natural selection on gene expression in rice." Nature 578(7796): 572-576.
  • Choi, J. Y., Z. N. Lye, S. C. Groen, X. Dai, P. Rughani, S. Zaaijer, E. D. Harrington, S. Juul and M. D. Purugganan (2020). "Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice." Genome Biol 21(1): 21.
  • Zaidem, M. L., S. C. Groen and M. D. Purugganan (2019). "Evolutionary and ecological functional genomics, from lab to the wild." Plant J 97(1): 40-55.
  • Purugganan, M. D. (2019). "Evolutionary Insights into the Nature of Plant Domestication." Curr Biol 29(14): R705-r714.
  • Hazzouri, K. M., M. Gros-Balthazard, J. M. Flowers, D. Copetti, A. Lemansour, M. Lebrun, K. Masmoudi, S. Ferrand, M. I. Dhar, Z. A. Fresquez, U. Rosas, J. Zhang, J. Talag, S. Lee, D. Kudrna, R. F. Powell, I. J. Leitch, R. R. Krueger, R. A. Wing, K. M. A. Amiri and M. D. Purugganan (2019). "Genome-wide association mapping of date palm fruit traits." Nat Commun 10(1): 4680.
  • Flowers, J. M., K. M. Hazzouri, M. Gros-Balthazard, Z. Mo, K. Koutroumpa, A. Perrakis, S. Ferrand, H. S. M. Khierallah, D. Q. Fuller, F. Aberlenc, C. Fournaraki and M. D. Purugganan (2019). "Cross-species hybridization and the origin of North African date palms." Proc Natl Acad Sci U S A 116(5): 1651-1658.
    
  • Choi, J. Y., M. Zaidem, R. Gutaker, K. Dorph, R. K. Singh and M. D. Purugganan (2019). "The complex geography of domestication of the African rice Oryza glaberrima." PLoS Genet 15(3): e1007414.
  • Wing, R. A., M. D. Purugganan and Q. Zhang (2018). "The rice genome revolution: from an ancient grain to Green Super Rice." Nat Rev Genet 19(8): 505-517.
  • Purugganan, M. D. (2018). "The Evolution of Plant Form: A Summary Perspective." Annual Plant Reviews online: 357-366.
  • Hazzouri, K. M., B. Khraiwesh, K. M. A. Amiri, D. Pauli, T. Blake, M. Shahid, S. K. Mullath, D. Nelson, A. L. Mansour, K. Salehi-Ashtiani, M. Purugganan and K. Masmoudi (2018). "Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism." Front Plant Sci 9: 156.
  • Choi, J. Y. and M. D. Purugganan (2018). "Multiple Origin but Single Domestication Led to Oryza sativa." G3 (Bethesda) 8(3): 797-803.
  • Choi, J. Y. and M. D. Purugganan (2018). "Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice." Mol Biol Evol 35(2): 365-382.
  • Choi, J. Y., A. E. Platts, D. Q. Fuller, Y. I. Hsing, R. A. Wing and M. D. Purugganan (2017). "The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice." Mol Biol Evol 34(4): 969-979.
  • Yuan, W., J. M. Flowers, D. J. Sahraie and M. D. Purugganan (2016). "Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment." G3 (Bethesda) 6(10): 3129-3138.
  • Yuan, W., J. M. Flowers, D. J. Sahraie, I. M. Ehrenreich and M. D. Purugganan (2016). "Extreme QTL mapping of germination speed in Arabidopsis thaliana." Mol Ecol 25(17): 4177-4196.
  • Van Andel, T. R., R. S. Meyer, S. A. Aflitos, J. A. Carney, M. A. Veltman, D. Copetti, J. M. Flowers, R. M. Havinga, H. Maat, M. D. Purugganan, R. A. Wing and M. E. Schranz (2016). "Tracing ancestor rice of Suriname Maroons back to its African origin." Nat Plants 2: 16149.
  • Meyer, R. S., J. Y. Choi, M. Sanches, A. Plessis, J. M. Flowers, J. Amas, K. Dorph, A. Barretto, B. Gross, D. Q. Fuller, I. K. Bimpong, M. N. Ndjiondjop, K. M. Hazzouri, G. B. Gregorio and M. D. Purugganan (2016). "Domestication history and geographical adaptation inferred from a SNP map of African rice." Nat Genet 48(9): 1083-1088.
  • Joly-Lopez, Z., J. M. Flowers and M. D. Purugganan (2016). "Developing maps of fitness consequences for plant genomes." Curr Opin Plant Biol 30: 101-107.
  • Hazzouri, K. M., J. M. Flowers, H. J. Visser, H. S. M. Khierallah, U. Rosas, G. M. Pham, R. S. Meyer, C. K. Johansen, Z. A. Fresquez, K. Masmoudi, N. Haider, N. El Kadri, Y. Idaghdour, J. A. Malek, D. Thirkhill, G. S. Markhand, R. R. Krueger, A. Zaid and M. D. Purugganan (2015). "Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop." Nat Commun 6: 8824.
  • Flowers, J. M., K. M. Hazzouri, G. M. Pham, U. Rosas, T. Bahmani, B. Khraiwesh, D. R. Nelson, K. Jijakli, R. Abdrabu, E. H. Harris, P. A. Lefebvre, E. F. Hom, K. Salehi-Ashtiani and M. D. Purugganan (2015). "Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii." Plant Cell 27(9): 2353-2369.
  • Purugganan, M. D. (2014). "An evolutionary genomic tale of two rice species." Nat Genet 46(9): 931-932.
  • Hazzouri, K. M., M. D. Purugganan and J. M. Flowers (2014). "Population Genomics of Plant Species." Genomes of Herbaceous Land Plants 69: 311-334.
  • Gerbault, P., R. G. Allaby, N. Boivin, A. Rudzinski, I. M. Grimaldi, J. C. Pires, C. Climer Vigueira, K. Dobney, K. J. Gremillion, L. Barton, M. Arroyo-Kalin, M. D. Purugganan, R. Rubio de Casas, R. Bollongino, J. Burger, D. Q. Fuller, D. G. Bradley, D. J. Balding, P. J. Richerson, M. T. Gilbert, G. Larson and M. G. Thomas (2014). "Story telling and story testing in domestication." Proc Natl Acad Sci USA 111(17): 6159-6164.
  • Fuller, D. Q., T. Denham, M. Arroyo-Kalin, L. Lucas, C. J. Stevens, L. Qin, R. G. Allaby and M. D. Purugganan (2014). "Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record." Proc Natl Acad Sci USA 111(17): 6147-6152.

  Publications by Group Members
  

  • Pires, R. C., A. Ferro, T. Capote, A. Usié, B. Correia, G. Pinto, E. Menéndez and L. Marum (2023). "Laser Microdissection of Woody and Suberized Plant Tissues for RNA-Seq Analysis." Mol Biotechnol 65(3): 419-432.
  • Smith, E. G., K. M. Hazzouri, J. Y. Choi, P. Delaney, M. Al-Kharafi, E. J. Howells, M. Aranda and J. A. Burt (2022). "Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs." Sci Adv 8(2): eabl7287.
  • Gros-Balthazard M. and J. M Flowers (2021). " A Brief History of the Origin of Domesticated Date Palms." SpringerLink (pp 55-74).
  • Sallon, S., E. Cherif, N. Chabrillange, E. Solowey, M. Gros-Balthazard, S. Ivorra, J. F. Terral, M. Egli and F. Aberlenc (2020). "Origins and insights into the historic Judean date palm based on genetic analysis of germinated ancient seeds and morphometric studies." Sci Adv 6(6): eaax0384.
  • Hazzouri, K. M., J. M. Flowers, D. Nelson, A. Lemansour, K. Masmoudi and K. M. A. Amiri (2020). "Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era." Front Plant Sci 11: 293.
    
  • Gros-Balthazard, M., V. Battesti, S. Ivorra, L. Paradis, F. Aberlenc, O. Zango, S. Zehdi-Azouzi, S. Moussouni, S. A. Naqvi, C. Newton and J. F. Terral (2020). "On the necessity of combining ethnobotany and genetics to assess agrobiodiversity and its evolution in crops: A case study on date palms (Phoenix dactylifera L.) in Siwa Oasis, Egypt." Evol Appl 13(8): 1818-1840.
  • Gros-Balthazard, M., W. Baker, I. Leitch, J. Pellicer, R. Powell and S. Bellot (2020). "Systematics and evolution of the genus Phoenix: towards understanding the date palm's origins." Springer, Cham (pp 29-54).
  • Veltman, M. A., J. M. Flowers, T. R. van Andel and M. E. Schranz (2019). "Origins and geographic diversification of African rice (Oryza glaberrima)." PLoS One 14(3): e0203508.
    
  • Gros-Balthazard, M., K. M. Hazzouri and J. M. Flowers (2018). "Genomic Insights into Date Palm Origins." Genes (Basel) 9(10).
    
  • Nelson, D. R., B. Khraiwesh, W. Fu, S. Alseekh, A. Jaiswal, A. Chaiboonchoe, K. M. Hazzouri, M. J. O'Connor, G. L. Butterfoss, N. Drou, J. D. Rowe, J. Harb, A. R. Fernie, K. C. Gunsalus and K. Salehi-Ashtiani (2017). "The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization." eLife 6.
    
