College of Agricultural Sciences &amp; Natural Resources &ndash; Research Output

2018

A microfluidic feed forward loop pulse generator for molecular communication

Deng, Y., Pierobon, M. & Nallanathan, A., Jan 10 2018, 2017 IEEE Global Communications Conference, GLOBECOM 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 1-7 7 p. (2017 IEEE Global Communications Conference, GLOBECOM 2017 - Proceedings; vol. 2018-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Pulse generators

Microfluidics

Communication

Pulse modulation

Information theory

1 Citation (Scopus)

Applying molecular communication theory to estimate information loss in cell signal transduction: An approach based on cancer transcriptomics

Sakkaff, Z., Immaneni, A. & Pierobon, M., Sep 5 2018, Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2018. Association for Computing Machinery, Inc, (Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2018).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Signal transduction

communication theory

Information theory

cancer

Genes

3 Citations (Scopus)

Estimating Information Exchange Performance of Engineered Cell-to-cell Molecular Communications: A Computational Approach

Harper, C., Pierobon, M. & Mazarini, M., Oct 8 2018, INFOCOM 2018 - IEEE Conference on Computer Communications. Institute of Electrical and Electronics Engineers Inc., Vol. 2018-April. p. 729-737 9 p. 8485834

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Communication

Communication systems

Cell engineering

Oncology

Tissue engineering

Estimating the Molecular Information Through Cell Signal Transduction Pathways

Sakkaff, Z., Immaneni, A. & Pierobon, M., Aug 24 2018, 2018 IEEE 19th International Workshop on Signal Processing Advances in Wireless Communications, SPAWC 2018. Institute of Electrical and Electronics Engineers Inc., 8445884. (IEEE Workshop on Signal Processing Advances in Wireless Communications, SPAWC; vol. 2018-June).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Signal transduction

Health

Internet

Communication

2017

4 Citations (Scopus)

A biological circuit design for modulated parity-check encoding in molecular communication

Marcone, A., Pierobon, M. & Magarini, M., Jul 28 2017, 2017 IEEE International Conference on Communications, ICC 2017. Institute of Electrical and Electronics Engineers Inc., 7997032

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Networks (circuits)

Communication

Modulators

Channel coding

Bioremediation

A frequency analysis on calcium T-type signaling in the nervous system

Khodaei, A., Vakilzadian, H. & Pierobon, M., Sep 27 2017, 2017 IEEE International Conference on Electro Information Technology, EIT 2017. IEEE Computer Society, p. 640-644 5 p. 8053442

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Neurology

Calcium

Depolarization

Power spectral density

Membranes

1 Citation (Scopus)

A new statistical model for genome-scale MicroRNA target prediction

Hakguder, Z., Liao, C., Shu, J. & Cui, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 101-107 7 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Statistical Models

MicroRNAs

Genes

Genome

Binding sites

A new system for human microRNA functional evaluation and network

Han, J., Shu, J. & Cui, J., Jan 17 2017, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc., p. 278-283 6 p. 7822531

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

MicroRNAs

Genes

Untranslated RNA

Gene Ontology

Gene Regulatory Networks

5 Citations (Scopus)

A parity check analog decoder for molecular communication based on biological circuits

Marcone, A., Pierobon, M. & Magarini, M., Oct 2 2017, INFOCOM 2017 - IEEE Conference on Computer Communications. Institute of Electrical and Electronics Engineers Inc., 8057131

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Networks (circuits)

Communication

Gene expression

Bit error rate

Medicine

A simulation model of glucose-insulin metabolism and implementation on OSG

Rad, M. G., Immaneni, A., McCabe, M., Pierobon, M. & Cui, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 1832-1839 8 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Insulin

Metabolism

Glucose

Adenosinetriphosphate

Adenosine Triphosphate

1 Citation (Scopus)

BioSIMP: Using Software Testing Techniques for Sampling and Inference in Biological Organisms

Cashman, M., Catlett, J. L., Cohen, M. B., Buan, N. R., Sakkaff, Z., Pierobon, M. & Kelley, C. A., Jun 29 2017, Proceedings - 2017 IEEE/ACM 12th International Workshop on Software Engineering for Science, SE4Science 2017. Institute of Electrical and Electronics Engineers Inc., p. 2-8 7 p. 7964305

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Software testing

Software engineering

Sampling

Ant colony optimization

Biological systems

Dictionary coded profiles and their use with nanopore sequencers

Murray, K., Dunigan, D. D. & Sayood, K., Sep 27 2017, 2017 IEEE International Conference on Electro Information Technology, EIT 2017. IEEE Computer Society, p. 422-426 5 p. 8053398

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Nanopores

Glossaries

Molecules

Genes

1 Citation (Scopus)

Digital modulation and achievable information rates of thru-body haptic communications

Hanisch, N. & Pierobon, M., Jan 1 2017, Disruptive Technologies in Sensors and Sensor Systems. Hall, R. D., Blowers, M. & Williams, J. (eds.). SPIE, 1020603. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 10206).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Information Rates

Haptics

Modulation

communication

modulation

2 Citations (Scopus)

End-to-end molecular communication channels in cell metabolism: An information theoretic study

Sakkaf, Z., Catlett, J. L., Cashman, M., Pierobon, M., Buan, N. R., Cohen, M. B. & Kelley, C. A., Sep 27 2017, Proceedings of the 4th ACM International Conference on Nanoscale Computing and Communication, NanoCom 2017. Association for Computing Machinery, Inc, 21

