2022

1. David R Nelson, Amphun Chaiboonchoe, Khaled M Hazzouri, Basel Khraiwesh, Amnah Alzahmi, Ashish Jaiswal, Guillermo Friis, John A Burt, Khaled MA Amiri, Kourosh Salehi-Ashtiani, Tissue-Specific Transcriptomes Outline Halophyte Adaptive Strategies in the Gray Mangrove (Avicennia marina). (2022), Agronomy 2022, 12(9), 2030; DOI:https://doi.org/10.3390/agronomy12092030
2. Khaled M Hazzouri, Naganeeswaran Sudalaimuthuasari, Esam Eldin Saeed, Biduth Kundu, Raja Saeed Al-Maskari, David Nelson, Alya Ali AlShehhi, Maryam Abdulla Aldhuhoori, Dhabiah Saleh Almutawa, Fatema Rashed Alshehhi, Jithin Balan, Sunil Mundra, Mohammad Alam, Kourosh Salehi-Ashtiani, Michael Purugganan, Khaled Amiri,Salt flat microbial diversity and dynamics across salinity gradient, Scientific Reports volume 12, Article number: 11293 (2022);DOI:https://doi.org/10.1038/s41598-022-15347-8
3. David Roy Nelson, Ala’a Al Hrout, Amnah Salem Alzahmi, Amphun Chaiboonchoe, Amr Amin, Kourosh Salehi-Ashtiani, Molecular Mechanisms behind Safranal’s Toxicity to HepG2 Cells from Dual Omics. (2022) Antioxidants 2022, 11(6), 1125; DOI:https://doi.org/10.3390/antiox11061125
4. Julien Olivet, Sibusiso B Maseko, Alexander N Volkov, Kourosh Salehi-Ashtiani, Kalyan Das, Michael A Calderwood, Jean-Claude Twizere, Christoph Gorgulla, A systematic approach to identify host targets and rapidly deliver broad-spectrum antivirals. (2022), Molecular Therapy, DOI:https://doi.org/10.1016/j.ymthe.2022.02.015.
5. Sibusiso B Maseko, Inge Van Molle, Karim Blibek, Christoph Gorgulla, Julien Olivet, Jeremy Blavier, Charlotte Vandermeulen, Stéphanie Skupiewski, Deeya Saha, Thandokuhle Ntombela, Julianne Lim, Frederique Lembo, Aurelie Beauvois, Malik Hamaidia, Jean-Paul Borg, Pascale Zimmermann, Frank Delvigne, Luc Willems, Johan Van Weyenbergh, Dae-Kyum Kim, Franck Dequiedt, Haribabu Arthanari, Kourosh Salehi-Ashtiani, Steven Ballet, Alexander N Volkov, Jean-Claude Twizere, Structural basis for targeting the human T-cell leukemia virus Tax oncoprotein and syntenin-1 interaction using a small molecule. bioRxiv March 18, 2022.;DOI: https://doi.org/10.1101/2021.08.25.457680

