Publications

Peer-Reviewed Publications

Adel M, Elbehery AHA, Aziz SK, Aziz RK, Grossart H-P, Siam R. (2016) Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments. Scientific Reports. 6:32704. doi: 10.1038/srep32704.

Elbaz NM, Ziko L, Siam R, Mamdouh W. (2016) Core-Shell Silver/Polymeric Nanoparticles-Based Combinatorial Therapy against Breast Cancer In-vitroScientific Reports. 6: 30729. doi:  10.1038/srep30729.

Mustafa, GA, Abd-Elgawad, A, Ouf, A, Siam, R. (2016) The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants. Environmental Pollution. Volume 214, Pages 892–902

The MetaSUB International Consortium. (2016) The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome.  3;4(1):24. doi: 10.1186/s40168-016-0168-z.

Elbehery AHA, Aziz RK, Siam R. (2016) Antibiotic resistome: improving detection and quantification accuracy for comparative metagenomics. OMICS: A Journal of Integrative Biology. 20(4): 229-238. doi:10.1089/omi.2015.0191.

 

​Sonbol SA, Ferreira AJS, Siam R. Red Sea Atlantis II brine pool nitrilase with unique thermostability profile and heavy metal tolerance. BMC Biotechnology. 2016;16:14. doi:10.1186/s12896-016-0244-2.

Antunes A, Alam I, Simões MF, Daniels C, Ferreira AJ, Siam R, El-Dorry H, Bajic VB. First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea. Genomics, Proteomics & Bioinformatics. 2015;13(5):304-309. doi:10.1016/j.gpb.2015.06.004.

 

Kopf A, Bicak M, Kottmann R, et al., 2015. The Ocean Sampling Day Consortium.
Gigascience. 2015 Jun 19;4:27. doi: 10.1186/s13742-015-0066-5. eCollection 2015.
 
Saadeldin MK, Shawer H, Mostafa A, Kassem NM, Amleh A, Siam R. (2015) New genetic variants of LATS1 detected in urinary bladder and colon cancer. Front Genet. 2015 Jan 13;5:425. doi: 10.3389/fgene.2014.00425. eCollection 2014.
 
Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy M, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R (2014): Aerobic Methanotrophic Communities in Red Sea Brine-Seawater Interfaces. Frontiers in Microbiology, 5:487. doi: 10.3389/fmicb.2014.00487

Mustafa GA, Abdel-Gawad A, Mahmoud, A, Siam, R (2014): Egypt’s Red Sea Coast: Phylogenetic analysis of cultured microbial consortia in industrialized sites. Frontiers in Microbiology, 5:363. doi: 10.3389/fmicb.2014.00363
 
Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang  G, Hikmawan T, Guan Y, Antunes, A, Siam R, El-Dorry H, Bajic VB and Stingl, U (2014): Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. ISME Journal. 2014 Aug 8. doi: 10.1038/ismej.2014.137.
 
Ferreira AJS, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, Stingl U, Archer JAC, Jankovic BR, Sogin M, Bajic VB, El-Dorry H (2014): Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS ONE. 2014 Jun 12;9(6):e97338. doi: 10.1371/journal.pone.0097338.
 
Demian P, Horton KC, Kajon A, Siam R, Hasanin AM, Elgohary Sheta A, Cornelius C, Gaynor AM. (2014) “Molecular identification of adenoviruses associated with respiratory infection in Egypt from 2003 to 2010.” BMC Infect Dis. 14(1):50.

Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB, Siam R, El-Dorry H. (2013). A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. J Biol Chem. 2013 Nov 26. [Epub ahead of print]

Mohamed YM, Ghazy MA, Sayed A, Ouf A, El-Dorry H, Siam R. (2013) “Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool”. Scientific Reports 3, Article number: 3358 doi:10.1038/srep03358

Thompson LR, Field C, Romanuk T, Ngugi D, Siam R, El Dorry H, Stingl U. (2013). Patterns of ecological specialization amongst microbial populations in the Red Sea and diverse oligotrophic marine environments. Ecol Evol. 3(6):1780-97. doi: 10.1002/ece3.593.

Siam R, Mustafa GA, Sharaf H, Moustafa A, Ramadan AR, et al. (2012). Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools. PLoS ONE 7(8): e42872. doi:10.1371/journal.pone.004287

Antunes A, Alam I, El Dorry H, Siam R, Robertson A, Bajic VB, Stingl U. (2011). Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake. Journal of Bacteriology. 193(17):4551-2.

ElHefnawi M, Hassan N, Kamar M, Siam R, Remoli AL, El-Azab I, AlAidy O, Marsili G, Sgarbanti M. (2011). The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus. Bioinformatics. 15; 27(24):3364-70.

ElHefnawi M, Alaidi O, Mohamed N, Kamar M, El-Azab I, Zada S, Siam R. (2011). Identification of novel conserved functional motifs across most Influenza A viral strains. Virology Journal. 27;8:44.

Siam, R., Harada, R., Cadieux, C., Battat, R., Vadnais, C., Nepveu, A. (2009). Transcriptional activation of the Lats1 tumor suppressor gene in tumors of CUX1 transgenic mice. Mol Cancer. 5(8):60.

