K. Salehi-Ashtiani

发表

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii[OPEN]

Erik F. Y. Hom, Kenan Jijakli, Gina M. Pham, 2015, Plant Cell.

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

István A. Kovács, Alexander T. Leighton, A. Barabasi, 2015, Cell.

The Landscape of C. elegans 3′UTRs

Sebastian D. Mackowiak, Emily K. Mis, F. Piano, 2010, Science.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Gloria M. Sheynkman, Alyce A. Chen, Bridget E. Begg, 2016, Cell.

Advances in microalgal research and engineering development.

Sarah Daakour, D. Nelson, K. Salehi-Ashtiani, 2019, Current opinion in biotechnology.

Algal Cell Factories: Approaches, Applications, and Potentials

D. Nelson, A. Chaiboonchoe, Basel Khraiwesh, 2016, Marine drugs.

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

Jason A. Papin, Roger L. Chang, Erik F. Y. Hom, 2011, Molecular systems biology.

RNA Catalysis in Model Protocell Vesicles

J. Szostak, I. Chen, K. Salehi-Ashtiani, 2005, Journal of the American Chemical Society.

SH3 interactome conserves general function over specific form

Gary D Bader, M. Vidal, D. Hill, 2013, Molecular systems biology.

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

S. Horvath, J. Sebat, D. Malhotra, 2014, Nature Communications.

A public genome-scale lentiviral expression library of human ORFs

Thomas M Green, W. Hahn, H. Hieronymus, 2011, Nature Methods.

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2012, PloS one.

Supplementary Figure and Table Legends

Julie M. Sahalie, M. Vidal, Haiyuan Yu, 2022 .

The completion of the Mammalian Gene Collection (MGC)

Richard A. Moore, Lillian D. Riddick, Charles L. G. Comstock, 2009 .

Metabolic network analysis integrated with transcript verification for sequenced genomes

Jason A. Papin, Roger L. Chang, Erik F. Y. Hom, 2009, Nature Methods.

next-generation sequencing to generate interactome datasets

David E Hill, Marc Vidal, Tong Hao, 2011 .

The in vitro selection world.

Amphun Chaiboonchoe, Joseph Koussa, Serdal Kirmizialtin, 2016, Methods.

Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling

D. Nelson, K. Jijakli, A. Chaiboonchoe, 2014, Front. Bioeng. Biotechnol..

Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation.

Jason A. Papin, Roger L. Chang, Haiyuan Yu, 2016, Molecular bioSystems.

Prospective Applications of Synthetic Biology for Algal Bioproduct Optimization

Laising Yen, K. Jijakli, A. Chaiboonchoe, 2015 .

Single-Cell Characterization of Microalgal Lipid Contents with Confocal Raman Microscopy

D. Nelson, K. Jijakli, S. Sharma, 2016 .

Posttranscriptional regulation of primate Ldhc mRNA by its AUUUA-like elements.

K. Salehi-Ashtiani, E. Goldberg, 1995, Molecular endocrinology.

Combined artificial high-silicate medium and LED illumination promote carotenoid accumulation in the marine diatom Phaeodactylum tricornutum

Ó. Rolfsson, S. Brynjólfsson, D. Nelson, 2019, Microbial Cell Factories.

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

Shayne D. Wierbowski, M. Vidal, Haiyuan Yu, 2020, Proceedings of the National Academy of Sciences.

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii

Gina M. Pham, D. Nelson, K. Jijakli, 2015 .

Supplemental Material for A massively parallel barcoded sequencing pipeline to generate the first ORFeome and interactome map for rice

Shayne D. Wierbowski, M. Vidal, Haiyuan Yu, 2020 .

An integrative Raman microscopy-based workflow for rapid in situ analysis of microalgal lipid bodies

D. Nelson, K. Jijakli, Tayebeh Bahmani, 2015, Biotechnology for Biofuels.

Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

Haiyuan Yu, T. Hao, Changyu Fan, 2011, BMC Genomics.

Molecular Mechanisms behind Safranal’s Toxicity to HepG2 Cells from Dual Omics

A. Chaiboonchoe, K. Salehi-Ashtiani, A. Amin, 2022, Antioxidants.

GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine Diatom

Sarah Daakour, S. Brynjólfsson, D. Nelson, 2020, iScience.

Toward Applications of Genomics and Metabolic Modeling to Improve Algal Biomass Productivity

D. Nelson, K. Jijakli, A. Chaiboonchoe, 2015 .

Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response

K. Jijakli, A. Chaiboonchoe, Basel Khraiwesh, 2015, Scientific Reports.

Salt flat microbial diversity and dynamics across salinity gradient

Alyas Ali Alshehhi, M. Purugganan, K. Hazzouri, 2022, Scientific Reports.