  • Douglas, G. M., G. Gos, K. A. Steige, A. Salcedo, K. Holm, E. B. Josephs, R. Arunkumar, J. A. Agren, K. M. Hazzouri, W. Wang, A. E. Platts, R. J. Williamson, B. Neuffer, M. Lascoux, T. Slotte and S. I. Wright (2015). "Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris." Proc Natl Acad Sci USA 112(9): 2806-2811.
    
  • Williamson, R. J., E. B. Josephs, A. E. Platts, K. M. Hazzouri, A. Haudry, M. Blanchette and S. I. Wright (2014). "Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora." PLoS Genet 10(9): e1004622.
  • Slotte, T., K. M. Hazzouri, J. A. Agren, D. Koenig, F. Maumus, Y. L. Guo, K. Steige, A. E. Platts, J. S. Escobar, L. K. Newman, W. Wang, T. Mandakova, E. Vello, L. M. Smith, S. R. Henz, J. Steffen, S. Takuno, Y. Brandvain, G. Coop, P. Andolfatto, T. T. Hu, M. Blanchette, R. M. Clark, H. Quesneville, M. Nordborg, B. S. Gaut, M. A. Lysak, J. Jenkins, J. Grimwood, J. Chapman, S. Prochnik, S. Shu, D. Rokhsar, J. Schmutz, D. Weigel and S. I. Wright (2013). "The Capsella rubella genome and the genomic consequences of rapid mating system evolution." Nat Genet 45(7): 831-835.
  • Brandvain, Y., T. Slotte, K. M. Hazzouri, S. I. Wright and G. Coop (2013). "Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella." PLoS Genet 9(9): e1003754.

   

• Adaptive Evolution in Invasive Species

  Principal Investigator: Stéphane Boissinot

  • Kassie, A., A. B. Simegn, B. A. Bogale, S. Goutte and S. Boissinot (2023). "Diversity, Distribution, and Habitat Association of Anuran Species from Keffa, Southwest Ethiopia." Diversity 15(2).
• Microbial Role in Coral Thermal Tolerance

  Principal Investigators: John Burt and Shady Amin

  • Mohamed, A. R., M. A. Ochsenkühn, A. Kazlak, A. Moustafa and S. A. Amin (2023). "The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions." FEMS Microbiol Rev.

  Publications by Group Members
  

  • Haydon, T. D., J. L. Matthews, J. R. Seymour, J. B. Raina, J. E. Seymour, K. Chartrand, E. F. Camp and D. J. Suggett (2023). "Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance." Proc Biol Sci 290(1992): 20221877.
• Comparative Genomics to Analyze Drought Tolerance in Crops

  Principal Investigator: Kenneth D. Birnbaum

  • Guillotin, B., R. Rahni, M. Passalacqua, M. A. Mohammed, X. Xu, S. K. Raju, C. O. Ramírez, D. Jackson, S. C. Groen, J. Gillis and K. D. Birnbaum (2023). "A pan-grass transcriptome reveals patterns of cellular divergence in crops." Nature.

CGSB Cores

• Bioinformatics Core
  • Gjorgjieva, T., A. Chaloemtoem, T. Shahin, O. Bayaraa, M. M. Dieng, M. Alshaikh, M. Abdalbaqi, J. Del Monte, G. Begum, C. Leonor, V. Manikandan, N. Drou, M. Arshad, M. Arnoux, N. Kumar, A. Jabari, A. Abdulle, G. ElGhazali, R. Ali, S. Y. Shaheen, J. Abdalla, F. Piano, K. C. Gunsalus, H. Daggag, H. Al Nahdi, H. Abuzeid and Y. Idaghdour (2023). "Systems genetics identifies miRNA-mediated regulation of host response in COVID-19." Hum Genomics 17(1): 49.
  • Pallichankandy, S., F. Thayyullathil, A. R. Cheratta, K. Subburayan, A. Alakkal, M. Sultana, N. Drou, M. Arshad, S. Tariq and S. Galadari (2023). "Targeting oxeiptosis-mediated tumor suppression: a novel approach to treat colorectal cancers by sanguinarine." Cell Death Discov 9(1): 94. 
  • Mughal, M. K., R. Giallo, M. Arshad, P. D. Arnold, K. Bright, E. M. Charrois, B. Rai, A. Wajid and D. Kingston (2023). "Trajectories of maternal depressive symptoms from pregnancy to 11 years postpartum: Findings from Avon Longitudinal Study of Parents and Children (ALSPAC) cohort." J Affect Disord 328: 191-199.
  • Charrois, E. M., M. K. Mughal, M. Arshad, A. Wajid, K. S. Bright, R. Giallo and D. Kingston (2022). "Patterns and predictors of depressive and anxiety symptoms in mothers affected by previous prenatal loss in the ALSPAC birth cohort." J Affect Disord 307: 244-253
  • AlHudaib, K. A., M. I. Almaghasla, S. M. El-Ganainy, M. Arshad, N. Drou and M. N. Sattar (2022). "High-Throughput Sequencing Identified Distinct Bipartite and Monopartite Begomovirus Variants Associated with DNA-Satellites from Tomato and Muskmelon Plants in Saudi Arabia." Plants (Basel) 12(1). 
  • Arshad, M. and A. Hannoufa (2022). "Alfalfa transcriptome profiling provides insight into miR156-mediated molecular mechanisms of heat stress tolerance." Genome 65(6): 315-330.
  • Sapudom, J., M. ElGindi, M. Arnoux, N. Drou, A. Garcia-Sabaté and J. C. M. Teo (2021). "Fibroblast Differentiation and Matrix Remodeling Impaired under Simulated Microgravity in 3D Cell Culture Model." International Journal of Molecular Sciences 22(21): 11911.
  • Gan, H. H., A. Twaddle, B. Marchand and K. C. Gunsalus (2021). "Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility." J Mol Biol 433(15): 167051.
  • Yousif, A., N. Drou, J. Rowe, M. Khalfan and K. C. Gunsalus (2020). "NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization." BMC Bioinformatics 21(1): 267.
    
  • Shibl, A. A., A. Isaac, M. A. Ochsenkuhn, A. Cardenas, C. Fei, G. Behringer, M. Arnoux, N. Drou, M. P. Santos, K. C. Gunsalus, C. R. Voolstra and S. A. Amin (2020). "Diatom modulation of select bacteria through use of two unique secondary metabolites." Proc Natl Acad Sci U S A 117(44): 27445-27455.
  • Dieng, M. M., A. Diawara, V. Manikandan, H. Tamim El Jarkass, S. S. Serme, S. Sombie, A. Barry, S. A. Coulibaly, A. Diarra, N. Drou, M. Arnoux, A. Yousif, A. B. Tiono, S. B. Sirima, I. Soulama and Y. Idaghdour (2020). "Integrative genomic analysis reveals mechanisms of immune evasion in P. falciparum malaria." Nat Commun 11(1): 5093.
  • Arshad, M., A. Puri, A. J. Simkovich, J. Renaud, M. Y. Gruber, F. Marsolais and A. Hannoufa (2020). "Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature." BMC Genomics 21(1): 758.
  • Arshad, M., M. K. Mughal, R. Giallo and D. Kingston (2020). "Predictors of child resilience in a community-based cohort facing flood as natural disaster." BMC Psychiatry 20(1): 543.
  • Abu-Helalah, M., B. Azab, R. Mubaidin, D. Ali, H. Jafar, H. Alshraideh, N. Drou and A. Awidi (2020). "BRCA1 and BRCA2 genes mutations among high risk breast cancer patients in Jordan." Sci Rep 10(1): 17573.
    
  • Xie, X., T. Venit, N. Drou and P. Percipalle (2018). "In Mitochondria β-Actin Regulates mtDNA Transcription and Is Required for Mitochondrial Quality Control." iScience 3: 226-237.
    
  • Xie, X., R. Jankauskas, A. M. A. Mazari, N. Drou and P. Percipalle (2018). "beta-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming." PLoS Genet 14(12): e1007846.
  • Xie, X., B. Almuzzaini, N. Drou, S. Kremb, A. Yousif, A. O. Farrants, K. Gunsalus and P. Percipalle (2018). "beta-Actin-dependent global chromatin organization and gene expression programs control cellular identity." FASEB J 32(3): 1296-1314.
  • Gruning, B., R. Dale, A. Sjodin, B. A. Chapman, J. Rowe, C. H. Tomkins-Tinch, R. Valieris, J. Koster and T. Bioconda (2018). "Bioconda: sustainable and comprehensive software distribution for the life sciences." Nat Methods 15(7): 475-476.
  • Nelson, D. R., B. Khraiwesh, W. Fu, S. Alseekh, A. Jaiswal, A. Chaiboonchoe, K. M. Hazzouri, M. J. O'Connor, G. L. Butterfoss, N. Drou, J. D. Rowe, J. Harb, A. R. Fernie, K. C. Gunsalus and K. Salehi-Ashtiani (2017). "The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization." Elife 6.