2021

1. A Alzahmi, S Daakour, DC El Assal, BS Dohai, A Chaiboonchoe, W Fu, DR Nelson, A Mystikou, K Salehi-Ashtiani, High-Throughput Metabolic Profiling for Model Refinements of Microalgae. (2021), J. Vis. Exp. (178), e61913, DOI: 10.3791/61913-v.
2. Maryam R. Al-Shehhi*, David Nelson, Rashed Farzanah, Rashid Alshihi, Kourosh Salehi-Ashtiani, Characterizing algal blooms in a shallow & a deep channel, Ocean and Coastal Management, Volume 213, 1 November 2021, https://doi.org/10.1016/j.ocecoaman.2021.105840.
3. Weiqi Fu, Bushra Dohai, Diana Charles El Assal, Sarah Daakour, Amnah Alzahmi, David R.Nelson, Ashish Jaiswal, Alexandra Mystikou, MeharSultana, JamesWeston, Kourosh Salehi-Ashtiani, Protocol to generate and characterize biofouling transformants of a model marine diatom, STAR Protocols, Volume 2, Issue 3, 17 September 2021, 100716. https://doi.org/10.1016/j.xpro.2021.100716.
4. Despoina Kerselidou, Bushra Saeed Dohai, David R Nelson, Sarah Daakour, Nicolas De Cock, Zahra Al Oula Hassoun, Dae-Kyum Kim, Julien Olivet, Diana C El Assal, Ashish Jaiswal, Amnah Alzahmi, Deeya Saha, Charlotte Pain, Filip Matthijssens, Pierre Lemaitre, Michael Herfs, Julien Chapuis, Bart Ghesquiere, Didier Vertommen, Verena Kriechbaumer, Kèvin Knoops, Carmen Lopez-Iglesias, Marc van Zandvoort, Jean-Charles Lambert, Julien Hanson, Christophe Desmet, Marc Thiry, Kyle J Lauersen, Marc Vidal, Pieter Van Vlierberghe, Franck Dequiedt, Kourosh Salehi-Ashtiani, Jean-Claude Twizere, Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Science Advances • 7 May 2021 • Vol 7, Issue 19 • DOI: 10.1126/sciadv.abe8349.
5. Yue Chen, Fei Qi, Fan Gao, Huifen Cao, Dongyang Xu, Kourosh Salehi-Ashtiani, Philipp Kapranov, Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nature Chemical Biology volume 17, pages 601–607 (2021).
6. David R Nelson, Khaled M Hazzouri, Kyle J Lauersen, Ashish Jaiswal, Amphun Chaiboonchoe, Alexandra Mystikou, Weiqi Fu, Sarah Daakour, Bushra Dohai, Amnah Alzahmi, David Nobles, Mark Hurd, Julie Sexton, Michael J Preston, Joan Blanchette, Michael W Lomas, Khaled MA Amiri, Kourosh Salehi-Ashtiani, Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution. Cell Host & Microbe, Volume 29, Issue 2, 10 February 2021, Pages 250-266.e8
7. Joseph Koussa, Burcu Vitrinel, Peter Whitney, Brian Kasper, Lara K Mahal, Christine Vogel, Kourosh Salehi-Ashtiani, Elodie Ghedin,Sex-specific glycosylation of secreted immunomodulatory proteins in the filarial nematode Brugia malayi. biorxiv (2021) doi: https://doi.org/10.1101/2021.02.24.432741.
8. Guillermo Friis, Joel Vizueta, Edward G Smith, David R Nelson, Basel Khraiwesh, Enas Qudeimat, Kourosh Salehi-Ashtiani, Alejandra Ortega, Alyssa Marshell, Carlos M Duarte, John A Burt, A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina. G3 Genes|Genomes|Genetics, Volume 11, Issue 1, January 2021, jkaa025, https://doi.org/10.1093/g3journal/jkaa025.
   
   

2020

1. Despoina Kerselidou, Bushra Saeed Dohai, David R Nelson, Sarah Daakour, Nicolas De Cock, Dae-Kyum Kim, Julien Olivet, Diana C El Assal, Ashish Jaiswal, Deeya Saha, Charlotte Pain, Filip Matthijssens, Pierre Lemaitre, Michael Herfs, Julien Chapuis, Bart Ghesquiere, Didier Vertommen, Verena Kriechbaumer, Kèvin Knoops, Carmen Lopez-Iglesias, Marc van Zandvoort, Jean-Charles Lambert, Julien Hanson, Christophe Desmet, Marc Thiry, Kyle J Lauersen, Marc Vidal, Pieter Van Vlierberghe, Franck Dequiedt, Kourosh Salehi-Ashtiani, Jean-Claude Twizere, Exostosin-1 Glycosyltransferase Regulates Endoplasmic Reticulum Architecture and Dynamics. (2022), Cold Spring Harbor Laboratory, DOI https://10.1101/2020.09.02.275925
2. Weiqi Fu, Amphun Chaiboonchoe, Bushra Dohai, Mehar Sultana, Kristos Baffour, Amnah Alzahmi, James Weston, Dina Al Khairy, Sarah Daakour, Ashish Jaiswal, David R Nelson, Alexandra Mystikou, Sigurdur Brynjolfsson, Kourosh Salehi-Ashtiani, GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine DiatomiScience, Volume 23, Issue 8, 21 August 2020, 101424
3. S. D. Wierbowski, 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, H. Yu. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. (2020) Proc. Natl. Acad. Sci. USA 17:11836-11842.
4. Maryam R Al Shehhi, David Nelson, Rashid R Alkhori, Rashid Alshihi, Kourosh Salehi-Ashtiani, Characterizing Algal blooms in a shallow and a deep channel over a decade (2008-2018), arXiv preprint arXiv:2003.05694, DOI https://doi.org/10.48550/arXiv.2003.05694

