Computer Science, VCU

Peer-reviewed publications.

 

Journals:

1.          Kamapantula, B, Abdelzaher, A, Ghosh, P., Mayo, M., Perkins, E., and Das, S.K. Leveraging the Robustness of Genetic Networks: A Case Study on Bio-inspired Wireless Sensor Topologies. Under review.

2.          Chaitankar, V., Ghosh P., Elasri, M, Gust, K., and Perkins, E. Exploiting higher order genetic structures for genome scale inference of transcriptional regulatory networks, Under review.

3.          Mayo, M, Perkins, EJ, Ghosh, P. Motif association models based on incoherent feed-forward loops. Under review.

4.          Chaitankar V, Barh D, Ramos R, Barbosa E, Fiaux K, Azevedo V, Silva A, Ghosh P. GENOTATOR: An automated tool towards assembly and annotation of genomes. Under review.

5.          Mayo, M, Abdelzaher, A, Perkins, EJ, Ghosh, P. Motif Participation by Genes in E. coli Transcriptional Networks, in press, Frontiers in Fractal Physiology, 2012.

6.          Hassan, S, Schneider, MP, Ramos, RT, Carneiro, A, Lima, AR, Guimarães, LC, Ali, A, Bakhtiar, S, Pereira, U, Santos, A, Soares, SC, Dorella, F, Pinto, A, Ribeiro, D, Barbosa, MS, Almeida, S, Abreu, VA, Aburjaile, F, Fiaux, KK, Barbosa, EG, Diniz, C, Rocha, F, Saxena, R, Tiwari, S, Zambare, V, Ghosh, P, Pacheco, LG, Dowson, C, Kumar, A, Barh, D, Miyoshi, A, Azevedo, V and Silva, A. Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 162, Isolated from Camel, in press, Journal of Bacteriology 2012.

7.          Achuthan, S., Chung, B.J., Ghosh P., Rangachari V. and Vaidya, A. A Modified Stokes Einstein Equation for Aβ Aggregation. BMC Bioinformatics 2011, 12(Suppl 10):S13, pp. 1-13.

8.          Mayo, M., Perkins, E. and Ghosh, P, First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. BMC Bioinformatics 2011, 12(Suppl 10):S18, pp. 1-14.

9.          Ghosh, S, Ghosh, P, Basu, K, Das, S, A discrete event based stochastic simulation platform for ‘in silico’ study of molecular level cellular dynamics. Journal of Biotechnology and Biomaterials 2011, Vol 1: 5, pp. 1-19.

10.        Cerdeira LT, Schneider MP, Pinto AC, de Almeida SS, Dos Santos AR, Barbosa EG, Ali A, Aburjaile FF, de Abreu VA, Guimarães LC, Soares Sde C, Dorella FA, Rocha FS, Bol E, Gomes de Sá PH, Lopes TS, Barbosa MS, Carneiro AR, Jucá Ramos RT, Coimbra NA, Lima AR, Barh D, Jain N, Tiwari S, Raja R, Zambare V, Ghosh P, Trost E, Tauch A, Miyoshi A, Azevedo V, Silva A. Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain CIP 52.97, Isolated from a Horse in Kenya. J Bacteriol. 2011 Dec; 193(24):7025-6.

11.        Ghosh, P., Kumar, A., Datta B. and Rangachari V., Protofibril elongation and association dynamics in the Aβ42 peptide aggregation pathway involved in Alzheimer’s disease. BMC Bioinformatics 2010, 11(Suppl 6):S24, doi:10.1186/1471-2105-11-S6-S24.

12.        Chaitankar, V, Zhang, C, Ghosh, P, Perkins, E, Gong, P, Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks, BMC Bioinformatics 2010, 11(Suppl 6):S19, doi:10.1186/1471-2105-11-S6-S19.

13.        Ghosh, P, Basu, K, Das, S, and Zhang, C. Discrete diffusion models to study the effects of Mg2+ concentration on the PhoPQ signal transduction system, in press, BMC Genomics 2010, 11(Suppl 3):S3, doi:10.1186/1471-2164-11-S3-S3.