  Supported Research

  • Gallardo-Dodd, C. J., C. Oertlin, J. Record, R. G. Galvani, C. Sommerauer, N. V. Kuznetsov, E. Doukoumopoulos, L. Ali, M. M. S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A. A. Sadova, S. M. Shulgina, V. A. Shmarov, O. V. Kutko, D. D. Vlasova, K. D. Orlova, M. P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S. A. Ponomarev and L. S. Westerberg (2023). "Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells." Sci Adv 9(34): eadg1610.
  • Venit, T., O. Sapkota, W. S. Abdrabou, P. Loganathan, R. Pasricha, S. R. Mahmood, N. H. El Said, S. Sherif, S. Thomas, S. Abdelrazig, S. Amin, D. Bedognetti, Y. Idaghdour, M. Magzoub and P. Percipalle (2023). "Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice." Nat Commun 14(1): 6328.
  • Ajouaou, Y., E. Magnani, B. Madakashira, E. Jenkins and K. C. Sadler (2023). "atm Mutation and Oxidative Stress Enhance the Pre-Cancerous Effects of UHRF1 Overexpression in Zebrafish Livers." Cancers 15(8): 2302.
  • Wilcox, J. J. S., B. Arca-Ruibal, J. Samour, V. Mateuta, Y. Idaghdour and S. Boissinot (2022). "Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux." Genome Biol Evol 14(6).
  • Smith, E. G., K. M. Hazzouri, J. Y. Choi, P. Delaney, M. Al-Kharafi, E. J. Howells, M. Aranda and J. A. Burt (2022). "Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs." Sci Adv 8(2): eabl7287.
  • Macchi, F., E. Edsinger and K. C. Sadler (2022). "Epigenetic machinery is functionally conserved in cephalopods." BMC Biol 20(1): 202.
  • Goutte, S., I. Hariyani, K. D. Utzinger, Y. Bourgeois and S. Boissinot (2022). "Genomic Analyses Reveal Association of ASIP with a Recurrently evolving Adaptive Color Pattern in Frogs." Mol Biol Evol 39(11).
  • Flowers, J. M., K. M. Hazzouri, A. Lemansour, T. Capote, M. Gros-Balthazard, S. Ferrand, M. Lebrun, K. M. A. Amiri and M. D. Purugganan (2022). "Patterns of Volatile Diversity Yield Insights Into the Genetics and Biochemistry of the Date Palm Fruit Volatilome." Frontiers in Plant Science 13.
  • Zhang C., F. Macchi, E. Magnani and K. C. Sadler. (2021). "Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver." Nat Commun 12(1): 4110.
  • Palanikumar L. , L. Karpauskaite,M. Al-Sayegh,I. Chehade,M. Alam,S. Hassan, D. Maity,L. Ali, M. Kalmouni, Y. Hunashal,J. Ahmed, T. Houhou, S. Karapetyan, Z. Falls, R. Samudrala, R. Pasricha, G. Esposito, A. J. Afzal, A. D.Hamilton, S. Kumar and M. Magzoub. (2021). "Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function." Nature Communications 12(1): 3962.
  • Mahmood, S. R., X. Xie, N. Hosny El Said, T. Venit, K. C. Gunsalus and P. Percipalle (2021). "β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture." Nature Communications 12(1): 5240.
  • Magnani, E., F. Macchi, B. P. Madakashira, C. Zhang, F. Alaydaroos and K. C. Sadler (2021). "uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements." Front Immunol 12: 627926.
  • Madakashira, B. P., C. Zhang, F. Macchi, E. Magnani and K. C. Sadler (2021). "Nuclear Organization during Hepatogenesis in Zebrafish Requires Uhrf1." Genes (Basel) 12(7).
  • Al-Sayegh, M., H. Ali, M. H. Jamal, M. ElGindi, T. Chanyong, K. Al-Awadi and M. Abu-Farha (2021). "Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis." Adipocyte 10(1): 1-20.
  • Abdrabou, W., M. Dieng, A. Diawara, S. S. Sermé, D. Almojil, S. Sombié, N. B. Henry, D. Kargougou, V. Manikandan, I. Soulama and Y. Idaghdour. (2021). "Metabolome modulation of the host adaptive immunity in human malaria." Nature Metabolism.
  • Venit, T., M. Dowaidar, M. Gestin, S. R. Mahmood, Ü. Langel and P. Percipalle (2020). "Transcriptional Profiling Reveals Ribosome Biogenesis, Microtubule Dynamics and Expression of Specific lncRNAs to be Part of a Common Response to Cell-Penetrating Peptides." Biomolecules 10(11).
  • Souza Bomfim, G. H., V. Costiniti, Y. Li, Y. Idaghdour and R. S. Lacruz (2020). "TRPM7 activation potentiates SOCE in enamel cells but requires ORAI." Cell Calcium 87: 102187.
  • Friis, G., J. Vizueta, D. R. Nelson, B. Khraiwesh, E. Qudeimat, K. Salehi-Ashtiani, A. Ortega, A. Marshell, C. M. Duarte and J. A. Burt (2020). "A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina." G3, 10.1093.
  • Aulestia, F. J., J. Groeling, G. H. S. Bomfim, V. Costiniti, V. Manikandan, A. Chaloemtoem, A. R. Concepcion, Y. Li, L. E. Wagner, 2nd, Y. Idaghdour, D. I. Yule and R. S. Lacruz (2020). "Fluoride exposure alters Ca(2+) signaling and mitochondrial function in enamel cells." Sci Signal 13(619).
  • Xie, X., M. Endara-Coll, R. Mahmood, R. Jankauskas, T. Gjorgjieva and P. Percipalle (2019). "Mitochondria-localized beta-actin is essential for priming innate antiviral immune signaling by regulating IRF3 protein stability." Cell Mol Immunol 16(10): 837-840.
  • Wang, S., C. Zhang, D. Hasson, A. Desai, S. SenBanerjee, E. Magnani, C. Ukomadu, A. Lujambio, E. Bernstein and K. C. Sadler (2019). "Epigenetic Compensation Promotes Liver Regeneration." Dev Cell 50(1): 43-56 e46.
  • Valles, Y., C. K. Inman, B. A. Peters, L. A. Wareth, A. Abdulle, H. Alsafar, F. A. Anouti, A. A. Dhaheri, D. Galani, M. Haji, A. A. Hamiz, A. A. Hosani, M. A. Houqani, A. Aljunaibi, M. Kazim, T. Kirchhoff, W. A. Mahmeed, F. A. Maskari, A. Alnaeemi, N. Oumeziane, R. Ramasamy, A. M. Schmidt, H. Valles, E. A. Zaabi, S. Sherman, R. Ali, J. Ahn and R. B. Hayes (2019). "Incense Burning is Associated with Human Oral Microbiota Composition." Sci Rep 9(1): 10039.
  • Nelson, D. R., A. Chaiboonchoe, W. Fu, K. M. Hazzouri, Z. Huang, A. Jaiswal, S. Daakour, A. Mystikou, M. Arnoux, M. Sultana and K. Salehi-Ashtiani (2019). "Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae." iScience 11: 450-465.
  • Hazzouri, K. M., M. Gros-Balthazard, J. M. Flowers, D. Copetti, A. Lemansour, M. Lebrun, K. Masmoudi, S. Ferrand, M. I. Dhar, Z. A. Fresquez, U. Rosas, J. Zhang, J. Talag, S. Lee, D. Kudrna, R. F. Powell, I. J. Leitch, R. R. Krueger, R. A. Wing, K. M. A. Amiri and M. D. Purugganan (2019). "Genome-wide association mapping of date palm fruit traits." Nat Commun 10(1): 4680.
  • Flowers, J. M., K. M. Hazzouri, M. Gros-Balthazard, Z. Mo, K. Koutroumpa, A. Perrakis, S. Ferrand, H. S. M. Khierallah, D. Q. Fuller, F. Aberlenc, C. Fournaraki and M. D. Purugganan (2019). "Cross-species hybridization and the origin of North African date palms." Proc Natl Acad Sci U S A 116(5): 1651-1658.
  • Bourgeois, Y., R. P. Ruggiero, J. D. Manthey and S. Boissinot (2019). "Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis." Genome Biol Evol 11(7): 2009-2022.
  • Bourgeois, Y. and S. Boissinot (2019). "Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer." Mol Ecol 28(15): 3523-3543.
  • Xie, X., R. Jankauskas, A. M. A. Mazari, N. Drou and P. Percipalle (2018). "beta-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming." PLoS Genet 14(12): e1007846.
  • Xie, X., M. Deliorman, M. A. Qasaimeh and P. Percipalle (2018). "The relative composition of actin isoforms regulates cell surface biophysical features and cellular behaviors." Biochim Biophys Acta Gen Subj 1862(5): 1079-1090.
  • Xie, X., B. Almuzzaini, N. Drou, S. Kremb, A. Yousif, A. O. Farrants, K. Gunsalus and P. Percipalle (2018). "beta-Actin-dependent global chromatin organization and gene expression programs control cellular identity." FASEB J 32(3): 1296-1314.
  • Valles, Y., C. K. Inman, B. A. Peters, R. Ali, L. A. Wareth, A. Abdulle, H. Alsafar, F. A. Anouti, A. A. Dhaheri, D. Galani, M. Haji, A. A. Hamiz, A. A. Hosani, M. A. Houqani, A. A. Junaibi, M. Kazim, T. Kirchhoff, W. A. Mahmeed, F. A. Maskari, A. Alnaeemi, N. Oumeziane, R. Ramasamy, A. M. Schmidt, M. Weitzman, E. A. Zaabi, S. Sherman, R. B. Hayes and J. Ahn (2018). "Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study." Sci Rep 8(1): 11327.
  • Reyes-Velasco, J., J. D. Manthey, X. Freilich and S. Boissinot (2018). "Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia." Mol Ecol 27(9): 2256-2270.
  • Reyes-Velasco, J., J. D. Manthey, Y. Bourgeois, X. Freilich and S. Boissinot (2018). "Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data." PLoS One 13(2): e0190440.
  • Konstantinides, N., K. Kapuralin, C. Fadil, L. Barboza, R. Satija and C. Desplan (2018). "Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features." Cell 174(3): 622-635 e613.
  • Gruning, B., R. Dale, A. Sjodin, B. A. Chapman, J. Rowe, C. H. Tomkins-Tinch, R. Valieris, J. Koster and T. Bioconda (2018). "Bioconda: sustainable and comprehensive software distribution for the life sciences." Nat Methods 15(7): 475-476.
  • Al-Hrout, A., A. Chaiboonchoe, B. Khraiwesh, C. Murali, B. Baig, R. El-Awady, H. Tarazi, A. Alzahmi, D. R. Nelson, Y. E. Greish, W. Ramadan, K. Salehi-Ashtiani and A. Amin (2018). "Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells." Sci Rep 8(1): 16951.
  • Smith, E. G., R. N. Ketchum and J. A. Burt (2017). "Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach." ISME J 11(6): 1500-1503.
  • Ruggiero, R. P., Y. Bourgeois and S. Boissinot (2017). "LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis." Front Genet 8: 44.
  • Fu, W., A. Chaiboonchoe, B. Khraiwesh, M. Sultana, A. Jaiswal, K. Jijakli, D. R. Nelson, A. Al-Hrout, B. Baig, A. Amin and K. Salehi-Ashtiani (2017). "Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency." Sci Adv 3(9): e1603096.
  • Hazzouri, K. M., J. M. Flowers, H. J. Visser, H. S. M. Khierallah, U. Rosas, G. M. Pham, R. S. Meyer, C. K. Johansen, Z. A. Fresquez, K. Masmoudi, N. Haider, N. El Kadri, Y. Idaghdour, J. A. Malek, D. Thirkhill, G. S. Markhand, R. R. Krueger, A. Zaid and M. D. Purugganan (2015). "Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop." Nat Commun 6: 8824.
• High-throughput Screening Core
  • Pearson, Y. E., S. Kremb, G. L. Butterfoss, X. Xie, H. Fahs and K. C. Gunsalus (2022). "A statistical framework for high-content phenotypic profiling using cellular feature distributions." Commun Biol 5(1): 1409.
  • Murade, C. U., S. Chadhuri, I. Nabita, H. Fahs, F. Refai, K. Gunsalus and G. Shubeita (2020). "A FRET-based Probe for High Throughput DNA Intercalator Drug Discovery and In Vivo Imaging." Biophysical Journal 118(3, Supplement 1): 315a.
  • Xie, X., T. Gjorgjieva, Z. Attieh, M. Dieng, M. Arnoux, M. Khair, Y. Moussa, F. Al Jallaf, N. Rahiman, C. Jackson, L.E. Messery, K. Pamplona, Z. Victoria, M. Zafar, R. Ali, F. Piano, K. C. Gunsalus, and Y. Idaghdour (2020). "Microfluidic Nano-Scale qPCR enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2." Processes 8, no. 11: 1425.
  • Xie, X., B. Almuzzaini, N. Drou, S. Kremb, A. Yousif, A. O. Farrants, K. Gunsalus and P. Percipalle (2018). "beta-Actin-dependent global chromatin organization and gene expression programs control cellular identity." FASEB J 32(3): 1296-1314.