2019

1. W. Fu, D.R. Nelson, A. Mystikou, S. Daakour, K. Salehi-Ashtiani. Advances in microalgal research and engineering development. Curr. Opin. Biotechnol., 59 (2019), pp. 157-164
2. David R. Nelson, Amphun Chaiboonchoe, Weiqi Fu, Khaled M. Hazzouri, Ziyuan Huang, Ashish Jaiswal, Sarah Daakour, Alexandra Mystikou, Marc Arnoux, Mehar Sultana, and Kourosh Salehi-Ashtiani, Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae. (2019) iScience/Cell 11, 450–465, January 25, 2019; PMID: 30684492 PMCID: PMC6348204 https://doi.org/10.1016/ j.isci.2018.12.035.
3. Weiqi Fu, Steinn Gudmundsson, Kristine Wichuk, Sirus Palsson, Bernhard O Palsson, Kourosh Salehi-Ashtiani, Sigurður Brynjólfsso (2019). Dataset on economic analysis of mass production of algae in LED-based photobioreactors. Data in Brief,22, 137-139. https://doi.org/10.1016/j.dib.2018.12.010
4. Weiqi Fu, Steinn Gudmundsson, Kristine Wichuk, Sirus Palsson, Bernhard O Palsson, Kourosh Salehi-Ashtiani, Sigurður Brynjólfsson (2019) Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris. Science of The Total Environment, Volume 654, Pages 275-283. https://doi.org/10.1016/j.scitotenv.2018.11.120

2018

1. Ala’a Al-Hrout, Amphun Chaiboonchoe, Basel Khraiwesh, Chandraprabha Murali, Badriya Baig, Raafat El-Awady, Hamadeh Tarazi, Amnah Alzahmi, David R Nelson, Yaser E Greish, Wafaa Ramadan, Kourosh Salehi-Ashtiani, Amr Amin.(2018) Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells (2018). Scientific reports, Volume 8, Pages 16951. https://www.nature.com/articles/s41598-018-34855-0
2. Zhiqian Yi, Yixi Su, Andreas Bergmann, Saevar Ingporsson, Ottar Rolfsson, Kourosh Salehi-Ashtiani, Sigurdur Brynjolfsson, Weiqi Fu, Chemical mutagenesis and fluorescence-based high-throughput screening for enhanced accumulation of carotenoids in a model marine diatom Phaeodactylum tricornutum. Mar. Drugs 2018, 16(8), 272; doi:10.3390/md16080272.
3. K. M. Hazzouri, 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, K. Masmoudi Mapping of HKT1; 5 gene in barley using GWAS approach and its implication in salt tolerance mechanism. Frontiers in Plant Science 9, 1-15. (2018).

2017

1. W. Fu, A. Chaiboonchoe, B. Khraiwesh, M. Sultana, A. Jaiswal, K. Jijakli, D. R. Nelson, A. Al-Hrout, B. Baig, A. Amin, K. Salehi-Ashtiani, Intracellular spectral recompositioning of light
   enhances algal photosynthetic efficiency. Sci. Adv. 3, e1603096 (2017).
2. D. R. Nelson, B. Khraiwesh, W. Fu, S. Alseekh, A. Jaiswal, A. Chaiboonchoe, K. Hazzouri, M. J. O’Connor, G. Butterfoss, N. Drou, J. D. Rowe, J. Harb, A. R. Fernie, K. C. Gunsalus, K. Salehi-Ashtiani (2017). The genome and phenome of the green alga Chloroidium sp. UTEX3007 reveal adaptive traits for desert acclimatization. eLife doi: 10.7554/eLife.25783. [Epub ahead of print]
3. B. Khraiwesh, K. Salehi-Ashtiani (2017). Alternative Poly(A) Tails Meet miRNA Targeting in Caenorhabditis elegans. Genetics 206(2):755-756. doi: 10.1534/genetics.117.202101.
4. W. Fu, D. R. Nelson, Z. Yi, M. Xu, B. Khraiwesh, K. Jijakli, A. Chaiboonchoe, A. Alzahmi, D. El-Khairy, S. Brynjolfsson, K. Salehi-Ashtiani.  Bioactive compounds from microalgae: Current development and prospects. In Studies in Natural Products Chemistry (Bioactive Natural Products), Ed. Atta-ur-Rahman. Vol. 54. Pp 199-217 (2017). Elsevier Science Publisher, Amsterdam, Netherlands.