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

M. Tabatabaei, A. Talebi, K. Salehi-Ashtiani, 2014 .

Tissue-Specific Transcriptomes Outline Halophyte Adaptive Strategies in the Gray Mangrove (Avicennia marina)

D. Nelson, A. Chaiboonchoe, K. Hazzouri, 2022, Agronomy.

Testis-specific expression of a metallothionein I-driven transgene correlates with undermethylation of the locus in testicular DNA.

C. Markert, K. Salehi-Ashtiani, E. Goldberg, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Saffron-Based Crocin Prevents Early Lesions of Liver Cancer: In vivo, In vitro and Network Analyses.

T. Adrian, A. Chaiboonchoe, K. Salehi-Ashtiani, 2016, Recent patents on anti-cancer drug discovery.

Closing the Gap between Bio-Based and Petroleum-Based Plastic through Bioengineering

J. Twizere, S. Amin, K. Salehi-Ashtiani, 2022, Microorganisms.

The ORFeome Collaboration: a genome-scale human ORF-clone resource

M. Diekhans, T. Moore, M. Vidal, 2016, Nature Methods.

Bioactive Compounds From Microalgae: Current Development and Prospects

S. Brynjólfsson, D. Nelson, K. Jijakli, 2017 .

Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells

M. Vidal, J. Lambert, D. Vertommen, 2021, Science Advances.

Exostosin-1 Glycosyltransferase Regulates Endoplasmic Reticulum Architecture and Dynamics

M. Vidal, J. Lambert, D. Vertommen, 2020, bioRxiv.

Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae

Sarah Daakour, D. Nelson, A. Chaiboonchoe, 2019, iScience.

Expression profile of Ldh-a in the developing rat (Rattus norvegicus) testis suggests regulation at the translational level.

K. Salehi-Ashtiani, E. Goldberg, 1995, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

Proteome expression moves in vitro: resources and tools for harnessing the human proteome

J. Hartley, K. Salehi-Ashtiani, D. Hill, 2008, Nature Methods.

COT/MAP3K8 drives resistance to RAF inhibition through MAP kinase pathway reactivation

Marc Vidal, Reinhard Dummer, William C. Hahn, 2010, Nature.

In vitro evolution suggests multiple origins for the hammerhead ribozyme

Jack W. Szostak, J. Szostak, K. Salehi-Ashtiani, 2001, Nature.

Hovlinc is a recently evolved class of ribozyme found in human lncRNA

P. Kapranov, K. Salehi-Ashtiani, Huifen Cao, 2021, Nature Chemical Biology.

Efficient targeted transcript discovery via array-based normalization of RACE libraries

Sylvain Foissac, Philipp Kapranov, Thomas R. Gingeras, 2008, Nature Methods.

Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii

K. Salehi-Ashtiani, J. Papin, 2012 .

Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism

M. Purugganan, M. Shahid, K. Hazzouri, 2018, Front. Plant Sci..

Differences in regulation of testis specific lactate dehydrogenase in rat and mouse occur at multiple levels

K. Salehi-Ashtiani, Erwin Goldberg, 1993, Molecular reproduction and development.

DNA methylation and expression of the genes coding for lactate dehydrogenases A and C during rodent spermatogenesis.

K. Salehi-Ashtiani, N. Hecht, J. Trasler, 1991, Biology of reproduction.

454 Data Fastq reads Trimmed reads Reads alignment Raw SNP / INDEL calls

S. Horvath, J. Sebat, D. Malhotra, 2014 .

Sex-specific glycosylation of secreted immunomodulatory proteins in the filarial nematode Brugia malayi

C. Vogel, E. Ghedin, K. Salehi-Ashtiani, 2021, bioRxiv.

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina

C. Duarte, D. Nelson, Basel Khraiwesh, 2020, bioRxiv.

Yeast one-hybrid assays for gene-centered human gene regulatory network mapping

David E Hill, Rachel Patton McCord, Heng Zhu, 2011, Nature Methods.

Expression ofneu and Neu differentiation factor in the olfactory mucosa of rat

A. Farbman, K. Salehi-Ashtiani, 1996, International Journal of Developmental Neuroscience.

Testis-Specific Gene Transcription

K. Salehi-Ashtiani, E. Goldberg, 1996 .

Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution.

M. Lomas, Sarah Daakour, D. Nelson, 2020, Cell host & microbe.

A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene

Andrej Lupták, J. Szostak, K. Salehi-Ashtiani, 2006, Science.

Metabolic systems analysis to advance algal biotechnology

Jason A Papin, K. Salehi-Ashtiani, Brian J Schmidt, 2010, Biotechnology journal.

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network.