  Supported Research

  • Xie, X., T. Venit, N. Drou and P. Percipalle (2018). "In Mitochondria β-Actin Regulates mtDNA Transcription and Is Required for Mitochondrial Quality Control." iScience 3: 226-237.
• Fluorescence Activated Cell Sorting Core
  • Pallichankandy, S., F. Thayyullathil, A. R. Cheratta, K. Subburayan, A. Alakkal, M. Sultana, N. Drou, M. Arshad, S. Tariq and S. Galadari (2023). "Targeting oxeiptosis-mediated tumor suppression: a novel approach to treat colorectal cancers by sanguinarine." Cell Death Discov 9(1): 94. 
  • Nelson, D. R., A. Chaiboonchoe, W. Fu, K. M. Hazzouri, Z. Huang, A. Jaiswal, S. Daakour, A. Mystikou, M. Arnoux, M. Sultana and K. Salehi-Ashtiani (2019). "Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae." iScience 11: 450-465.
    
  • Fu, W., A. Chaiboonchoe, B. Khraiwesh, M. Sultana, A. Jaiswal, K. Jijakli, D. R. Nelson, A. Al-Hrout, B. Baig, A. Amin and K. Salehi-Ashtiani (2017). "Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency." Sci Adv 3(9): e1603096.
    
  • Abdrabu, R., S. K. Sharma, B. Khraiwesh, K. Jijakli, D. R. Nelson, A. Alzahmi, J. Koussa, M. Sultana, S. Khapli, R. Jagannathan and K. Salehi-Ashtiani (2016). Single-Cell Characterization of Microalgal Lipid Contents with Confocal Raman Microscopy. Essentials of Single-Cell Analysis: Concepts, Applications and Future Prospects. F.-G. Tseng and T. S. Santra. Berlin, Heidelberg, Springer Berlin Heidelberg: 363-382.

  Supported Research
  

  • Thayyullathil, F., A. R. Cheratta, A. Alakkal, K.Subburayan, S. Pallichankandy, Y. A. Hannun, & S. Galadari (2021). “Acid sphingomyelinase-dependent autophagic degradation of GPX4 is critical for the execution of ferroptosis”. Cell death & disease, 12(1), 26.
  • L. Palanikumar, L. Karpauskaite,M. Al-Sayegh,I. Chehade, M. Alam, S. Hassan, D. Maity, L. Ali, M. Kalmouni, Y. Hunashal, J. Ahmed, T. Houhou, S. Karapetyan, Z. Falls, R. Samudrala, R. Pasricha, G. Esposito, A. J. Afzal, A. D.Hamilton, S. Kumar and M. Magzoub. (2021). "Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function." Nature Communications 12(1): 3962.
  • Al-Sayegh, M., H. Ali, M. H. Jamal, M. ElGindi, T. Chanyong, K. Al-Awadi and M. Abu-Farha (2021). "Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis." Adipocyte 10(1): 1-20.
  • Abdrabou, W., M. Dieng, A. Diawara, S. S. Sermé, D. Almojil, S. Sombié, N. B. Henry, D. Kargougou, V. Manikandan, I. Soulama and Y. Idaghdour. (2021). "Metabolome modulation of the host adaptive immunity in human malaria." Nature Metabolism 3(7): 1001-1016.
  • Wang, H., F. Franco, Y. C. Tsui, X. Xie, M. P. Trefny, R. Zappasodi, S. R. Mohmood, J. Fernandez-Garcia, C. H. Tsai, I. Schulze, F. Picard, E. Meylan, R. Silverstein, I. Goldberg, S. M. Fendt, J. D. Wolchok, T. Merghoub, C. Jandus, A. Zippelius and P. C. Ho (2020). "CD36-mediated metabolic adaptation supports regulatory T cell survival and function in tumors." Nat Immunol 21(3): 298-308.
    
  • Subburayan K., F. Thayyullathil, S. Pallichankandy, AR. Cheratta, S. Galadari. (2020) “Superoxide-mediated ferroptosis in human cancer cells induced by sodium selenite”. Transl Oncol. 13(11):100843. 
    
  • Sharma, S. K., S. Al Hosani, M. Kalmouni, A. R. Nair, L. Palanikumar, R. Pasricha, K. C. Sadler, M. Magzoub and R. Jagannathan (2020). "Supercritical CO2 Processing Generates Aqueous Cisplatin Solutions with Enhanced Cancer Specificity." ACS Omega 5(9): 4558-4567.
    
  • Palanikumar, L., S. Al-Hosani, M. Kalmouni, H. O. Saleh and M. Magzoub (2020). "Hexokinase II-Derived Cell-Penetrating Peptide Mediates Delivery of MicroRNA Mimic for Cancer-Selective Cytotoxicity." Biochemistry 59(24): 2259-2273.
  • Palanikumar, L., S. Al-Hosani, M. Kalmouni, V. P. Nguyen, L. Ali, R. Pasricha, F. N. Barrera and M. Magzoub (2020). "pH-responsive high stability polymeric nanoparticles for targeted delivery of anticancer therapeutics." Commun Biol 3(1): 95.
  • Xie, X., M. Endara-Coll, R. Mahmood, R. Jankauskas, T. Gjorgjieva and P. Percipalle (2019). "Mitochondria-localized beta-actin is essential for priming innate antiviral immune signaling by regulating IRF3 protein stability." Cell Mol Immunol 16(10): 837-840.
  • Wang, S., C. Zhang, D. Hasson, A. Desai, S. SenBanerjee, E. Magnani, C. Ukomadu, A. Lujambio, E. Bernstein and K. C. Sadler (2019). "Epigenetic Compensation Promotes Liver Regeneration." Dev Cell 50(1): 43-56 e46.
  • u, W., D. R. Nelson, A. Mystikou, S. Daakour and K. Salehi-Ashtiani (2019). "Advances in microalgal research and engineering development." Curr Opin Biotechnol 59: 157-164.
  • Xie, X., T. Venit, N. Drou and P. Percipalle (2018). "In Mitochondria Beta-Actin Regulates mtDNA Transcription and Is Required for Mitochondrial Quality Control." iScience 3: 226-237.
    