14.        Chaitankar, V, Zhang, C, Ghosh, P, Perkins, E, Gong, P, Deng, Y. Reverse engineering of gene regulatory networks using predictive minimum description length principle, BMC Systems Biology 4(1): S7, pp. 1- 12, 2010.

15.        Choe, H, Ghosh, P and Das, S, QoS-Aware Adaptive Data Reporting in Wireless Sensor Networks, Elsevier Computer Communications, 33:11, pp. 1244-1254, 2010.

16.        Ghosh, P, Dullea, R, Fischer, J, Turi, T, Sarver, R, Zhang, C, Poland, B and Das, S. Comparing 2-nt 3’ overhangs against blunt ended siRNAs: A systems biology based study, BMC Genomics 10(1): S17, pp. 1-14, 2009.

17.        Ghosh, P, Ghosh, S, Basu, K and Das, S, Parametric modeling of protein-DNA binding kinetics: A Discrete Event based Simulation approach, Journal of Discrete Applied Mathematics, 157(10): 2395-2415, 2009.

18.        Ghosh, P, and Das, S, Mobility-aware Cost-efficient Job Scheduling for Single-class Grid jobs in a generic Mobile Grid Architecture. Elsevier Future Generation Computer Systems, vol. 26:8, pp. 1356-1367, 2010.

19.        Ghosh, P, Ghosh, S, Basu, K and Das, S. Holding Time Estimation for Reactions in Stochastic Event-based Simulation of Complex Biological Systems, Elsevier Simulation Modeling Practice and Theory, 2008, 16(10): 1615-1639.

20.        Ghosh, P, Basu, K and Das, S, Improving End-to-End Quality of Service in Online Multiplayer Wireless Gaming Networks. Elsevier Computer Communications, special issue on End-to-end Support over Heterogeneous Wired-Wireless Networks, 31(11): 2685-2698 (2008).

21.        Mazloom, A, Ghosh, P, Basu, K and Das, S, CoCONet: A Collision-free Container-based Core Optical Network, Elsevier Computer Networks Journal, 52(10): 2013-2032 (2008).

22.        Ghosh, P, Ghosh, S, Basu, K, Das, S, and Daeffler, S. A Computationally Fast and Parametric Model to estimate Protein-Ligand Docking time for Stochastic Event based Simulation, LNCS Transactions on Computational Systems Biology (TCSB VIII), 2007, LNBI 4780, pp. 14-41.

23.        Ghosh, P, Basu, K and Das, S, A Game Theory based Pricing Strategy to support Single/Multi-Class Job Allocation Schemes for Bandwidth Constrained Distributed Systems. IEEE Transactions on Parallel and Distributed Systems, 2007, Volume 18, Issue 3, pp. 289-306.

24.        Ghosh, P, Basu, K and Das, S, A Novel Photonic Container Switched Architecture and Scheduler to Design the Core Transport Network. IEEE Transactions on Computers, 2007, Volume 56, Issue 8, pp. 1087-1104.

25.        Lin, H, Ghosh, P and Das, P, Wireless Networks Revenue Optimization through Overload Control with Priority Services, in the Journal of Communications (JCM), issue 4, 2006, Volume 1, Issue 4, pp. 22-30.

26.        Ghosh, P, Roy, N, Basu, K and Das, S, A Pricing Strategy for Job Allocation in Mobile Grids using a Non-cooperative bargaining Theory Framework, in Special Issue on Design and Performance of Networks for Super-Cluster and Grid-Computing, JPDC, 2005, Volume 65, Issue 11, pp. 1366-1383.

 

Book Chapters:

27.        Chaitankar V, Ghosh P, Barh D, Azevedo V: Computational Regulomics: Information Theoretic Approaches Towards Regulatory Network Inference. In press, “Animal Biotechnology: Models in Discovery and Translation” Edt by Verma and Singh. Elsevier, USA.