2016

1. K. Jijakli, B. Khraiwesh, , W. Fu, L. Luo, A. Alzahmi, J. Koussa, A. Chaiboonchoe, S. Kirmizialtin, L.Yen, K. Salehi-Ashtiani. (2016). "The In Vitro Selection World. Methods". 10.1016/j.ymeth.2016.06.003.
2. A. Chaiboonchoe, L. Ghamsari, B. Dohai, P. Ng,  B. Khraiwesh, A. Jaiswal, J. Koussa, D. R. Nelson, H. Cai, X. Yan, R.L. Chang, J. Papin, Haiyuan Yu, Santhanam Balaji, K. Salehi-Ashtiani. (2016) "Systems level analyses of Chlamydomonas reinhardtii metabolic network reveal variability in evolutionary co-conservation". Mol. BioSyst. (EPUB ahead of print).DOI: 10.1039/C6MB00237D.
3. Weiqi Fu, Basel Khraiwesh, Hongbing Liu, and Lei Kai, Advances in Biotechnology for Sustainable Development, BioMed Research International, Volume 2016 (2016), Article ID 7154916.
4. S. Wiemann, C. Pennacchio, Y. Hu, P. Hunter, M. Harbers, A. Amiet, G. Bethel, M. Busse, P. Carninci, M. Diekhans, I. Dunham, T. Hao, J.W. Harper, Y Hayashizaki, O. Heil, S. Hennig, A. Hotz-Wagenblatt, W. Jang, A. Jocker, J. Kawai, C. Koenig, B. Korn, C. Lambert, A. LeBeau, S. Lu, J. Maurer, T. Moore, O. Ohara, J. Park, A. Rolfs, K. Salehi-Ashtiani, C. Seiler, B. Simmons, A. van Brabant Smith, J. Steel, L. Wagner, T. Weaver, R. Wellenreuther, S. Yang, M. Vidal, D.S. Gerhard, J. LaBaer, G. Temple, D.E. Hill (2016). The ORFeome Collaboration: A genome-scale human ORF-clone resource. Nature Methods 13, 191-192.
5. C.N. Chiu, J. Rihel, D.A. Lee, C. Singh, E.A. Mosser, S. Chen, V. Sapin, U. Pham, J. Engle, B.J. Niles, C.J. Montz, S. Chakravarthy, S. Zimmerman, K. Salehi-Ashtiani, K, M. Vidal, A.F. Schier, D.A. Prober (2016). "A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States".     Neuron 89:842-856.
6. X. Yang, J. Coulombe-Huntington, S. Kang, G.M. Sheynkman, T. Hao, A. Richardson, S. Sun, F. Yang, Y. A. Shen, R. R. Murray, K. Spirohn, B. E. Begg, M. Duran-Frigola, A. MacWilliams, S. J. Pevzner, Q. Zhong, S. A. Trigg, S. Tam, L. Ghamsari, N. Sahni, S. Yi, M. D. Rodriguez, D. Balcha, G. Tan, M. Costanzo, B. Andrews, C. Boone, X. J. Zhou, K. Salehi-Ashtiani, B. Charloteaux, A. A. Chen, M. A. Calderwood, P. Aloy, F. P. Roth, D. E. Hill, L. M. Iakoucheva, Y. Xia, M. Vidal (2016). "Widespread expansion of protein interaction capabilities by alternative splicing". Cell 164:805–817.
7. Rasha Abdrabu, Sudhir Kumar Sharma, Basel Khraiwesh, Kenan Jijakli, David R. Nelson, Amnah Alzahmi, Joseph Koussa, Mehar Sultana, Sachin Khapli, Ramesh Jagannathan, Kourosh Salehi-Ashtiani "Single Cell Characterization of Microalgal Lipid Contents with Confocal Raman Microscopy. In Essentials of Single-Cell Analysis: Concepts, Applications and Future Prospects", Eds. F.-G. Tseng and T. S. Santra. pp 363-382 (2016). Springer.
8. Fu, W.; Chaiboonchoe, A.; Khraiwesh, B.; Nelson, D.R.; Al-Khairy, D.; Mystikou, A.; Alzahmi, A.; Salehi-Ashtiani, K. Algal Cell Factories: Approaches, Applications, and Potentials. Mar. Drugs 2016, 14, 225.

