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152. Clinically-actionable colorectal cancer plasma and tissue proteomic biosignatures

Author

Baker, Mark S., primary, Mahboob, Sadia, additional, Mohamedali, Abidali, additional, Cantor, David, additional, Ranganathan, Shoba, additional, Pascovici, Dana, additional, Wu, Jemma, additional, Zaw, Thiri, additional, Chapuis, Pierre, additional, Chan, Charles, additional, Dent, Owen, additional, Nice, Ed, additional, and Ahn, Seong Beom, additional

Published
2018
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155. A bioinformatics potpourri

Author

Schönbach, Christian, primary, Li, Jinyan, additional, Ma, Lan, additional, Horton, Paul, additional, Sjaugi, Muhammad Farhan, additional, and Ranganathan, Shoba, additional

Published
2018
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162. Accelerating the search for the missing proteins in the human proteome

Author

Baker, Mark S., primary, Ahn, Seong Beom, additional, Mohamedali, Abidali, additional, Islam, Mohammad T., additional, Cantor, David, additional, Verhaert, Peter D., additional, Fanayan, Susan, additional, Sharma, Samridhi, additional, Nice, Edouard C., additional, Connor, Mark, additional, and Ranganathan, Shoba, additional

Published
2017
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166. Radial behavior of the average local ionization energies of atoms.

Author

Politzer, Peter, Murray, Jane S., Grice, M. Edward, Brinck, Tore, and Ranganathan, Shoba

Subjects
ATOMS, IONIZATION (Atomic physics), HELIUM, KRYPTON, HARTREE-Fock approximation
Abstract

The radial behavior of the average local ionization energy I(r) has been investigated for the atoms He–Kr, using ab initio Hartree–Fock atomic wave functions. I(r) is found to decrease in a stepwise manner with the inflection points serving effectively to define boundaries between electronic shells. There is a good inverse correlation between polarizability and the ionization energy in the outermost region of the atom, suggesting that I(r) may be a meaningful measure of local polarizabilities in atoms and molecules. [ABSTRACT FROM AUTHOR]

Published
1991
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167. Systems Proteomics View of the Endogenous Human Claudin Protein Family

Author

Liu, Fei, primary, Koval, Michael, additional, Ranganathan, Shoba, additional, Fanayan, Susan, additional, Hancock, William S., additional, Lundberg, Emma K., additional, Beavis, Ronald C., additional, Lane, Lydie, additional, Duek, Paula, additional, McQuade, Leon, additional, Kelleher, Neil L., additional, and Baker, Mark S., additional

Published
2016
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173. Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

Author

Xinrui Zhou, Jie Zheng, Ivan, Fransiskus Xaverius, Rui Yin, Ranganathan, Shoba, Chow, Vincent T. K., and Chee-Keong Kwoh

Subjects
BINDING site assay, AVIAN influenza A virus, INFECTION, PANDEMICS, HEMAGGLUTININ
Abstract

Background: Influenza viruses are undergoing continuous and rapid evolution. The fatal influenza A/H7N9 has drawn attention since the first wave of infections in March 2013, and raised more grave concerns with its increased potential to spread among humans. Experimental studies have revealed several host and virulence markers, indicating differential host binding preferences which can help estimate the potential of causing a pandemic. Here we systematically investigate the sequence pattern and structural characteristics of novel influenza A/H7N9 using computational approaches. Results: The sequence analysis highlighted mutations in protein functional domains of influenza viruses. Molecular docking and molecular dynamics simulation revealed that the hemagglutinin (HA) of A/Taiwan/1/2017(H7N9) strain enhanced the binding with both avian and human receptor analogs, compared with the previous A/Shanghai/02/2013(H7N9) strain. The Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) calculation revealed the change of residue-ligand interaction energy and detected the residues with conspicuous binding preference. Conclusion: The results are novel and specific to the emerging influenza A/Taiwan/1/2017(H7N9) strain compared with A/Shanghai/02/2013(H7N9). Its enhanced ability to bind human receptor analogs, which are abundant in the human upper respiratory tract, may be responsible for the recent outbreak. Residues showing binding preference were detected, which could facilitate monitoring the circulating influenza viruses. [ABSTRACT FROM AUTHOR]

Published
2018
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174. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