  • Xie, X. and P. Percipalle (2018). "Elevated transforming growth factor beta signaling activation in beta-actin-knockout mouse embryonic fibroblasts enhances myofibroblast features." J Cell Physiol 233(11): 8884-8895.
    
  • Xie, X., M. Deliorman, M. A. Qasaimeh and P. Percipalle (2018). "The relative composition of actin isoforms regulates cell surface biophysical features and cellular behaviors." Biochim Biophys Acta Gen Subj 1862(5): 1079-1090.
    
  • Konstantinides, N., K. Kapuralin, C. Fadil, L. Barboza, R. Satija and C. Desplan (2018). "Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features." Cell 174(3): 622-635 e613.
  • Al-Hrout, A., A. Chaiboonchoe, B. Khraiwesh, C. Murali, B. Baig, R. El-Awady, H. Tarazi, A. Alzahmi, D. R. Nelson, Y. E. Greish, W. Ramadan, K. Salehi-Ashtiani and A. Amin (2018). "Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells." Sci Rep 8(1): 16951.
  • Nelson, D. R., B. Khraiwesh, W. Fu, S. Alseekh, A. Jaiswal, A. Chaiboonchoe, K. M. Hazzouri, M. J. O'Connor, G. L. Butterfoss, N. Drou, J. D. Rowe, J. Harb, A. R. Fernie, K. C. Gunsalus and K. Salehi-Ashtiani (2017). "The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization." Elife 6.
  • Sharma, S. K., D. R. Nelson, R. Abdrabu, B. Khraiwesh, K. Jijakli, M. Arnoux, M. J. O'Connor, T. Bahmani, H. Cai, S. Khapli, R. Jagannathan and K. Salehi-Ashtiani (2015). "An integrative Raman microscopy-based workflow for rapid in situ analysis of microalgal lipid bodies." Biotechnol Biofuels 8: 164.
  • Flowers, J. M., K. M. Hazzouri, G. M. Pham, U. Rosas, T. Bahmani, B. Khraiwesh, D. R. Nelson, K. Jijakli, R. Abdrabu, E. H. Harris, P. A. Lefebvre, E. F. Hom, K. Salehi-Ashtiani and M. D. Purugganan (2015). "Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii." Plant Cell 27(9): 2353-2369.

• Algal Genomics and Synthetic Biology

  Principal Investigator: Kourosh Salehi-Ashtiani

  • Al-Khairy, D., W. Fu, A. S. Alzahmi, J. C. Twizere, S. A. Amin, K. Salehi-Ashtiani and A. Mystikou (2022). "Closing the Gap between Bio-Based and Petroleum-Based Plastic through Bioengineering." Microorganisms 10(12).
  • Nelson, D. R., A. Chaiboonchoe, K. M. Hazzouri, B. Khraiwesh, A. Alzahmi, A. Jaiswal, G. Friis, J. A. Burt, K. M. A. Amiri and K. Salehi-Ashtiani (2022). "Tissue-Specific Transcriptomes Outline Halophyte Adaptive Strategies in the Gray Mangrove (Avicennia marina)." Agronomy 12(9): 2030.
  • Hazzouri, K. M., N. Sudalaimuthuasari, E. E. Saeed, B. Kundu, R. S. Al-Maskari, D. Nelson, A. A. AlShehhi, M. A. Aldhuhoori, D. S. Almutawa, F. R. Alshehhi, J. Balan, S. Mundra, M. Alam, K. Salehi-Ashtiani, M. Purugganan and K. M. A. Amiri (2022). "Salt flat microbial diversity and dynamics across salinity gradient." Sci Rep 12(1): 11293.
    
  • Kerselidou, D., B. S. Dohai, D. R. Nelson, S. Daakour, N. De Cock, Z. A. O. Hassoun, D. K. Kim, J. Olivet, D. C. El Assal, A. Jaiswal, A. Alzahmi, D. Saha, C. Pain, F. Matthijssens, P. Lemaitre, M. Herfs, J. Chapuis, B. Ghesquiere, D. Vertommen, V. Kriechbaumer, K. Knoops, C. Lopez-Iglesias, M. van Zandvoort, J. C. Lambert, J. Hanson, C. Desmet, M. Thiry, K. J. Lauersen, M. Vidal, P. Van Vlierberghe, F. Dequiedt, K. Salehi-Ashtiani and J. C. Twizere (2021). "Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells." Sci Adv 7(19).
  • Alzahmi, A., S. Daakour, D. C. El Assal, B. S. Dohai, A. Chaiboonchoe, W. Fu, D. R. Nelson, A. Mystikou and K. Salehi-Ashtiani (2021). "High-Throughput Metabolic Profiling for Model Refinements of Microalgae." J Vis Exp (178).
  • Al-Shehhi, M. R., D. Nelson, R. Farzanah, R. Alshihi and K. Salehi-Ashtiani (2021). "Characterizing algal blooms in a shallow & a deep channel." Ocean & Coastal Management 213: 105840.
  • Nelson, D. R., K. M. Hazzouri, K. J. Lauersen, A. Jaiswal, A. Chaiboonchoe, A. Mystikou, Weiqi Fu, S. Daakour, A. Alzahmi, D. Nobles, M. Hurd, J. Sexton, M. Preston, J. Blanchette, M. Lomas, K. Salehi-Ashtiani (2021) “Large-scale sequencing of diverse microalgal genomes reveals a genic basis for salt tolerance.” Cell Host & Microbe 1934-6069.
  • Fu, W., B. Dohai, D. C. El Assal, S. Daakour, A. Alzahmi, D. R. Nelson, A. Jaiswal, A. Mystikou, M. Sultana, J. Weston and K. Salehi-Ashtiani (2021). "Protocol to generate and characterize biofouling transformants of a model marine diatom." STAR Protocols 2(3): 100716.
  • Friis, G., J. Vizueta, E. G. Smith, D. R. Nelson, B. Khraiwesh, E. Qudeimat, K. Salehi-Ashtiani, A. Ortega, A. Marshell, C. M. Duarte and J. A. Burt (2020). "A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina." G3 10.1093.
  • Wierbowski, S. D., T. V. Vo, P. Falter-Braun, T. O. Jobe, L. H. Kruse, X. Wei, J. Liang, M. J. Meyer, N. Akturk, C. A. Rivera-Erick, N. A. Cordero, M. I. Paramo, E. E. Shayhidin, M. Bertolotti, N. D. Tippens, K. Akther, R. Sharma, Y. Katayose, K. Salehi-Ashtiani, T. Hao, P. C. Ronald, J. R. Ecker, P. A. Schweitzer, S. Kikuchi, H. Mizuno, D. E. Hill, M. Vidal, G. D. Moghe, S. R. McCouch and H. Yu (2020). "A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice." Proc Natl Acad Sci U S A 117(21): 11836-11842.
    
  • Fu, W., A. Chaiboonchoe, B. Dohai, M. Sultana, K. Baffour, A. Alzahmi, J. Weston, D. Al Khairy, S. Daakour, A. Jaiswal, D. R. Nelson, A. Mystikou, S. Brynjolfsson and K. Salehi-Ashtiani (2020). "GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine Diatom." iScience 23(8): 101424.
    
  • Al Shehhi, M., D. Nelson, R. R Alkhori, R. Alshihi, K. Salehi-Ashtiani (2020). "Characterizing Algal blooms in a shallow and a deep channel over a decade (2008-2018)." Quantitative Biology > Populations and Evolution - Cornell University.
  • Yi, Z., Y. Su, P. Cherek, D. R. Nelson, J. Lin, O. Rolfsson, H. Wu, K. Salehi-Ashtiani, S. Brynjolfsson and W. Fu (2019). "Combined artificial high-silicate medium and LED illumination promote carotenoid accumulation in the marine diatom Phaeodactylum tricornutum." Microb Cell Fact 18(1): 209.
    
  • Nelson, D. R., A. Chaiboonchoe, W. Fu, K. M. Hazzouri, Z. Huang, A. Jaiswal, S. Daakour, A. Mystikou, M. Arnoux, M. Sultana and K. Salehi-Ashtiani (2019). "Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae." iScience 11: 450-465.
    
  • Fu, W., D. R. Nelson, A. Mystikou, S. Daakour and K. Salehi-Ashtiani (2019). "Advances in microalgal research and engineering development." Curr Opin Biotechnol 59: 157-164.
    
  • Hazzouri, K. M., B. Khraiwesh, K. M. A. Amiri, D. Pauli, T. Blake, M. Shahid, S. K. Mullath, D. Nelson, A. L. Mansour, K. Salehi-Ashtiani, M. Purugganan and K. Masmoudi (2018). "Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism." Front Plant Sci 9: 156.
    
  • Al-Hrout, A., A. Chaiboonchoe, B. Khraiwesh, C. Murali, B. Baig, R. El-Awady, H. Tarazi, A. Alzahmi, D. R. Nelson, Y. E. Greish, W. Ramadan, K. Salehi-Ashtiani and A. Amin (2018). "Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells." Sci Rep 8(1): 16951.
    
