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Items: 48

1.

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

Al-Hrout A, Chaiboonchoe A, Khraiwesh B, Murali C, Baig B, El-Awady R, Tarazi H, Alzahmi A, Nelson DR, Greish YE, Ramadan W, Salehi-Ashtiani K, Amin A.

Sci Rep. 2018 Nov 16;8(1):16951. doi: 10.1038/s41598-018-34855-0.

PMID:
30446676
2.

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

Fu W, Gudmundsson S, Wichuk K, Palsson S, Palsson BO, Salehi-Ashtiani K, Brynjólfsson S.

Sci Total Environ. 2018 Nov 9;654:275-283. doi: 10.1016/j.scitotenv.2018.11.120. [Epub ahead of print]

PMID:
30445327
3.

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

Yi Z, Su Y, Xu M, Bergmann A, Ingthorsson S, Rolfsson O, Salehi-Ashtiani K, Brynjolfsson S, Fu W.

Mar Drugs. 2018 Aug 4;16(8). pii: E272. doi: 10.3390/md16080272.

4.

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

Hazzouri KM, Khraiwesh B, Amiri KMA, Pauli D, Blake T, Shahid M, Mullath SK, Nelson D, Mansour AL, Salehi-Ashtiani K, Purugganan M, Masmoudi K.

Front Plant Sci. 2018 Feb 19;9:156. doi: 10.3389/fpls.2018.00156. eCollection 2018.

5.

Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency.

Fu W, Chaiboonchoe A, Khraiwesh B, Sultana M, Jaiswal A, Jijakli K, Nelson DR, Al-Hrout A, Baig B, Amin A, Salehi-Ashtiani K.

Sci Adv. 2017 Sep 1;3(9):e1603096. doi: 10.1126/sciadv.1603096. eCollection 2017 Sep.

6.

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

Nelson DR, Khraiwesh B, Fu W, Alseekh S, Jaiswal A, Chaiboonchoe A, Hazzouri KM, O'Connor MJ, Butterfoss GL, Drou N, Rowe JD, Harb J, Fernie AR, Gunsalus KC, Salehi-Ashtiani K.

Elife. 2017 Jun 17;6. pii: e25783. doi: 10.7554/eLife.25783.

7.

Alternative Poly(A) Tails Meet miRNA Targeting in Caenorhabditis elegans.

Khraiwesh B, Salehi-Ashtiani K.

Genetics. 2017 Jun;206(2):755-756. doi: 10.1534/genetics.117.202101. No abstract available.

8.

Algal Cell Factories: Approaches, Applications, and Potentials.

Fu W, Chaiboonchoe A, Khraiwesh B, Nelson DR, Al-Khairy D, Mystikou A, Alzahmi A, Salehi-Ashtiani K.

Mar Drugs. 2016 Dec 13;14(12). pii: E225. Review.

9.

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

Chaiboonchoe A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, Salehi-Ashtiani K.

Mol Biosyst. 2016 Jul 19;12(8):2394-407. doi: 10.1039/c6mb00237d.

PMID:
27357594
10.

The in vitro selection world.

Jijakli K, Khraiwesh B, Fu W, Luo L, Alzahmi A, Koussa J, Chaiboonchoe A, Kirmizialtin S, Yen L, Salehi-Ashtiani K.

Methods. 2016 Aug 15;106:3-13. doi: 10.1016/j.ymeth.2016.06.003. Epub 2016 Jun 14. Review.

11.

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

Chiu CN, Rihel J, Lee DA, Singh C, Mosser EA, Chen S, Sapin V, Pham U, Engle J, Niles BJ, Montz CJ, Chakravarthy S, Zimmerman S, Salehi-Ashtiani K, Vidal M, Schier AF, Prober DA.

Neuron. 2016 Feb 17;89(4):842-56. doi: 10.1016/j.neuron.2016.01.007.

12.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M.

Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.

13.

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

Khraiwesh B, Qudeimat E, Thimma M, Chaiboonchoe A, Jijakli K, Alzahmi A, Arnoux M, Salehi-Ashtiani K.

Sci Rep. 2015 Nov 30;5:17434. doi: 10.1038/srep17434.

14.

