Publications

Principal Investigator: Claude Desplan 

• 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.
  
• 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.
• 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.
• 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. and C. Desplan (2016). "Re-utilization of a transcription factor." Elife 5.
• 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.
• 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.
• 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.
• 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.
• Wernet, M. F. and C. Desplan (2015). "Brain Wiring in the Fourth Dimension." Cell 162(1): 20-22.
• 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.
• 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

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.

Principal Investigator: Gordon J. Fishell

• 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.
• 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.
  
• 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.
• Pouchelon, G., Y. Bollmann, E. Fisher, C. K. Agba, Q. Xu, K. D. Ritola, A. M. Mirow, S. Kim, R. Cossart and G. Fishell (2020). "The organization and developmental establishment of cortical interneuron presynaptic circuits." bioRxiv: 2020.2009.2017.302117.
• 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.

Principal Investigators: Justin Blau and Dipesh Chaudhury

• 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.
• Hackley, C. R., E. O. Mazzoni and J. Blau (2018). "cAMPr: A single-wavelength fluorescent sensor for cyclic AMP." Sci Signal 11(520).
• 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.
• Lymer, S. and J. Blau (2016). "Do Flies Count Sheep or NMDA Receptors to Go to Sleep?" Cell 165(6): 1310-1311.
• 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.

Principal Investigators: Kristin Gunsalus

• 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.
• 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.

• 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.
• 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.
• 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.
• 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.

Publications by group members

• 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.
• 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.
• 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.

Principal Investigator: John Burt

• 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 (2021). "A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina." G3 (Bethesda) 250-266.e8.
• 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.
  
• 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." bioRxiv: 2020.2005.2030.124800. Preprint.  

Publications by group members

• 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.

Principal Investigator: Kourosh Salehi-Ashtiani

• 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.
• 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 (2021). "A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina." G3 (Bethesda) 250-266.e8.
• Nelson, D. R., K. M. Hazzouri, K. J. Lauersen, A. Jaiswal, A. Chaiboonchoe, A. Mystikou, W. Fu, S. Daakour, B. Dohai, A. Alzahmi, D. Nobles, M. Hurd, J. Sexton, M. J. Preston, J. Blanchette, M. W. Lomas, K. M. A. Amiri and K. Salehi-Ashtiani (2021). "Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution." Cell Host Microbe 1934-6069
  
• 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.
  
• 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." bioRxiv: 2020.2005.2030.124800. Preprint.
• 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. Preprint.
• 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.
  
• Koussa, J., A. Chaiboonchoe and K. Salehi-Ashtiani (2014). "Computational approaches for microalgal biofuel optimization: a review." Biomed Res Int 2014: 649453. (Review article)
  
• 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.

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.

Publications by group members

• 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.
• 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.
• 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.
• 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.

Principal Investigator: Michael Purugganan

• 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.
• 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
• 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.
• 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.
  
• 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.
• 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.
• Hazzouri, K. M., M. D. Purugganan and J. M. Flowers (2014). "Population Genomics of Plant Species." Genomes of Herbaceous Land Plants 69: 311-334.

Publications by group members

• 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.
• 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.
• 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., 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." Preprint.
• 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.
• 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. Preprint

Principal Investigators: Stéphane Boissinot and Youssef Idaghdour

• 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.

Bioinformatics Core

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
  
• 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., 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.

High-throughput Screening Core

• 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., 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.

Fluorescence Activated Cell Sorting Core

• 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.
• 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. (Chapter Book)