  • Nelson, D. R., B. Khraiwesh, W. Fu, S. Alseekh, A. Jaiswal, A. Chaiboonchoe, K. M. Hazzouri, M. J. O'Connor, G. L. Butterfoss, N. Drou, J. D. Rowe, J. Harb, A. R. Fernie, K. C. Gunsalus and K. Salehi-Ashtiani (2017). "The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization." Elife 6.
    
  • Khraiwesh, B. and K. Salehi-Ashtiani (2017). "Alternative Poly(A) Tails Meet miRNA Targeting in Caenorhabditis elegans." Genetics 206(2): 755-756.
    
  • Fu, W., A. Chaiboonchoe, B. Khraiwesh, M. Sultana, A. Jaiswal, K. Jijakli, D. R. Nelson, A. Al-Hrout, B. Baig, A. Amin and K. Salehi-Ashtiani (2017). "Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency." Sci Adv 3(9): e1603096.
    
  • Jijakli, K., B. Khraiwesh, W. Fu, L. Luo, A. Alzahmi, J. Koussa, A. Chaiboonchoe, S. Kirmizialtin, L. Yen and K. Salehi-Ashtiani (2016). "The in vitro selection world." Methods 106: 3-13.
  • Fu, W., A. Chaiboonchoe, B. Khraiwesh, D. R. Nelson, D. Al-Khairy, A. Mystikou, A. Alzahmi and K. Salehi-Ashtiani (2016). "Algal Cell Factories: Approaches, Applications, and Potentials." Mar Drugs 14(12).
  • Chaiboonchoe, A., L. Ghamsari, B. Dohai, P. Ng, B. Khraiwesh, A. Jaiswal, K. Jijakli, J. Koussa, D. R. Nelson, H. Cai, X. Yang, R. L. Chang, J. Papin, H. Yu, S. Balaji and K. Salehi-Ashtiani (2016). "Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation." Mol Biosyst 12(8): 2394-2407.
  • Sharma, S. K., D. R. Nelson, R. Abdrabu, B. Khraiwesh, K. Jijakli, M. Arnoux, M. J. O'Connor, T. Bahmani, H. Cai, S. Khapli, R. Jagannathan and K. Salehi-Ashtiani (2015). "An integrative Raman microscopy-based workflow for rapid in situ analysis of microalgal lipid bodies." Biotechnol Biofuels 8: 164.
    
  • Khraiwesh, B., E. Qudeimat, M. Thimma, A. Chaiboonchoe, K. Jijakli, A. Alzahmi, M. Arnoux and K. Salehi-Ashtiani (2015). "Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response." Sci Rep 5: 17434.
    
  • Flowers, J. M., K. M. Hazzouri, G. M. Pham, U. Rosas, T. Bahmani, B. Khraiwesh, D. R. Nelson, K. Jijakli, R. Abdrabu, E. H. Harris, P. A. Lefebvre, E. F. Hom, K. Salehi-Ashtiani and M. D. Purugganan (2015). "Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii." Plant Cell 27(9): 2353-2369.
    
  • Chaiboonchoe, A., B. S. Dohai, H. Cai, D. R. Nelson, K. Jijakli and K. Salehi-Ashtiani (2014). "Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling." Front Bioeng Biotechnol 2: 68.
  • Mangone, M., A. P Manoharan, D.Thierry-Mieg, J. Thierry-Mieg, T. Han, S. D. Mackowiak, E. Mis, C. Zegar, M. R. Gutwein, V. Khivansara, O. Attie, K. Chen, K. Salehi-Ashtiani, M. Vidal, T. T. Harkins, P. Bouffard, Y. Suzuki, S. Sugano, Y. Kohara, N. Rajewsky, F. Piano, K. C. Gunsalus and J. K. Kim . (2010). "The landscape of C. elegans 3'UTRs." Science 329(5990): 432-435.

  Chapter Books
  

  • Fu, W., D. R. Nelson, Z. Yi, M. Xu, B. Khraiwesh, K. Jijakli, A. Chaiboonchoe, A. Alzahmi, D. Al-Khairy, S. Brynjolfsson and K. Salehi-Ashtiani (2017). Chapter 6 - Bioactive Compounds From Microalgae: Current Development and Prospects. Studies in Natural Products Chemistry. R. Atta ur, Elsevier. 54: 199-225. 
  • Abdrabu, R., S. K. Sharma, B. Khraiwesh, K. Jijakli, D. R. Nelson, A. Alzahmi, J. Koussa, M. Sultana, S. Khapli, R. Jagannathan and K. Salehi-Ashtiani (2016). Single-Cell Characterization of Microalgal Lipid Contents with Confocal Raman Microscopy. Essentials of Single-Cell Analysis: Concepts, Applications and Future Prospects. F.-G. Tseng and T. S. Santra. Berlin, Heidelberg, Springer Berlin Heidelberg: 363-382. 
  • Salehi-Ashtiani, K., J. Koussa, B. S. Dohai, A. Chaiboonchoe, H. Cai, K. A. D. Dougherty, D. R. Nelson, K. Jijakli and B. Khraiwesh (2015). Toward Applications of Genomics and Metabolic Modeling to Improve Algal Biomass Productivity. Biomass and Biofuels from Microalgae: Advances in Engineering and Biology. N. R. Moheimani, M. P. McHenry, K. de Boer and P. A. Bahri. Cham, Springer International Publishing: 173-189. 
  • Khraiwesh, B., K. Jijakli, J. Swift, A. Chaiboonchoe, R. Abdrabu, P.-W. Chao, L. Yen and K. Salehi-Ashtiani (2015). Prospective Applications of Synthetic Biology for Algal Bioproduct Optimization. Biomass and Biofuels from Microalgae: Advances in Engineering and Biology. N. R. Moheimani, M. P. McHenry, K. de Boer and P. A. Bahri. Cham, Springer International Publishing: 137-154. 
    
  • Jijakli, K., R. Abdrabu, B. Khraiwesh, D. R. Nelson, J. Koussa and K. Salehi-Ashtiani (2015). Molecular Genetic Techniques for Algal Bioengineering. Biomass and Biofuels from Microalgae: Advances in Engineering and Biology. N. R. Moheimani, M. P. McHenry, K. de Boer and P. A. Bahri. Cham, Springer International Publishing: 155-171.
  • Koussa, J., A. Chaiboonchoe and K. Salehi-Ashtiani (2014). "Computational approaches for microalgal biofuel optimization: a review." Biomed Res Int 2014: 649453.

  Publications by Group Members
  

  • Orfanidis, S., V. Papathanasiou, N. Mittas, T. Theodosiou, A. Ramfos, S. Tsioli, M. Kosmidou, A. Kafas, A. Mystikou and A. Papadimitriou (2020). "Further improvement, validation, and application of CymoSkew biotic index for the ecological status assessment of the Greek coastal and transitional waters." Ecological Indicators 118: 106727.
  • Hazzouri, K. M., N. Sudalaimuthuasari, B. Kundu, D. Nelson, M. A. Al-Deeb, A. Le Mansour, J. J. Spencer, C. Desplan and K. M. A. Amiri (2020). "The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface." Commun Biol 3(1): 323.
  • Hazzouri, K. M., J. M. Flowers, D. Nelson, A. Lemansour, K. Masmoudi and K. M. A. Amiri (2020). "Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era." Front Plant Sci 11: 293.
  • Fu, W., B. Khraiwesh, H. Liu and L. Kai (2016). "Advances in Biotechnology for Sustainable Development." Biomed Res Int 2016: 7154916. 
    
  • Khan, M. S., B. Khraiwesh, G. Pugalenthi, R. S. Gupta, J. Singh, S. K. Duttamajumder and R. Kapur (2014). "Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)." FEBS Open Bio 4: 533-541.
• Cortical Interneurons

  Principal Investigator: Gordon J. Fishell
  

  • Pouchelon, G., D. Dwivedi, Y. Bollmann, C. K. Agba, Q. Xu, A. M. C. Mirow, S. Kim, Y. Qiu, E. Sevier, K. D. Ritola, R. Cossart and G. Fishell (2021). "The organization and development of cortical interneuron presynaptic circuits are area specific." Cell Rep 37(6): 109993.
  • Ibrahim, L. A., S. Huang, M. Fernandez-Otero, M. Sherer, Y. Qiu, S. Vemuri, Q. Xu, R. Machold, G. Pouchelon, B. Rudy and G. Fishell (2021). "Bottom-up inputs are required for establishment of top-down connectivity onto cortical layer 1 neurogliaform cells." Neuron 109(21): 3473-3485.e3475.
  • Favuzzi, E., S. Huang, G. A. Saldi, L. Binan, L. A. Ibrahim, M. Fernandez-Otero, Y. Cao, A. Zeine, A. Sefah, K. Zheng, Q. Xu, E. Khlestova, S. L. Farhi, R. Bonneau, S. R. Datta, B. Stevens and G. Fishell (2021). "GABA-receptive microglia selectively sculpt developing inhibitory circuits." Cell 184(15): 4048-4063 e4032.
  • Vormstein-Schneider, D., J. D. Lin, K. A. Pelkey, R. Chittajallu, B. Guo, M. A. Arias-Garcia, K. Allaway, S. Sakopoulos, G. Schneider, O. Stevenson, J. Vergara, J. Sharma, Q. Zhang, T. P. Franken, J. Smith, L. A. Ibrahim, M. A. KJ, E. Sabri, S. Huang, E. Favuzzi, T. Burbridge, Q. Xu, L. Guo, I. Vogel, V. Sanchez, G. A. Saldi, B. L. Gorissen, X. Yuan, K. A. Zaghloul, O. Devinsky, B. L. Sabatini, R. Batista-Brito, J. Reynolds, G. Feng, Z. Fu, C. J. McBain, G. Fishell and J. Dimidschstein (2020). "Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans." Nat Neurosci 23, 1629-1636.
    