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

Amin A, Hamza AA, Daoud S, Khazanehdari K, Hrout AA, Baig B, Chaiboonchoe A, Adrian TE, Zaki N, Salehi-Ashtiani K.

Recent Pat Anticancer Drug Discov. 2016;11(1):121-33.

PMID:
26522014
15.

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

Sharma SK, Nelson DR, Abdrabu R, Khraiwesh B, Jijakli K, Arnoux M, O'Connor MJ, Bahmani T, Cai H, Khapli S, Jagannathan R, Salehi-Ashtiani K.

Biotechnol Biofuels. 2015 Oct 6;8:164. doi: 10.1186/s13068-015-0349-1. eCollection 2015.

16.

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

Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EF, Salehi-Ashtiani K, Purugganan MD.

Plant Cell. 2015 Sep;27(9):2353-69. doi: 10.1105/tpc.15.00492. Epub 2015 Sep 21.

17.

Widespread macromolecular interaction perturbations in human genetic disorders.

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 AJM, Lindquist S, Vidal M.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

18.

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

Chaiboonchoe A, Dohai BS, Cai H, Nelson DR, Jijakli K, Salehi-Ashtiani K.

Front Bioeng Biotechnol. 2014 Dec 10;2:68. doi: 10.3389/fbioe.2014.00068. eCollection 2014.

19.

Computational approaches for microalgal biofuel optimization: a review.

Koussa J, Chaiboonchoe A, Salehi-Ashtiani K.

Biomed Res Int. 2014;2014:649453. doi: 10.1155/2014/649453. Epub 2014 Sep 21. Review.

20.

Integrated analysis of gene network in childhood leukemia from microarray and pathway databases.

Chaiboonchoe A, Samarasinghe S, Kulasiri D, Salehi-Ashtiani K.

Biomed Res Int. 2014;2014:278748. doi: 10.1155/2014/278748. Epub 2014 Apr 15.

21.

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

Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM.

Nat Commun. 2014 Apr 11;5:3650. doi: 10.1038/ncomms4650.

22.

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.

23.

Evidence for transcript networks composed of chimeric RNAs in human cells.

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, Gelpí 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, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

24.

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

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.

Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764.

25.

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

Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S4. doi: 10.1186/1471-2164-12-S1-S4.

26.

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

Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA.

Mol Syst Biol. 2011 Aug 2;7:518. doi: 10.1038/msb.2011.52.

27.

A public genome-scale lentiviral expression library of human ORFs.

Yang X, Boehm JS, Yang X, Salehi-Ashtiani K, Hao T, Shen Y, Lubonja R, Thomas SR, Alkan O, Bhimdi T, Green TM, Johannessen CM, Silver SJ, Nguyen C, Murray RR, Hieronymus H, Balcha D, Fan C, Lin C, Ghamsari L, Vidal M, Hahn WC, Hill DE, Root DE.

Nat Methods. 2011 Jun 26;8(8):659-61. doi: 10.1038/nmeth.1638.

28.

Next-generation sequencing to generate interactome datasets.

Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P, Vidal M.

Nat Methods. 2011 Jun;8(6):478-80. doi: 10.1038/nmeth.1597. Epub 2011 Apr 24.

29.

COT drives resistance to RAF inhibition through MAP kinase pathway reactivation.

Johannessen CM, Boehm JS, Kim SY, Thomas SR, Wardwell L, Johnson LA, Emery CM, Stransky N, Cogdill AP, Barretina J, Caponigro G, Hieronymus H, Murray RR, Salehi-Ashtiani K, Hill DE, Vidal M, Zhao JJ, Yang X, Alkan O, Kim S, Harris JL, Wilson CJ, Myer VE, Finan PM, Root DE, Roberts TM, Golub T, Flaherty KT, Dummer R, Weber BL, Sellers WR, Schlegel R, Wargo JA, Hahn WC, Garraway LA.

Nature. 2010 Dec 16;468(7326):968-72. doi: 10.1038/nature09627. Epub 2010 Nov 24.

30.

Metabolic systems analysis to advance algal biotechnology.

Schmidt BJ, Lin-Schmidt X, Chamberlin A, Salehi-Ashtiani K, Papin JA.