Author

Horvatovich, Péter, primary, Lundberg, Emma K., additional, Chen, Yu-Ju, additional, Sung, Ting-Yi, additional, He, Fuchu, additional, Nice, Edouard C., additional, Goode, Robert J., additional, Yu, Simon, additional, Ranganathan, Shoba, additional, Baker, Mark S., additional, Domont, Gilberto B., additional, Velasquez, Erika, additional, Li, Dong, additional, Liu, Siqi, additional, Wang, Quanhui, additional, He, Qing-Yu, additional, Menon, Rajasree, additional, Guan, Yuanfang, additional, Corrales, Fernando J., additional, Segura, Victor, additional, Casal, J. Ignacio, additional, Pascual-Montano, Alberto, additional, Albar, Juan P., additional, Fuentes, Manuel, additional, Gonzalez-Gonzalez, Maria, additional, Diez, Paula, additional, Ibarrola, Nieves, additional, Degano, Rosa M., additional, Mohammed, Yassene, additional, Borchers, Christoph H., additional, Urbani, Andrea, additional, Soggiu, Alessio, additional, Yamamoto, Tadashi, additional, Salekdeh, Ghasem Hosseini, additional, Archakov, Alexander, additional, Ponomarenko, Elena, additional, Lisitsa, Andrey, additional, Lichti, Cheryl F., additional, Mostovenko, Ekaterina, additional, Kroes, Roger A., additional, Rezeli, Melinda, additional, Végvári, Ákos, additional, Fehniger, Thomas E., additional, Bischoff, Rainer, additional, Vizcaíno, Juan Antonio, additional, Deutsch, Eric W., additional, Lane, Lydie, additional, Nilsson, Carol L., additional, Marko-Varga, György, additional, Omenn, Gilbert S., additional, Jeong, Seul-Ki, additional, Lim, Jong-Sun, additional, Paik, Young-Ki, additional, and Hancock, William S., additional

Published
2015
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175. A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes’ stages A-D colorectal cancers

Author

Mahboob, Sadia, primary, Ahn, Seong Beom, additional, Cheruku, Harish R, additional, Cantor, David, additional, Rennel, Emma, additional, Fredriksson, Simon, additional, Edfeldt, Gabriella, additional, Breen, Edmond J, additional, Khan, Alamgir, additional, Mohamedali, Abidali, additional, Muktadir, Md Golam, additional, Ranganathan, Shoba, additional, Tan, Sock-Hwee, additional, Nice, Edouard, additional, and Baker, Mark S, additional

Published
2015
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176. Coherence analysis discriminates between retroviral integration patterns in CD34+ cells transduced under differing clinical trial conditions

Author

Hallwirth, Claus V, primary, Garg, Gagan, additional, Peters, Timothy J, additional, Kramer, Belinda A, additional, Malani, Nirav V, additional, Hyman, Jessica, additional, Ruan, Xiaoan, additional, Ginn, Samantha L, additional, Hetherington, Nicola A, additional, Veeravalli, Lavanya, additional, Shahab, Atif, additional, Ranganathan, Shoba, additional, Wei, Chia-Lin, additional, Liddle, Christopher, additional, Thrasher, Adrian J, additional, Bushman, Frederic D, additional, Buckley, Michael J, additional, and Alexander, Ian E, additional

Published
2015
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177. Massively Parallel Sequencing and Analysis of the Necatoramericanus Transcriptome

Author

Cantacessi, Cinzia, Mitreva, Makedonka, Jex, Aaron R., Young, Neil D., Campbell, Bronwyn E., Hall, Ross S., Doyle, Maria A., Rabelo, Elida M., Ranganathan, Shoba, Sternberg, Paul W., Loukas, Alex, and Gasser, Robin B.

Subjects
Other medical sciences, parasitic diseases
Abstract

Background: The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses. Methodology/PrincipalFindings:A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%), proteinase inhibitors (7.8%) or calcium-binding EF-hand proteins (6.7%). Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%), oxidative phosphorylation (63%) and/or proteases (60%); most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins) were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins) or amino acid metabolism (e.g., asparagine t-RNA synthetase). Conclusions: This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human hookworm, A. duodenale, for both fundamental and applied purposes, including the prevalidation of anti-hookworm drug targets.

Published
2010

180. Characterization of the Interaction between Heterodimeric αvβ6 Integrin and Urokinase Plasminogen Activator Receptor (uPAR) Using Functional Proteomics

Author

Ahn, Seong Beom, primary, Mohamedali, Abidali, additional, Anand, Samyuktha, additional, Cheruku, Harish R., additional, Birch, Debra, additional, Sowmya, Gopichandran, additional, Cantor, David, additional, Ranganathan, Shoba, additional, Inglis, David W., additional, Frank, Ronald, additional, Agrez, Michael, additional, Nice, Edouard C., additional, and Baker, Mark S., additional

Published
2014
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181. Whole genome sequences of nematodes of the order Strongylida

Author

Casser, Robin B., Ranganathan, Shoba, Baillie, David, Sternberg, Paul W., Mitreva, Makedonka, Mardis, Elaine, and Wilson, Richard K.