28.        Barh, D, Yiannakopoulou, EC, Salawu, EO, Bhattacharjee, A, Chowbina, S, Ghosh, P, Azevedo, V: In silico Disease Models, In press, “Animal Biotechnology: Models in Discovery and Translation” Edt by Verma and Singh. Elsevier, USA.

29.        Chaitankar, V, Zhang, C, Ghosh, P, Perkins, E, Gong, P, Deng, Y. Predictive minimum description length principle approach to infer gene regulatory networks, Springer Adv Exp Med Biol. 2011;696:37-43.

 

Genome Sequences:

30.        Cerdeira LT, Carneiro AR, Bol E, Barbosa MS, Coimbra N, Ramos RTJ, Almeida SS, Santos AR, Soares SC, Pinto AC, Ali A, Barbosa E, Dorella FA, Rocha FS, Guimaraes LG, Figueira F, Ghosh P, Zambare V, Barve N, Tiwari S, Barh D, Miyoshi A, Schneider MPC, Azevedo V, Silva A. Corynebacterium pseudotuberculosis CIP 52.97, complete genomeGenBank: CP003061

31.         Cerdeira L, Schneider MPC, Barbosa MS, Ramos RTJ, Carneiro AR, Santos RS, Lima M, DAFonseca V, Almeida SS, Santos AR, Soares SC, Pinto AC, AliA, Barbosa E, Dorella FA, Rocha FS, Guimaraes LG, Belchior SB, Ghosh P, Zambare V, Barve N, Tiwari S, Barh D, Miyoshi A, Azevedo V. Corynebacterium pseudotuberculosis PAT10, complete genome. GenBank: CP002924.1

32.         Silva A, Ramos R, Carneiro A, Almeida S, Barbosa S,  Pinto AC, Cerdeira L, Santos A, Soares S, Guimaraes L, Barbosa E, Figueira F, Souza F, Abreu VC, Dorella F, Pacheco L, Ghosh P, Zambare V, Barve N, Tiwari S, Barh D, Miyoshi A, Schneider MP, and Azevedo V. Corynebacterium pseudotuberculosis 316, complete genome. GenBank: CP003077.1

33.         Silva A, Cerdeira L, Bol E, Barbosa MS, Muller B, Helden PV, Santos A R, Ramos RTJ, Carneiro A R, Guimaraes LC, Aburjaile F F, Padua UD, Arbosa E, Fiaux KK,  Diniz CAA, Soares SC, Pinto AC, Almeida SS, Abreu VAC, Hassan SS, Khatri G, Rahangdale S, Gupta K, Verma A, Ghosh P, Zambare V, Kumavath RN, Barh D, Miyoshi A, Schneider MPC, and Azevedo V. Corynebacterium pseudotuberculosis P54B96, complete genome. GenBank: CP003385.1

34.         Silva A, Lopes T, Ramos RTJ, Carneiro AR, Barbosa MS, Santos AR, Guimaraes LC, Aburjaile FF, Padua Ud, Barbosa E, Fiaux KK, Diniz CA, Soares SC, Pinto AC, Almeida SS, Abreu VAC, Hassan SS, Khatri G, Rahangdale S, Gupta K, Verma A, Kumavath RN, Ghosh P, Zambare V, Barh D, Miyoshi A, Schneider MPC, and Azevedo V. Corynebacterium pseudotuberculosis 267, complete genome. GenBank: CP003407.1

35.         Silva A, Saleh,M , Selim SA, Cerdeira L, Ramos RT, Carneiro AR, Barbosa S, Santos A, Soares S, Guimaraes L, Diniz CA, Fiaux K, Hassan SS, Ali A, Barbosa E, Figueira F, Pinto AC, Almeida S, Abreu VC, Dorella F, Pacheco L, Souza F, Ghosh P, Zambare V, Barh D, Miyoshi A, Schneider MP,  and Azevedo V.  Corynebacterium pseudotuberculosis 31, complete genome. GenBank:  CP003421.1