M. Vidal, C. Kiel, P. Lehner, 2009, Genome research.

Chemical Mutagenesis and Fluorescence-Based High-Throughput Screening for Enhanced Accumulation of Carotenoids in a Model Marine Diatom Phaeodactylum tricornutum

Ó. Rolfsson, A. Bergmann, S. Brynjólfsson, 2018, Marine drugs.

Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency

D. Nelson, K. Jijakli, A. Chaiboonchoe, 2017, Science Advances.

Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells

Amr Amin, Amphun Chaiboonchoe, D. Nelson, 2018, Scientific Reports.

Structural basis for targeting the human T-cell leukemia virus Tax oncoprotein and syntenin-1 interaction using a small molecule

Sibusiso B. Maseko, F. Dequiedt, J. Twizere, 2022, bioRxiv.

Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris.

B. Palsson, S. Brynjólfsson, Steinn Gudmundsson, 2019, The Science of the total environment.

The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

Amphun Chaiboonchoe, Alisdair R Fernie, Saleh Alseekh, 2017, eLife.

Molecular Genetic Techniques for Algal Bioengineering

D. Nelson, K. Jijakli, Basel Khraiwesh, 2015 .

Computational Approaches for Microalgal Biofuel Optimization: A Review

Amphun Chaiboonchoe, Joseph Koussa, A. Chaiboonchoe, 2014, BioMed research international.

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing

Weidong Tian, David E Hill, Marc Vidal, 2008, Nature Methods.

interaction network Analysis of the human E 2 ubiquitin conjugating enzyme protein

M. Vidal, C. Kiel, P. Lehner, 2009 .

Analysis of the human E 2 ubiquitin conjugating enzyme protein interaction network

M. Vidal, C. Kiel, P. Lehner, 2009 .

Protocol to generate and characterize biofouling transformants of a model marine diatom

Sarah Daakour, D. Nelson, K. Salehi-Ashtiani, 2021, STAR protocols.

Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction

C. Van Lint, J. Twizere, F. Delvigne, 2023, bioRxiv.

Ultrastructural Variability in the Locomotor Cortex of the Ciliated Protozoa, Mytilophilus pacificae

K. Salehi-Ashtiani, GREGORY A. ANTIPA, 1997, The Journal of eukaryotic microbiology.

A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States

A. Schier, D. Prober, M. Vidal, 2016, Neuron.

Characterizing algal blooms in a shallow & a deep channel

K. Salehi-Ashtiani, Rashed Farzanah, D. Nelson, 2021 .

Characterizing Algal blooms in a shallow and a deep channel over a decade (2008-2018).

D. Nelson, K. Salehi-Ashtiani, M. A. Shehhi, 2020, 2003.05694.

Integrated Analysis of Gene Network in Childhood Leukemia from Microarray and Pathway Databases

S. Samarasinghe, D. Kulasiri, A. Chaiboonchoe, 2014, BioMed research international.

The completion of the Mammalian Gene Collection (MGC).

Ryan D. Morin, Richard A. Moore, Lillian D. Riddick, 2009, Genome research.

SH3 interactome conserves general function over specific form

Gary D Bader, M. Vidal, Xiaofeng Xin, 2013, Molecular systems biology.

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2012, PloS one.

COT/MAP3K8 drives resistance to RAF inhibition through MAP kinase pathway reactivation

T. Golub, W. Hahn, H. Hieronymus, 2010, Nature.

Leveraging the Power of Next-generation Sequencing to Generate Interactome Datasets Hhs Public Access Online Methods Protein Complementation Assay (pca) Nucleic Acid Programmable Protein Array in Wells (wnappa) Supplementary Material

Julie M. Sahalie, M. Vidal, Haiyuan Yu, 2022 .

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Gloria M. Sheynkman, Alyce A. Chen, Bridget E. Begg, 2016, Cell.

Leveraging the power of next-generation sequencing to generate interactome datasets

Julie M. Sahalie, M. Vidal, Haiyuan Yu, 2011, Nature methods.

Evidence for transcript networks composed of chimeric RNAs in human cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2017 .

Evidence for transcript networks composed of chimeric RNAs in human cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2014 .

A public genome-scale lentiviral expression library of human ORFs

Thomas M Green, W. Hahn, H. Hieronymus, 2011, Nature Methods.

Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity.

Sarah Daakour, J. Twizere, W. Ratcliff, 2024, Molecular plant.

Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics

Sarah Daakour, J. Twizere, K. Salehi-Ashtiani, 2024, Microorganisms.

Molecular Systems Biology Peer Review Process File Sh3 Interactome Conserves General Function over Specific Form Transaction Report

Gary D Bader, M. Vidal, Xiaofeng Xin, 2022 .