Spencer, W., Siam, R., Ouimet, M.C., Bastedo, D.P., Marczynski, G.T. (2009). CtrA, a global response regulator uses a distinct second category of weak DNA binding sites for cell cycle transcription control in Caulobacter crescentus. Journal of Bacteriology. 191(17):5458-70.

Gendoo, D.M.A., El-Hefnawi, M.M., Werner, M., Siam, R. (2008). Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions. Virology Journal. 5:91-101.

Siam, R., Gómez, E.B., Forsburg, S.L. (2007). Schizosaccharomyces pombe Rad4/Cut5 protein modification and chromatin binding changes in DNA damage. DNA Cell Biology. 26(8):565-75.

Siam, R., Dolan, W.P., Forsburg, S.L. (2004). Choosing and using S. pombe plasmids. Methods. 33:189-98.

Siam, R., Brassinga, A.K.C., Marczynski G.T. (2003). A dual binding site for integration host factor and the response regulator CtrA inside the Caulobacter crescentus replication origin. Journal of Bacteriology. 185: 5563-5572.

Siam, R. and Marczynski, G.T. (2003). Glutamate at the phosphorylation site of response regulator CtrA provides essential activities without increasing DNA binding. Nucleic Acids Research. 31 (6): 1775-1779.

Brassinga, A.K.C., Siam, R., McSween, W., Winkler, H., Woods, W., Marczynski G.T. (2001) Conserved response regulator CtrA and IHF binding sites in the proteobacteria Caulobacter crescentus and Rickettsia prowazekii chromosomal replication origins. Journal of Bacteriology, 184: 5789-5799.

Brassinga, A.K.C., Siam, R., Marczynski G.T. (2001). Conserved gene cluster at replication origins of Caulobacter crescentus and Rickettsia prowazekii. Journal of Bacteriology, 183:1824-1829.

Siam, R. and Marczynski, G.T. (2000). Cell cycle regulator phosphorylation stimulates two distinct modes of binding at a chromosome replication origin. The EMBO Journal, 19:1138-1147.

 

Selected Conference Presentations

2013    FEMS 2013 5th Congress of European Microbiologists Leipzig, Germany, July 21 - 25, 2013
Lotaief, M.M., Moustafa, A., Ghazy, M. , Sayed, A. , Ouf, A., Dorry, H. and Siam, R. “CRISPR Diversity in Red Sea Brine Pools”.

2011    111th AMERICAN SOCIETY FOR MICROBIOLOGY General Meeting New Orleans, USA. May 21, 2011.
Mohamed, Y., Ghazy, M., Sayed, A., Sharaf, H., El Dorry, H. F. A., Siam, R. "Isolating a Thermostable Lipase from the Atlantis II Brine Pool".

11th CONFERENCE ON BACTERIAL GENETICS AND ECOLOGY
BAGECO, Corfu, Greece. May 29, 2011. Farag, I., Ghazy, M., Sayed, A., Sharaf, H., Ferreira, A. J.S., El Dorry, H. F. A., Siam, R. "Improving microbial survival by a unique Acylhomoserine Lactone synthase (AHLS) revealed through metagenomic and functional analysis of Red Sea Atlantis II Brine Pool".

INTEGRATIVE ECOLOGICAL GENOMICS, CONFERENCES JACQUES MONOD, Roscoff
(Brittany), France. November 15, 2011. Mustafa, G. A., Moustafa, A., Sharaf, H. (Author), Ramadan, A. R. (Author), Sogin, M., Ferreira, A. J.S., El Dorry, H. F. A., Siam, R. "Unique Biodiversity of the Red Sea Brine Floor Revealed by Comparative Taxonomic Analysis of Atlantis II and Discovery Deep Brine sediments".

DEPARTMENT OF ENERGY-JOINT GENOME INSTITUTE
Walnut Creek, CA, USA. March 2011 Ghazy, M., Shibl, A., Mofeed, N., El-Said, N., Siam, R., El Dorry, H. F. A. "Isolation of genes encoding potential cellulase, xylanase, and DNA polymerase from metagenomic fosmid library of Red Sea’s Atlantis II Hot Deep-Sea Brine".

XIII INTERNATIONAL SMYPOSIUM FOR RESPIRATORY VIRUSES
La Marcae group, GEIS-supported, Rome, Italy. March 12, 2011 Demian, P., Pethers, J., Coon, R., Myers, C. A., Naguib, A., El-Gohary, A., Siam, R., Kajon, A., Cornelius, C. "Molecular typing of adenoviruses associated with respiratory infection in Egypt from 2003 to 2010_Abstract.docxMolecular typing of adenoviruses associated with respiratory infection in Egypt from 2003 to 2010.”

2010    110th AMERICAN SOCIETY FOR MICROBIOLOGY General Meeting May 23 - 27, 2010 San Diego, California, USA.
Rania Siam, Ari J. S. Ferreira, Amged Ouf, Hazem Sharaf, Felipe S. Chambergo, Rehab Z. Abdallah, Eman Ramadan, Ahmed Shibl, Joao C. Setubal and Hamza El-Dorry. "Metagenomic Analysis of the Red Sea Atlantis II Brine Pools Reveals Novel Signature Sequences."