Biotechnol J. 2010 Jul;5(7):660-70. doi: 10.1002/biot.201000129. Review.

PMID:
20665641
31.

The landscape of C. elegans 3'UTRs.

Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak SD, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK.

Science. 2010 Jul 23;329(5990):432-5. doi: 10.1126/science.1191244. Epub 2010 Jun 3.

32.

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.

Salehi-Ashtiani K, Lin C, Hao T, Shen Y, Szeto D, Yang X, Ghamsari L, Lee H, Fan C, Murray RR, Milstein S, Svrzikapa N, Cusick ME, Roth FP, Hill DE, Vidal M.

Genome Res. 2009 Dec;19(12):2334-42. doi: 10.1101/gr.098640.109. Epub 2009 Oct 2.

33.

The completion of the Mammalian Gene Collection (MGC).

MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S.

Genome Res. 2009 Dec;19(12):2324-33. doi: 10.1101/gr.095976.109. Epub 2009 Sep 18.

34.

Metabolic network analysis integrated with transcript verification for sequenced genomes.

Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA.

Nat Methods. 2009 Aug;6(8):589-92. doi: 10.1038/nmeth.1348. Epub 2009 Jul 13.

35.

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

Markson G, Kiel C, Hyde R, Brown S, Charalabous P, Bremm A, Semple J, Woodsmith J, Duley S, Salehi-Ashtiani K, Vidal M, Komander D, Serrano L, Lehner P, Sanderson CM.

Genome Res. 2009 Oct;19(10):1905-11. doi: 10.1101/gr.093963.109. Epub 2009 Jun 23.

36.

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

Hartley JL, Salehi-Ashtiani K, Hill DE.

Nat Methods. 2008 Dec;5(12):1001-2. doi: 10.1038/nmeth1208-1001. No abstract available.

PMID:
19034266
37.

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

Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, Lin C, Makowski K, Shen L, Murray RR, Szeto D, Tusneem N, Smith DR, Cusick ME, Hill DE, Roth FP, Vidal M.

Nat Methods. 2008 Jul;5(7):597-600. doi: 10.1038/nmeth.1224. Epub 2008 Jun 15.

38.

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

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, Harrow J, Makrythanasis P, Vidal M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigó R.

Nat Methods. 2008 Jul;5(7):629-35. doi: 10.1038/nmeth.1216. Epub 2008 May 25.

39.

A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene.

Salehi-Ashtiani K, Lupták A, Litovchick A, Szostak JW.

Science. 2006 Sep 22;313(5794):1788-92.

40.

RNA catalysis in model protocell vesicles.

Chen IA, Salehi-Ashtiani K, Szostak JW.

J Am Chem Soc. 2005 Sep 28;127(38):13213-9.

41.

In vitro evolution suggests multiple origins for the hammerhead ribozyme.

Salehi-Ashtiani K, Szostak JW.

Nature. 2001 Nov 1;414(6859):82-4.

PMID:
11689947
42.

Ultrastructural variability in the locomotor cortex of the ciliated protozoa, Mytilophilus pacificae.

Salehi-Ashtiani K, Antipa GA.

J Eukaryot Microbiol. 1997 Sep-Oct;44(5):471-9.

PMID:
9304816
43.

Expression of neu and Neu differentiation factor in the olfactory mucosa of rat.

Salehi-Ashtiani K, Farbman AI.

Int J Dev Neurosci. 1996 Nov;14(7-8):801-11.

PMID:
9010726
44.

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

Salehi-Ashtiani K, Goldberg E.

Mol Endocrinol. 1995 Dec;9(12):1782-90.

PMID:
8614414
45.

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

Salehi-Ashtiani K, Goldberg E.

Comp Biochem Physiol B Biochem Mol Biol. 1995 Mar;110(3):623-7.

PMID:
7584835
46.

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

Salehi-Ashtiani K, Widrow RJ, Markert CL, Goldberg E.

Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8886-90.

47.
48.

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

Alcivar AA, Trasler JM, Hake LE, Salehi-Ashtiani K, Goldberg E, Hecht NB.

Biol Reprod. 1991 Mar;44(3):527-35.

PMID:
2015369

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