  • Pelkey, K. A., D. Calvigioni, C. Fang, G. Vargish, T. Ekins, K. Auville, J. C. Wester, M. Lai, C. Mackenzie-Gray Scott, X. Yuan, S. Hunt, D. Abebe, Q. Xu, J. Dimidschstein, G. Fishell, R. Chittajallu and C. J. McBain (2020). "Paradoxical network excitation by glutamate release from VGluT3(+) GABAergic interneurons." Elife 9.
    
  • Wamsley, B., L. A. Ibrahim, N. Yusuf, E. Fisher, X. H. Jaglin, Q. Xu, L. Guo, A. Khodadadi-Jamayran, E. Favuzzi, Y. Yuan, J. Dimidschstein, R. Darnell and G. Fishell (2019). "Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing." bioRxiv: 845230.
    
  • Wilson, D. E., G. B. Smith, A. L. Jacob, T. Walker, J. Dimidschstein, G. Fishell and D. Fitzpatrick (2017). "GABAergic Neurons in Ferret Visual Cortex Participate in Functionally Specific Networks." Neuron 93(5): 1058-1065 e1054.
  • Dimidschstein, J., Q. Chen, R. Tremblay, S. L. Rogers, G. A. Saldi, L. Guo, Q. Xu, R. Liu, C. Lu, J. Chu, J. S. Grimley, A. R. Krostag, A. Kaykas, M. C. Avery, M. S. Rashid, M. Baek, A. L. Jacob, G. B. Smith, D. E. Wilson, G. Kosche, I. Kruglikov, T. Rusielewicz, V. C. Kotak, T. M. Mowery, S. A. Anderson, E. M. Callaway, J. S. Dasen, D. Fitzpatrick, V. Fossati, M. A. Long, S. Noggle, J. H. Reynolds, D. H. Sanes, B. Rudy, G. Feng and G. Fishell (2016). "A viral strategy for targeting and manipulating interneurons across vertebrate species." Nat Neurosci 19(12): 1743-1749.

  Publications by Group Members

  • Liu, H., A. Rastogi, P. Narain, Q. Xu, M. Sabanovic, A. D. Alhammadi, L. Guo, J. L. Cao, H. Zhang, H. Aqel, V. Mlambo, R. Rezgui, B. Radwan and D. Chaudhury (2021). "Blunted diurnal firing in lateral habenula projections to dorsal raphe nucleus and delayed photoentrainment in stress-susceptible mice." PLoS Biol 19(3): e3000709.
    
• Mangrove Adaptation Evolution

  Principal Investigator: John Burt

  • Friis, G., E. G. Smith, C. E. Lovelock, A. Ortega, A. Marshell, C. M. Duarte and J. A. Burt (2024). "Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula." Mol Ecol: e17260.
  • Smith, E. G., K. M. Hazzouri, J. Y. Choi, P. Delaney, M. Al-Kharafi, E. J. Howells, M. Aranda and J. A. Burt (2022). "Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs." Sci Adv 8(2): eabl7287.
    