2015

1. Basel Khraiwesh, Enas Qudeimat, Manjula Thimma, Amphun Chaiboonchoe, Kenan Jijakli, Amnah Alzahmi, Marc Arnoux & Kourosh Salehi-Ashtiani, (2015), "Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response", Scientific Reports 5, Article number: 17434 (2015), 30 November 2015; doi:10.1038/srep17434
2. Amin A*, Hamza AA, Daoud S, Khazanehdari K, Al Hrout A, Baig B, Chaiboonchoe A, Adrian TE, Zaki N, Salehi-Ashtiani K. (2015). "Saffron-Based Crocin Prevents Early Lesions of Liver Cancer: In Vivo, In Vitro and Network Analyses". Recent Pat Anticancer Drug Discovery.
3. J. M. Flowers, K. M. Hazzouri, G. M. Pham, U. Rosas, T. Bahmani, B. Khraiwesh, David R. Nelson, Kenan Jijakli, Rasha Abdrabu, E. H. Harris, P. A. Lefebvre, E. F.Y. Hom, K. Salehi-Ashtiani,  M. D. Purugganan (2015). "Whole genome re-sequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii". Plant Cell, 27(9) 2352-2369.
4. S. Kumar Sharma, D. R. Nelson,  R. Abdrabu, Basel Khraiwesh, Kenan Jajkli, M. J. O'Connor, T. Bahmani, H. Cai, S. Khapli, Jagannathan, K. Salehi- Ashtiani. (2015) "An integrative Raman microscopy-based workflow for rapid in situ analysis of microalgal lipid bodies". Biotechnology for Biofuels. 8:164 . 
   DOI: 10.1186/s13068-015-0349-1.
5. Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJ, Lindquist S, Vidal M. (2015): "Widespread macromolecular interaction perturbations in human genetic disorders". Cell Apr 23;161(3):647-60. doi: 10.1016/j.cell.2015.04.013. 
6. Khraiwesh B, Jijakli K, Swift J, Chaiboonchoe A, Abdrabu R, Chao P-W, Yen L, Salehi-Ashtiani K (2015): "Prospective Applications of Synthetic Biology for Algal Bioproduct Optimization". In: Moheimani NR, McHenry MP, de Boer K, Bahri PA (eds) Biomass and Biofuels from Microalgae, Biofuel and Biorefinery Technologies. Springer International Publishing, pp 137-154. doi:10.1007/978-3-319-16640-7_8.
7. Salehi-Ashtiani K, Koussa J, Dohai B, Chaiboonchoe A, Cai H, Dougherty KD, Nelson D, Jijakli K, Khraiwesh B (2015): "Toward Applications of Genomics and Metabolic Modeling to Improve Algal Biomass Productivity". In: Moheimani NR, McHenry MP, de Boer K, Bahri PA (eds) Biomass and Biofuels from Microalgae, Biofuel and Biorefinery Technologies. Springer International Publishing, pp 173-189. doi:10.1007/978-3-319-16640-7_10.
8. Jijakli K, Abdrabu R, Khraiwesh B, Nelson D, Koussa J, Salehi-Ashtiani K (2015): "Molecular Genetic Techniques for Algal Bioengineering". In: Moheimani NR, McHenry MP, de Boer K, Bahri PA (eds) Biomass and Biofuels from Microalgae, Biofuel and Biorefinery Technologies. Springer International Publishing, pp 155-171. doi:10.1007/978-3-319-16640-7_9.
9. Weiqi Fu, Kristine Wichuk, Sigurour Brynjolfsson (13 April 2015) "Developing diatoms for value-added products: challenges and opportunities" New Biotechnology, European Federation of Biotechnology (EFB). doi:10.1016/j.nbt.2015.03.016