Subjects
Other medical sciences
Abstract

The order Strongylida (clade V) represents parasites most closely related to C. elegans, and the group most likely to benefit from the comparative value of its genome sequence. C. elegans has already served as an essential guide for exploring the genomes of other nematode species. However, transcriptomic data from parasitic nematode species, generated by EST approaches, have already served as a boon for C. elegans biology, as they confirm gene predictions and add depth to analyses of structure-function. Here, we propose sequencing the genomes of 20 species, members of the order Strongylida (‘strongylids’). Strongylids, including human hookworms and many intestinal parasites of livestock, are relatively closely related to one another and may have resulted from a recent radiation. To advance and facilitate molecular studies of strongylid parasites, an expressed sequence tag (EST)-based gene discovery program has been carried out, as a part of a broad study of the transcriptomes of members of the phylum Nematoda. More than 60,000 ESTs have been generated for key parasites of human and domestic animals, and for model parasitic species belonging to order Strongylida (comprising 83% of all clade V non-Caenorhabditis ESTs), and deposited in the public databases. Although the transcriptomic data hold promise for the development of novel control strategies for these important pathogens, emerging whole genome data will be pivotal in a more comprehensive approach to identify alternative control strategies, which is increasingly pressing as levels of parasite resistance to available drugs is rising, making some treatment strategies that worked just 5 years ago, ineffective. Also, some drug treatments and environmental nematocideecological contamination.

Published
2007

182. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

Author

Schönbach, Christian, Verma, Chandra, Bond, Peter J., and Ranganathan, Shoba

Subjects
BIOINFORMATICS, MOLECULAR biology, NUCLEOTIDE sequencing, RNA analysis, NUCLEOTIDE sequence
Abstract

The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017. [ABSTRACT FROM AUTHOR]

Published
2016
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183. The Asia-Pacific regional perspective on bioinformatics

Author

Miyano, Satoru and Ranganathan, Shoba

Subjects
Asia -- Research, Pacific Rim -- Research, Australia -- Research, Computational biology -- Research, Biological research -- Research, Molecular biology -- Research, Business, Computers, Computers and office automation industries, Electronics
Abstract

An overview is presented of bioinformatics reserch, service and education in the Asia-Pacific region. That area includes the Asian and Australian continents, as well as the Pacific Rim countries.

Published
2001

185. Transcriptome analysis reveals pathogenicity and evolutionary history of the pathogenic oomycete Pythium insidiosum

Author

Krajaejun, Theerapong, primary, Lerksuthirat, Tassanee, additional, Garg, Gagan, additional, Lowhnoo, Tassanee, additional, Yingyong, Wanta, additional, Khositnithikul, Rommanee, additional, Tangphatsornruang, Sithichoke, additional, Suriyaphol, Prapat, additional, Ranganathan, Shoba, additional, and Sullivan, Thomas D., additional

Published
2014
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187. Genome of the human hookworm Necator americanus

Author

Tang, Yat T, primary, Gao, Xin, additional, Rosa, Bruce A, additional, Abubucker, Sahar, additional, Hallsworth-Pepin, Kymberlie, additional, Martin, John, additional, Tyagi, Rahul, additional, Heizer, Esley, additional, Zhang, Xu, additional, Bhonagiri-Palsikar, Veena, additional, Minx, Patrick, additional, Warren, Wesley C, additional, Wang, Qi, additional, Zhan, Bin, additional, Hotez, Peter J, additional, Sternberg, Paul W, additional, Dougall, Annette, additional, Gaze, Soraya Torres, additional, Mulvenna, Jason, additional, Sotillo, Javier, additional, Ranganathan, Shoba, additional, Rabelo, Elida M, additional, Wilson, Richard K, additional, Felgner, Philip L, additional, Bethony, Jeffrey, additional, Hawdon, John M, additional, Gasser, Robin B, additional, Loukas, Alex, additional, and Mitreva, Makedonka, additional

Published
2014
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196. Simple re-instantiation of small databases using cloud computing

Author

Tan, Tin Wee, primary, Xie, Chao, additional, De Silva, Mark, additional, Lim, Kuan Siong, additional, Patro, C Pawan K, additional, Lim, Shen Jean, additional, Govindarajan, Kunde Ramamoorthy, additional, Tong, Joo Chuan, additional, Choo, Khar Heng, additional, Ranganathan, Shoba, additional, and Khan, Asif M, additional

Published
2013
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