  • Nelson, D. R., A. Chaiboonchoe, K. M. Hazzouri, B. Khraiwesh, A. Alzahmi, A. Jaiswal, G. Friis, J. A. Burt, K. M. A. Amiri and K. Salehi-Ashtiani (2022). "Tissue-Specific Transcriptomes Outline Halophyte Adaptive Strategies in the Gray Mangrove (Avicennia marina)." Agronomy 12(9): 2030.
  • Ketchum, R. N., P. L. Davidson, E. G. Smith, G. A. Wray, J. A. Burt, J. F. Ryan and A. M. Reitzel (2022). "A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes." Genome Biol Evol 14(10).
  • Howells, E. J., M. Hagedorn, M. J. H. Van Oppen and J. A. Burt (2022). "Challenges of sperm cryopreservation in transferring heat adaptation of corals across ocean basins." PeerJ 10: e13395.
  • Al-Khairy, D., W. Fu, A. S. Alzahmi, J. C. Twizere, S. A. Amin, K. Salehi-Ashtiani and A. Mystikou (2022). "Closing the Gap between Bio-Based and Petroleum-Based Plastic through Bioengineering." Microorganisms 10(12).
  • Torquato, F., J. Bouwmeester, P. Range, A. Marshell, M. A. Priest, J. A. Burt, P. R. Møller and R. Ben-Hamadou (2021). "Population genetic structure of a major reef-building coral species Acropora downingi in northeastern Arabian Peninsula." Coral Reefs.
  • Melville-Rea, H., C. Eayrs, N. Anwahi, J. A. Burt, D. Holland, F. Samara, F. Paparella, A. H. Al Murshidi, M. R. Al-Shehhi and D. M. Holland (2021). "A Roadmap for Policy-Relevant Sea-Level Rise Research in the United Arab Emirates." Frontiers in Marine Science 8.
  • Mateos-Molina, D., E. Ben Lamine, M. Antonopoulou, J. A. Burt, H. S. Das, S. Javed, J. Judas, S. B. Khan, S. B. Muzaffar, N. Pilcher, C. J. Rodriguez-Zarate, O. J. S. Taylor and S. Giakoumi (2021). "Synthesis and evaluation of coastal and marine biodiversity spatial information in the United Arab Emirates for ecosystem-based management." Marine Pollution Bulletin 167: 112319.
  •  Le Quesne, W. J. F., L. Fernand, T. S. Ali, O. Andres, M. Antonpoulou, J. A. Burt, W. W. Dougherty, P. J. Edson, J. El Kharraz, J. Glavan, R. J. Mamiit, K. D. Reid, A. Sajwani and D. Sheahan (2021). "Is the development of desalination compatible with sustainable development of the Arabian Gulf?" Mar Pollut Bull 173(Pt A): 112940.
  • Ketchum, R. N., E. G. Smith, G. O. Vaughan, D. McParland, N. Al-Mansoori, J. A. Burt and A. M. Reitzel (2021). "Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients." Mol Ecol 30(15): 3869-3881.
  • Howells, E. J., D. Abrego, Y. J. Liew, J. A. Burt, E. Meyer and M. Aranda (2021). "Enhancing the heat tolerance of reef-building corals to future warming." Sci Adv 7(34).
  • De Verneil, A., J. A. Burt, M. Mitchell and F. Paparella (2021). "Summer Oxygen Dynamics on a Southern Arabian Gulf Coral Reef." Frontiers in Marine Science 8(1676).
  • Bouwmeester, J., R. Riera, P. Range, R. Ben-Hamadou, K. Samimi-Namin and J. Burt (2021). "Coral and Reef Fish Communities in the Thermally Extreme Persian/Arabian Gulf: Insights into Potential Climate Change Effects" 63-86.
  • Baird, A. H., J. R. Guest, A. J. Edwards, A. G. Bauman, J. Bouwmeester, H. Mera, D. Abrego, M. Alvarez-Noriega, R. C. Babcock, M. B. Barbosa, V. Bonito, J. Burt, P. C. Cabaitan, C. F. Chang, S. Chavanich, C. A. Chen, C. J. Chen, W. J. Chen, F. C. Chung, S. R. Connolly, V. R. Cumbo, M. Dornelas, C. Doropoulos, G. Eyal, L. Eyal-Shaham, N. Fadli, J. Figueiredo, J. F. Flot, S. H. Gan, E. Gomez, E. M. Graham, M. Grinblat, N. Gutiérrez-Isaza, S. Harii, P. L. Harrison, M. Hatta, N. A. J. Ho, G. Hoarau, M. Hoogenboom, E. J. Howells, A. Iguchi, N. Isomura, E. A. Jamodiong, S. Jandang, J. Keyse, S. Kitanobo, N. Kongjandtre, C. Y. Kuo, C. Ligson, C. H. Lin, J. Low, Y. Loya, E. A. Maboloc, J. S. Madin, T. Mezaki, C. Min, M. Morita, A. Moya, S. H. Neo, M. R. Nitschke, S. Nojima, Y. Nozawa, S. Piromvaragorn, S. Plathong, E. Puill-Stephan, K. Quigley, C. Ramirez-Portilla, G. Ricardo, K. Sakai, E. Sampayo, T. Shlesinger, L. Sikim, C. Simpson, C. A. Sims, F. Sinniger, D. A. Spiji, T. Tabalanza, C. H. Tan, T. I. Terraneo, G. Torda, J. True, K. Tun, K. Vicentuan, V. Viyakarn, Z. Waheed, S. Ward, B. Willis, R. M. Woods, E. S. Woolsey, H. H. Yamamoto and S. Yusuf (2021). "An Indo-Pacific coral spawning database." Sci Data 8(1): 35.
  • Mateos-Molina, D., M. Antonopoulou, R. Baldwin, I. Bejarano, J. A. Burt, J. A. García-Charton, S. M. Al-Ghais, J. Walgamage and O. J. S. Taylor (2020). "Applying an integrated approach to coastal marine habitat mapping in the north-western United Arab Emirates." Mar Environ Res 161: 105095.
  • Liew, Y. J., E. J. Howells, X. Wang, C. T. Michell, J. A. Burt, Y. Idaghdour and M. Aranda (2020). "Intergenerational epigenetic inheritance in reef-building corals." Nature Climate Change 10(3): 254-259.
  •  Ketchum, R. N., E. G. Smith, M. B. DeBiasse, G. O. Vaughan, D. McParland, W. B. Leach, N. Al-Mansoori, J. F. Ryan, J. A. Burt and A. M. Reitzel (2020). "Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient." Genome Biol Evol 12(10): 1819-1829.
  •  Howells, E. J., A. G. Bauman, G. O. Vaughan, B. C. C. Hume, C. R. Voolstra and J. A. Burt (2020). "Corals in the hottest reefs in the world exhibit symbiont fidelity not flexibility." Mol Ecol 29(5): 899-911.
  • Friis, G., J. Vizueta, D. R. Nelson, B. Khraiwesh, E. Qudeimat, K. Salehi-Ashtiani, A. Ortega, A. Marshell, C. M. Duarte and J. A. Burt (2020). "A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina." G3, 10.1093.
  • Friis, G. and J. A. Burt (2020). "Evolution of mangrove research in an extreme environment: Historical trends and future opportunities in Arabia." Ocean & Coastal Management 195: 105288. (Review article)
  • Clarke, S. A., L. Vilizzi, L. Lee, L. E. Wood, W. J. Cowie, J. A. Burt, R. J. E. Mamiit, H. Ali, P. I. Davison, G. V. Fenwick, R. Harmer, M. E. Skóra, S. Kozic, L. R. Aislabie, A. Kennerley, W. J. F. Le Quesne, G. H. Copp and P. D. Stebbing (2020). "Identifying potentially invasive non-native marine and brackish water species for the Arabian Gulf and Sea of Oman." Glob Chang Biol 26(4): 2081-2092.
  • Brandl, S. J., J. L. Johansen, J. M. Casey, L. Tornabene, R. A. Morais and J. A. Burt (2020). "Extreme environmental conditions reduce coral reef fish biodiversity and productivity." Nat Commun 11(1): 3832.
  • Torquato, F., P. Range, R. Ben-Hamadou, E. E. Sigsgaard, P. F. Thomsen, R. Riera, M. L. Berumen, J. A. Burt, D. A. Feary, A. Marshell, D. D'Agostino, J. D. DiBattista and P. R. Møller (2019). "Consequences of marine barriers for genetic diversity of the coral-specialist yellowbar angelfish from the Northwestern Indian Ocean." Ecol Evol 9(19): 11215-11226.
  • Hume, B. C. C., E. G. Smith, M. Ziegler, H. J. M. Warrington, J. A. Burt, T. C. LaJeunesse, J. Wiedenmann and C. R. Voolstra (2019). "SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling." Mol Ecol Resour 19(4): 1063-1080.
  • Burt, J. A. and A. Bartholomew (2019). "Towards more sustainable coastal development in the Arabian Gulf: Opportunities for ecological engineering in an urbanized seascape." Mar Pollut Bull 142: 93-102.
  • Riegl, B., M. Johnston, S. Purkis, E. Howells, J. Burt, S. C. C. Steiner, C. R. C. Sheppard and A. Bauman (2018). "Population collapse dynamics in Acropora downingi, an Arabian/Persian Gulf ecosystem-engineering coral, linked to rising temperature." Glob Chang Biol 24(6): 2447-2462.
  • Kirk, N. L., E. J. Howells, D. Abrego, J. A. Burt and E. Meyer (2018). "Genomic and transcriptomic signals of thermal tolerance in heat-tolerant corals (Platygyra daedalea) of the Arabian/Persian Gulf." Mol Ecol 27(24): 5180-5194.
  • Ketchum, R. N., M. B. DeBiasse, J. F. Ryan, J. A. Burt and A. M. Reitzel (2018). "The complete mitochondrial genome of the sea urchin,." Mitochondrial DNA B Resour 3(2): 1225-1227.
  • Hume, B. C. C., C. D'Angelo, E. G. Smith, J. R. Stevens, J. A. Burt and J. Wiedenmann (2018). "Validation of the binary designation Symbiodinium thermophilum (Dinophyceae)." J Phycol 54(5): 762-764.
  • Ziegler, M., C. Arif, J. A. Burt, S. Dobretsov, C. Roder, T. C. LaJeunesse and C. R. Voolstra (2017). "Biogeography and molecular diversity of coral symbionts in the genus." J Biogeogr 44(3): 674-686.
  • Smith, E. G., R. N. Ketchum and J. A. Burt (2017). "Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach." ISME J 11(6): 1500-1503.
  • Pratchett, M. S., A. H. Baird, A. G. Bauman and J. A. Burt (2017). "Abundance and composition of juvenile corals reveals divergent trajectories for coral assemblages across the United Arab Emirates." Mar Pollut Bull 114(2): 1031-1035.
  • Hadaidi, G., T. Röthig, L. K. Yum, M. Ziegler, C. Arif, C. Roder, J. Burt and C. R. Voolstra (2017). "Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas." Sci Rep 7: 45362.
  • Vaughan, G. O. and J. A. Burt (2016). "The changing dynamics of coral reef science in Arabia." Mar Pollut Bull 105(2): 441-458.
  • Shuail, D., J. Wiedenmann, C. D'Angelo, A. H. Baird, M. S. Pratchett, B. Riegl, J. A. Burt, P. Petrov and C. Amos (2016). "Local bleaching thresholds established by remote sensing techniques vary among reefs with deviating bleaching patterns during the 2012 event in the Arabian/Persian Gulf." Mar Pollut Bull 105(2): 654-659.
  • Hume, B. C., C. R. Voolstra, C. Arif, C. D'Angelo, J. A. Burt, G. Eyal, Y. Loya and J. Wiedenmann (2016). "Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change." Proc Natl Acad Sci U S A 113(16): 4416-4421.
  • Howells, E. J., R. N. Ketchum, A. G. Bauman, Y. Mustafa, K. D. Watkins and J. A. Burt (2016). "Species-specific trends in the reproductive output of corals across environmental gradients and bleaching histories." Mar Pollut Bull 105(2): 532-539.
  • Howells, E. J., D. Abrego, E. Meyer, N. L. Kirk and J. A. Burt (2016). "Host adaptation and unexpected symbiont partners enable reef-building corals to tolerate extreme temperatures." Glob Chang Biol 22(8): 2702-2714.
  • Grizzle, R. E., K. M. Ward, R. M. AlShihi and J. A. Burt (2016). "Current status of coral reefs in the United Arab Emirates: Distribution, extent, and community structure with implications for management." Mar Pollut Bull 105(2): 515-523.
  • Cavalcante, G. H., D. A. Feary and J. A. Burt (2016). "The influence of extreme winds on coastal oceanography and its implications for coral population connectivity in the southern Arabian Gulf." Mar Pollut Bull 105(2): 489-497.
  • Bento, R., A. S. Hoey, A. G. Bauman, D. A. Feary and J. A. Burt (2016). "The implications of recurrent disturbances within the world's hottest coral reef." Mar Pollut Bull 105(2): 466-472.
  • D'Angelo, C., B. C. Hume, J. Burt, E. G. Smith, E. P. Achterberg and J. Wiedenmann (2015). "Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf." ISME J 9(12): 2551-2560.

  Publications by Group Members
  

  • Sanchez-Donoso, I., S. Ravagni, J. D. Rodríguez-Teijeiro, M. J. Christmas, Y. Huang, A. Maldonado-Linares, M. Puigcerver, I. Jiménez-Blasco, P. Andrade, D. Gonçalves, G. Friis, I. Roig, M. T. Webster, J. A. Leonard and C. Vilà (2021). "Massive genome inversion drives coexistence of divergent morphs in common quails." Curr Biol S0960-9822(21)01543-8.
    
  • Friis, G. and B. Mila (2020). "Change in sexual signaling traits outruns morphological divergence across an ecological gradient in the postglacial radiation of the songbird genus Junco." J Evol Biol 33: 1276– 1293.
• Falcon Population and Conservation Genomics

  Principal Investigators: Stéphane Boissinot and Youssef Idaghdour

  • Wilcox, J. J. S., B. Arca-Ruibal, J. Samour, V. Mateuta, Y. Idaghdour and S. Boissinot (2022). "Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux." Genome Biol Evol 14(6).
  • Almojil, D., Y. Bourgeois, M. Falis, I. Hariyani, J. Wilcox and S. Boissinot (2021). "The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes." Genes (Basel) 12(6).
  • Wilcox, J. J. S., S. Boissinot and Y. Idaghdour (2019). "Falcon genomics in the context of conservation, speciation, and human culture." Ecol Evol 9(24): 14523-14537.
  • Ruggiero, R. P., Y. Bourgeois and S. Boissinot (2017). "LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis." Front Genet 8:44.

  Publications by Group Members

  • Wilcox, J. J. S., J. J. Lopez-Cotto and H. Hollocher (2021). "Historical contingency, geography, and anthropogenic patterns of exposure drive the evolution of host-switching in the Blastocystis species-complex." Parasitology: 1-37.