9th INTERNATIONAL CONGRESS ON HALOPHILIC MICROORGANISMS
June 29 - July 3, 2010 Beijing, China. Ahmed Shibl, Mohamed Maged, Ari J S Ferreira, Hazem Sharaf, Ulrich Stingl, André Antunes, João C Setubal, Rania Siam and Hamza El Dorry. "Mining the Red Sea’s Atlantis II hot deep-sea brine for halophilic proteins."
8th INTERNATIONAL CONGRESS ON EXTREMOPHILES

September 12 - 16, 2010, São Miguel, Azores, Portugal. Rehab Zohier Abdallah, Amged Ouf, Ari Jose Scattone Ferreira, Hazem Sharaf, Joao Carlos Setubal, Hamza El-Dorry and Rania Siam (2010) "Comparative Genomics of Methanogens and Methanotrophs in the Red Sea Atlantis II Deep Brine".
Eman Ramadan, Ari J S Ferreira, Adam Dawe, Amgad Ouf, Hazem Sharaf, João C Setubal, Rania Siam and Hamza El Dorry. "Insights into sulfur metabolism in the microbial community of the Red Sea Atlantis II brine pool as revealed by whole-genome shotgun metagenomics approach."

13th INTERNATIONAL SYMPOSIUM ON MICROBIAL ECOLOGY
August 22 - 27, 2010 Seattle, Washington, USA. Luke R. Thompson, Ahmed Said, Ari J. S. Ferreira, Adam Dawe, Minna Lehvaslaiho, Allan Kamau, Intikhab Alam, Boris Jankovic, John Archer, Heikki Lehvaslaiho, Rania Siam, Vladimir B. Bajic, Hamza El Dorry, Ulrich Stingl. (2010) “A metagenomic analysis of Prochlorococcus in the Red Sea”

INTERNATIONAL CONFERENCE ON EMERGING INFECTIOUS DISEASES
July 11 - 14, Atlanta, Georgia, 2010. Diaa El-Din A. Mahmoud, Rania E. Siam, Cecilia A. DeMattos, Salwa F. Ahmed, Sherif A. Elfayoumy, Ahmed S. Abdel-Ghani, Pola N. Demian, Carlos C. Demattos. (2010) “Molecular Characterization of Influenza B Viruses in Egypt from 1999 to 2008.”

2009    AMERICAN UNIVERSITY IN CAIRO ANNUAL RESEARCH CONFERENCE Coordinator “Biotechnology and Pharmaceutical Research and Development in Egypt” Workshop.
Mourad, L., Nicklasson, M., Siam, R., and Pimentel, G. (2009), “Molecular Characterization of extendedspectrum b-lactamases producing Klebsiella pneumoniae and Escherichia coli from hospitalized patients in Oman”. BMC Proceedings 2009, 3(Suppl 3):O10 (1 July 2009).

Boutrous, M. and Siam, R. (2009), “Lats1 differential expression in selected human cancers”, BMC Proceedings 2009, 3(Suppl 3):O8 (1 July 2009).

2008    ASIA-PACIFIC REGIONAL S. POMBE MEETING, Singapore. Title: S. pombe Rad4/Cut5 role in spindle checkpoint pathway-selected for oral presentation.
BIOVISION Conference
April 12 - 16, 2008, Bibliotheca Alexandrina. Title: Rad4 protein in S. pombe in response to DNA damaging agents Authors: Amged Ouf and Rania Siam

2007    INTEGRATED METABOLISM and GENOMICS, American Society for Microbiology, Montreal, Quebec, Canada
Marczynski,G.T., Spencer, W., Ouimet, M.C. and Siam R. (2007), “A New Mode of DNA Binding for a Global Regulator of Transcription and Chromosome Replication,” 2nd American Society for Microbiology Conference on Integrated Metabolism and Genomics, Page 35-36.
   
THE EUROPEAN CANCER CONFERENCE ECCO 14, Barcelona, Spain. Siam, R., Harada, R., Cadieux, C., Leduay, L. and Nepveu, N., (2007), “In vitro and in vivo activation of the tumor suppressor Lats1 by the transcriptional regulator CDP/Cux,” European Journal of Cancer Supplements, Vol 5 No 4, Page 68.

1999    99th AMERICAN SOCIETY FOR MICROBIOLOGY General Meeting, Los Angeles, California Presentation Title: In vitro Interaction of Integration Host Factor with the Replication Origin of C. crescentus

1998    98th AMERICAN SOCIETY FOR MICROBIOLOGY General Meeting, Atlanta, Georgia Invited Speaker -American society for Microbiology meeting, Presentation Title: In vitro Interaction of the Response Regulator CtrA with the Replication Origin of C. crescentus
PROKARYOTIC REPLICATION MEETING, Norway Presentation Title: The Master Regulator Cell Cycle Transcription Regulator A and C. crescentus

1997   CANADIAN SOCIETY FOR MICROBIOLOGY, Sherbrooke, Canada Presentation Title: Transcription in and around the Replication Origin of C. crescentus