36.         Silva A, Ramos R , Carneiro,A R , Cerdeira,L , BarbosaS, Santos A, Soares S, Guimaraes L, Diniz CAA, Fiaux K, Hassan SS, Ali A, Barbosa E, Figueira F, Pinto AC, Almeida S, Abreu VC, Dorella F, Pacheco L, Souza F, Dowson CG, Ghosh P, Zambare V, Barh D, Miyoshi A, Schneider MP,  Azevedo V.  Corynebacterium pseudotuberculosis 258, complete genome. GenBank:  CP003540.1

37.        Silva A, Ramos R, Carneiro AR,  Barbosa S,  Santos A, Soares S,  Guimaraes L,  Diniz CAA,  Fiaux K,  Hassan SS, Ali A,  Barbosa E,  Figueira F,  Pinto AC, Almeida S, Abreu VC,  Dorella F,  Pacheco L,  Dowson CG,  Souza F, Ghosh P,  Zambare V,  Barh D, Miyoshi A,  Schneider MP,  Azevedo V. Corynebacterium pseudotuberculosis Cp162, complete genome. GenBank:  CP003652.1

 

Conference Proceedings:

38. Chaitankar, V., Ghosh P., Elasri, M, Gust, K., and Perkins, E. Genome scale inference of transcriptional regulatory networks using mutual information on complex interactions, To appear ACM BCB Workshop on Biological Network Analysis and Applications in Translational and Personalized Medicine (BNA-M), 2012.

39. Chaitankar, V., Ghosh P., Elasri, M, Gust, K., and Perkins, E. sCoIn: A Scoring algorithm based on COmplex INteractions for reverse engineering regulatory networks, Under Review.

40. Nazi, A, Raj, M, Francesco, M.D, Ghosh, P, Das, S.K. Robust Deployment of Wireless Sensor Networks using Gene Regulatory Networks, Under Review.

41. Nazi, A, Raj, M, Francesco, M.D, Ghosh, P, Das, S.K. Robust Routing Topology with Maximum Coverage in Wireless Sensor Networks using Gene Regulatory Networks, Under Review.

42. Kamapantula, B, Abdelzaher, A, Ghosh, P., Mayo, M., Perkins, E., and Das, S.K. Performance of Wireless Sensor Topologies Inspired by E. coli Genetic Networks, PerSens Workshop (part of PerCom 2012), pp. 302-307.

43. Ghosh, P. Can biological network topologies benefit engineered systems? NSF Sponsored Workshop on “Biologically Inspired Networking”, July 2011.

44. Mayo, M., Perkins, E., and Ghosh, P. Downstream Exploration of DNA-Bound Searching Proteins: a Diffusion-Reaction Model, IEEE BIBE 2011, pp. 21-26.

45. Ghosh, P., Datta B., and Rangachari V., Computational predictions for the lag-times and nucleation mass involved in Aβ42 peptide aggregation. Bioinformatics 2012, pp. 312-316.

46. Chaitankar, V., Ghosh P., and Perkins, E. S-REVEAL: A Scalable implementation of REVEAL for gene regulatory network reconstruction, IEEE ISDA 2011, pp. 1-6.

47. Chaitankar, V., Ghosh P., Elasri, M., and Perkins, E. A scalable gene regulatory network reconstruction algorithm combining gene knock-out data, BiCob 2011, pp. 74-79.

48. Ghosh, P., Mayo, M., Chaitankar, V., Habib, T., Perkins, E., and Das, S.K. Robust topology and attractor dynamics of gene regulatory networks inspire fault-tolerant wireless sensor network designs, PerSens Workshop (part of PerCom 2011), pp. 160-165.

49. Ghosh, P., Kumar, A., Datta B. and Rangachari V., Estimating the dynamics of protofibril elongation involved in Aβ42 peptide aggregation in Alzheimer’s disease. ACM Bioinformatics and Computational Biology, 2010, pp. 451-453.