2014

1. Khan, S. M., Khraiwesh, B., Ganesan, P., Gupta, R.S., Singh, J., Duttamajumder, K. S., Kapur R. (2014): "Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)". FEBS Open Bio. 10; 4:533-41.
2. A. Chaiboonchoe, B.S. Dohai, H. Cai, D.R. Nelson, K. Jijakli,K. Salehi-Ashtiani (2014). "Microalgal metabolic network model refinement through high throughput functional metabolic profiling". Frontiers in Bioengineering and Biotechnology; 2:1-12.
3. J. Koussa, A. Chaiboonchoe,K. Salehi-Ashtiani (2014). "Computational Approaches for Microalgal Biofuel Optimization: A Review". BioMed Research International; 2014: Article ID 649453.
4. A. F. Talebi, M. Tohidfar, A. Bagheri, S. R. Lyon,K. Salehi-Ashtiani, M. Tabatabaei (2014). "Manipulation of carbon flux into fatty acid biosynthesis pathway in Dunaliella salina using AccD and ME genes to enhance lipid content and to improve produced biodiesel quality". Biofuel Res. J. 1 (3):391-397.
5. R. Corominas, X. Yang, G. N. Lin, S. Kang, Y. Shen, L. Ghamsari, M. Broly, M. Rodriguez, S. Tam, S. A. Wanamaker, M. Tasan, I. Lemmens, X. Kuang, N. Zhao, D. Malhotra, J. J. Michaelson, V.Vacic, S. Horvath, K. Salehi-Ashtiani, F. P. Roth, J. Tavernier, D. Korkin, J. Sebat, D. E. Hill, T. Hao, M. Vidal, L. M. Iakoucheva (2014). "Autism-centered interactome network reveals functional links between genetic risk factors for ASD". Nature Communications; 5:3650.
6. Amphun Chaiboonchoe, Sandhya Samarasinghe, Don Kulasiri, and Kourosh Salehi-Ashtiani (2014) "Integrated Analysis of Gene Network in Childhood Leukemia from Microarray and Pathway Databases", BioMed Research International, vol 2014, Article ID 278748, 7 pages.

2013

1. Khraiwesh, B. and Qudeimat, E. (2013): "Abiotic Stress‐Responsive Small RNA‐Mediated Plant Improvement Under a Changing Climate", in Climate Change and Plant Abiotic Stress Tolerance (eds N. Tuteja and S. S. Gill), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527675265.ch18.
2. SH3 interactome conserves general function over specific form. Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD. Mol Syst Biol. 2013;9:652. doi: 10.1038/msb.2013.9. PMID: 23549480 [PubMed - in process]

2012 and earlier

1. Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpi JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigo R, Gingeras TR."Evidence for transcript networks composed of chimeric RNAs in human cells". PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4. PMID: 22238572 [PubMed - indexed for MEDLINE]
2. Xiaoping Yang, Jesse S Boehm, Xinping Yang, Kourosh Salehi-Ashtiani, et.al “A public genome-scale lentiviral expression library of human ORFs” ; Nature Methods  8, 659–661 (2011) doi:10.1038/nmeth.1638.
3. Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong JS, Jiang L, MacWilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J, Walhout AJ. "Yeast one-hybrid assays for gene-centered human gene regulatory network mapping". Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764. PMID: 22037702 [PubMed - indexed for MEDLINE]
4. Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K., "Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii". BMC Genomics. 2011 Jun 15;12 Suppl 1:S4. doi: 10.1186/1471-2164-12-S1-S4. PMID: 21810206 [PubMed - indexed for MEDLINE]
5. R.L. Chang, L. Ghamsari, A. Manichaikul, E.F. Hom, S. Balaji, W. Fu, Y. Shen, T. Hao, B.Ø. Palsson,K. Salehi-Ashtiani§, J.A. Papin§. "Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism". Molecular Systems Biology. 7:518, 2011. (§= corresponding author)
6. C.M. Johannessen et al. "COT drives resistance to RAF inhibition through MAPkinase pathway reactivation". Nature 468:968-972, 2010.
7. M. Mangone et al. "The landscape of C. elegans 3'UTRs". Science 329:432-435, 2010.
8. A. Manichaikul, L. Ghamsari, E.F. Hom, C. Lin, R.R. Murray, R.L. Chang, S. Balaji, T. Hao, Y. Shen, A.K. Chavali, I. Thiele, X. Yang, C. Fan, E. Mello, D.E. Hill, M. Vidal, K. Salehi-Ashtiani§, J.A. Papin§."Metabolic network analysis integrated with transcript verification for sequence genomes". Nature Methods6: 589-592, 2009. (§= corresponding author)
9. K. Salehi-Ashtiani§ et al."Isoform discovery using targeted cloning, “deep well” pooling, and parallel sequencing". Nature Methods, 5:597-600, 2008. (§= corresponding author)
10. K. Salehi-Ashtiani, A. Luptak, A. Litovchick, J.W. Szostak. "A Genome-wide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene". Science; 313:1788-1792, 2006.
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