50. Chaitankar, V, Zhang, C, Ghosh, P, Perkins, E, Gong, P. Effects of CDNA microarray data size on gene regulatory network inference accuracy, ACM Bioinformatics and Computational Biology, 2010, pp. 410-413.

51. Ghosh, P, Ghosh, S, Basu, K and Das, S. In-silico effects of Mg2+ concentration on the PhoPQ signal transduction syst.m International Joint Conferences on Bionformatics, Systems Biology and Intelligent Computing (IJCBS) 2009, pp 405-411.

52. Chaitankar, V, Zhang, C, Ghosh, P, Perkins, E, Gong, P, Deng, Y. A novel Gene regulatory network inference algorithm using the predictive minimum description length principle and conditional mutual information. International Joint Conferences on Bionformatics, Systems Biology and Intelligent Computing (IJCBS) 2009, pp. 487-490.

53. Choe, H, Ghosh, P and Das, S, Cross-Layer Design for Adaptive Data Reporting in Wireless Sensor Networks. The 1st International Workshop on Information Quality and Quality of Service for Pervasive Computing (IQ2S 2009), held in conjunction with Percom 2009, TX, USA, pp. 1-6.

54. Pal, S, Ghosh, P, Kundu, S, Basu, K and Das, S, Emancipating the IEEE 802.11 Network from Handoff Delay. 17th IEEE International Workshop on Quality of Service (IWQoS 2009), pp. 1-6.

55. Choe, H, Ghosh, P, Basu, K and Das, S, Class-Based Data Reporting Scheme in Heterogeneous Wireless Sensor Networks. The 18th IEEE International Conference on Computer Communications and Networks (ICCCN 2009), pp. 1-6.

56. Ghosh, P, Ghosh, S, Basu, K and Das, S. A Markov Model based Analysis of Stochastic Biochemical Systems. LSS Computational Systems Bioinformatics Conf (CSB) 2007, pp. 121-132.

57. Ghosh, P, Ghosh, S, Basu, K, Das, S, and Daeffler, S. Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2007,  pp. 439-446.

58. Ghosh, S, Ghosh, P, Basu, K and Das, S, Modeling the stochastic dynamics of gene expression in single cells: A Birth and Death Markov Chain Analysis. IEEE International Conference on Bioinformatics and Biomedicine, 2007, pp. 308-316.

59. Ghosh, S, Ghosh, P, Basu, K and Das, S, Modeling the stochastic dynamics of protein synthesis: A discrete event simulation approach. Biotechnology and Bioinformatics Symposium (BIOT-2007), Colorado Springs, 2007, pp. 1-6.

60. Ghosh, P, Roy, N, Basu, K and Das, S, Wilson, P and Das, P, A Case Study-based Performance Evaluation Framework for CSCF Processes on a Blade-Server. 3rd IEEE International Conference on Networking and Services, 2007, pp. 87-96.

61. Ghosh, P, Roy, N and Das, S, Mobility-based Cost-efficient Job Scheduling in Mobile grids. 1st IEEE International Workshop on Context-Awareness and Mobility in Grid Computing, 2007, Brazil, pp. 701-706.

62. Pal, S, Ghosh, P, Kundu, S, Mazloom, A and Das, S, Two Phase Scheduling Algorithm for Maximizing the Number of Satisfied Users in Multi-Rate Wireless Systems. IEEE International Symposium on a World of Wireless, Mobile and Multimedia Networks (WOWMOM 2007), Finland, pp. 1-9.

63. Ghosh, P, Ghosh, S, Basu, K, Das, S. "An Analytical Model to Estimate the time taken for Cytoplasmic Reactions for Stochastic Simulation of Complex Biological Systems", IEEE Granular Computing Conference, 2006, pp. 79-84.

64. Ghosh, P, Ghosh, S, Basu, K, Das, S, and Daeffler, S. "Stochastic Modeling of Cytoplasmic Reactions in Complex Biological Systems", International Conference on Computational Science and its Applications, ICCSA 2006, pp. 566-576.

65. Ghosh, P, Ghosh, S, Basu, K, Das, S, and Daeffler, S. "Modeling the Diffusion process in Stochastic Event based Simulation of the PhoPQ system", International Symposium on Computational Biology and Bioinformatics (ISBB 2006), December, 2006, Bhubaneshwar, India, pp. 1-6.

66. Ghosh, P, Ghosh, S, Basu, K, Das, S, and Daeffler, S. A stochastic model to estimate the time taken for protein-ligand docking. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2006, Toronto, Canada, pp. 1-8.

67. Ghosh, S, Ghosh, P, Basu, K, Das, S, and Daeffler, S. “iSimBioSys: A Discrete Event Simulation Platform for 'in silico' Study of Biological Systems”, IEEE 39th Annual Simulation Symposium, 2006 pp. 204-213.

68. Ghosh, P, Mazloom, A, Basu, K and Das, S, A Centrally-Scheduled Photonic Container Switched Architecture For The Core Transport Network. Pacific Telecommunication Council Conference, 2006, Hawaii, USA, pp. 1-17 (best paper award).

69. Ghosh, P, Basu, K and Das, S, Cost-Optimal Job Allocation Schemes for Bandwidth-Constrained Distributed Computing Systems. 12th Annual IEEE International Conference on High Performance Computing (HiPC), 2005, Goa, India, pp. 40-50.

70. Ghosh, P, Basu, K and Das, S, A Novel Photonic Container Switched OBS Architecture and Nonpreemptive Scheduler for the Core Transport Network. 19th International Teletraffic Congress (ITC19), 2005, China, pp. 1-10.

71. Ghosh, P, Basu, K and Das, S, A Photonic Container Switched Transport Network to Support Long-Haul Traffic at the Core. Second IEEE International Conference on Broadband Networks (Broadnets Optical networking Symposium), 2005, Boston, USA, pp. 104-113.

72. Ghosh, P, Basu, K and Das, S, A Cross-Layer Design to Improve Quality of Service in Online Multiplayer Wireless Gaming Networks. Second IEEE International Conference on Broadband Networks (Broadnets Applications/Services Symposium), 2005, Boston, USA, pp. 875-884.

73. Ghosh, S, Ghosh, P, Basu, K and Das, S, GaMa: An Evolutionary Algorithmic Approach for the Design of Mesh-Based Radio Access Networks. 30th IEEE Conference on Local Computer Networks (LCN), 2005, Sydney, pp. 374-381.

74. Sanyal, S, Ghosh, P, Basu, K and Das, S, Towards the Optimal design of an Enterprise Network: A genetic algorithm perspective. XVth International Symposium on Services and Local Access (ISSLS), 2004, UK, pp. 1-7.

75. Ghosh, P, Roy, N, Basu, K and Das, S, A Game Theory based Pricing Strategy for Job allocation in Mobile Grids. 18th IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2004, USA, pp. 82-91.

 

Selected Extended Abstracts:

76. Ghosh, P., Datta B. and Rangachari V., In silico hypotheses of the Aβ42 peptide aggregation process in Alzheimer’s disease. IEEE ICCABS 2011.

77. Chaitankar, V., Ghosh P., Elasri, M., and Perkins, E. Gene Regulatory Network Inference Using Time Lagged Context Likelyhood of Relatedness, IEEE ICCABS 2011.

78. Ghosh, P., Kumar, A., Datta B. and Rangachari V., Molecular level simulation of competing pathways in AB42 peptide aggregation towards a realistic understanding of Alzheimer’s disease. MCBIOS 2010.

79. Chaitankar, V, Zhang, C, Ghosh, P, Perkins. Transcriptional time lagged information approach to improving the accuracy of gene regulatory network reconstruction. MCBIOS 2010. Received Best poster award.

80. Ghosh, P, Squires, B, Basu, K, Das, S and Scheuermann, R. A Stochastic Model to study the Influenza Molecular Infection Machinery, The Sixth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society MCBIOS 2009, Feb, 2009, Starkville, MS.

81. Squires, B, Ghosh, P, Basu, K, Das, S, Scheuermann, R. FluSim - An Influenza Virus Molecular Infection Model and Discrete Event, Stochastic Simulation , Immunobiology and Pathogenesis of Influenza Infection Conference, June, 2008, Georgia, also at BIOT 2008.

82. Samik Ghosh, A. R Mazloom, Preetam Ghosh, Kalyan Basu and Sajal K Das, Connecting the dots: An integrated database for studying cellular dynamics. Eighth International Conference on Systems Biology (ICSB), Oct 2007, USA.

83. Ghosh, S, Ghosh, P, Basu, K and Das, S, A Hybrid Simulation Framework for genome scale study of molecular dynamics in Escherichia Coli. Seventh International Conference on Systems Biology (ICSB 2006), Oct 9-13, Japan.

84. Basu, K, Ghosh, S, Ghosh, P and Das, S. Genome scale cell modeling using stochastic discrete event simulation. (poster paper) accepted for publication at the Conference on Stochastic Networks (SNC 2006), UIUC, 2006.

85. Ghosh, P, Ghosh, S, Basu, K and Das, S. A Diffusion Model to Estimate the Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks. (poster paper) IEEE Computational Systems Bioinformatics Conference (CSB) 2005, Stanford University, USA, pp. 19-21.

86. Ghosh, S, Ghosh, P, Basu, K and Das, S, iSimBioSys: An `In Silico’ Discrete Event Simulation Framework for Modeling Biological Systems. (poster paper) IEEE Computational Systems Bioinformatics Conference (CSB) 2005, Stanford University, USA pp. 170-171.

87. P. Ghosh, S. Ghosh, K. Basu, S K Das, Parametric and Stochastic Modeling of Molecular Reactions in the Cell. Dallas Area Bioinformatics and Computational Biology Workshop (DABC) 2006, U.T. SouthWestern Medical Center, USA.

88. M. Mayo, P. Ghosh, T. Habib, N. Reyero, V. Chaitankar and E. Perkins, Robust topology and attractor dynamics of gene regulatory networks can inspire fault-tolerant wireless sensor network design, Army Network Science Conference 2010.

89. Datta, B, Ghosh, P, Rangachari, V. A computational prediction of the nucleation mass in the Aβ42 peptide aggregation pathway, MCBIOS 2011.

90. Clyde Sims, Preetam Ghosh, Modeling AB aggregation pathways in Alzheimer’s Disease, Mississippi Academy of Sciences, 2010.

91. Ghosh, P. Can biological network topologies benefit engineered systems? NSF Workshop on “Biologically Inspired Networking”, July 2011.

92. Kurt A Gust, Vijender Chaitankar, Preetam Ghosh, Mitchell S Wilbanks, Xianfeng Chen, Craig A McFarland, Larry Talent, Edward J Perkins. Use of mutual information theory to decipher the impacts of multiple stressors from molecular through whole-organism level effects. SETAC 2012.

 

Technical Reports:

93. P. Ghosh, S. Ghosh, K. Basu, S. Das, S. Daefler, "Estimation of the holding Time for Cytoplasmic Reactions in Stochastic Event Based Modeling of Complex Biological Networks", TR CSE-2005-09.

94.        P. Ghosh, S. Ghosh, K. Basu, S. Das, S. Daefler, "Transient analysis of Diffusion for charged molecules to model the input process in a stochastic event based simulation framework for the PhoPQ signal transduction system ", TR CSE-2005-07.

95.        P. Ghosh, Shashikant Maheshwari and Giridhar Mandyam, A Dynamic Packetization Scheme to Improve Transport Layer Performance in Online Multiplayer Wireless Gaming. Technical Report, Nokia Research Centre, Irving, Dallas, 2004.

 

Publications