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Chemical compounds

Ecology

Chemical industry

Controllability

Metabolism

MiRDR-OSG: MicroRNA dynamic regulation analysis utilizing open science grid

Shu, J. & Cui, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 1846-1851 6 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

MicroRNAs

RNA

Gene expression

Pipelines

Throughput

4 Citations (Scopus)

The Gaussian approximation in soft detection for molecular communication via biological circuits

Marcone, A., Pierobon, M. & Magarini, M., Dec 19 2017, 18th IEEE International Workshop on Signal Processing Advances in Wireless Communications, SPAWC 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-July. p. 1-6 6 p. 8227764

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Networks (circuits)

Communication

Molecules

Chemical reactions

Communication systems

2 Citations (Scopus)

When technology meets technology: Retrained 'Inception V3' classifier for NGS based pathogen detection

Sinha, R. & Clarke, J. L., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 1-5 5 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Pathogens

Classifiers

Technology

Metagenomics

Nucleotides

2016

6 Citations (Scopus)

An intra-body linear channel model based on neuronal subthreshold stimulation

Khodaei, A. & Pierobon, M., Jul 12 2016, 2016 IEEE International Conference on Communications, ICC 2016. Institute of Electrical and Electronics Engineers Inc., 7511483

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Neurons

Communication systems

Neurophysiology

Neurology

Telecommunication networks

9 Citations (Scopus)

Mutual information upper bound of molecular communication based on cell metabolism

Pierobon, M., Sakkaff, Z., Catlett, J. L. & Buan, N. R., Aug 9 2016, SPAWC 2016 - 17th IEEE International Workshop on Signal Processing Advances in Wireless Communications. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-August. 7536835

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Metabolism

Communication

Chemical reactions

Biotechnology

Chemical analysis

2 Citations (Scopus)

Subthreshold linear modeling of dendritic trees: A computational approach

Khodaei, A. & Pierobon, M., Oct 13 2016, 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-October. p. 235-238 4 p. 7590683

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Neurons

Carisoprodol

Nervous System

Electric Stimulation

Linear Models

2 Citations (Scopus)

The assurance timeline: Building assurance cases for synthetic biology

Cohen, M. B., Firestone, J. & Pierobon, M., Jan 1 2016, Computer Safety, Reliability, and Security, SAFECOMP 2016 - Workshops ASSURE, DECSoS, SASSUR, and TIPS, Proceedings. Guiochet, J., Schoitsch, E., Bitsch, F. & Skavhaug, A. (eds.). Springer Verlag, p. 75-86 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9923 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Synthetic Biology

Drug Delivery

Pollution

Drug delivery

Computer programming languages

2015

A biochemical filter for frequency-based signal reception in molecular communication

Laddomada, M. & Pierobon, M., 2015, 2015 IEEE Global Communications Conference, GLOBECOM 2015. Institute of Electrical and Electronics Engineers Inc., 7417148

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

communication

Communication

communication system

biology

Communication systems

4 Citations (Scopus)

A crosstalk-based linear filter in biochemical signal transduction pathways for the internet of bio-things

Laddomada, M. & Pierobon, M., Aug 4 2015, 2015 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2015 - Proceedings. Institute of Electrical and Electronics Engineers Inc., Vol. 2015-August. p. 5520-5524 5 p. 7179027

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Signal transduction

Crosstalk

Internet

Notch filters

Chemical reactions

2 Citations (Scopus)

An optical biosensor for detection of pathogen biomarkers from Shiga toxin-producing Escherichia coli in ground beef samples

Lamoureux, L., Adams, P., Banisadr, A., Stromberg, Z., Graves, S., Montano, G., Moxley, R. A. & Mukundan, H., 2015, Progress in Biomedical Optics and Imaging - Proceedings of SPIE. SPIE, Vol. 9310. 931004

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Shiga Toxin

Shiga-Toxigenic Escherichia coli

Beef

pathogens

biomarkers

Human absorbable microRNA prediction based on an ensemble manifold ranking model

Shu, J., Chiang, K., Zhao, D. & Cui, J., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 295-300 6 p. 7359697. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

MicroRNAs

RNA

Viruses

Genes

Experiments

2014

10 Citations (Scopus)

A molecular communication system model based on biological circuits

Pierobon, M., Jan 1 2014, Proceedings of the 1st ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2014. Association for Computing Machinery, 2619958. (Proceedings of the 1st ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2014).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Communication systems

Networks (circuits)

Communication

Bearings (structural)

Molecules

2013

2 Citations (Scopus)

Molecular communication model of nanoparticle-body interactions in Particulate Drug Delivery Systems

Chahibi, Y., Pierobon, M. & Song, S. O., Jan 1 2013, Conference Record of the 47th Asilomar Conference on Signals, Systems and Computers. IEEE Computer Society, p. 1051-1055 5 p. 6810452. (Conference Record - Asilomar Conference on Signals, Systems and Computers).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Nanoparticles

Pharmacokinetics

Communication

Advection

Communication systems

2012

26 Citations (Scopus)

Intersymbol and co-channel interference in diffusion-based molecular communication

Pierobon, M. & Akyildiz, I. F., Dec 1 2012, 2012 IEEE International Conference on Communications, ICC 2012. p. 6126-6131 6 p. 6364970. (IEEE International Conference on Communications).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Communication

Modulation

Intersymbol interference

Molecules

Fluidics

2011

5 Citations (Scopus)

Autohydrolytic production of feruloylated arabinoxylan hydrolysates from cereal processing coproducts for food applications

Rose, D. J., Jan 1 2011, Advances in Cereal Science: Implications to Food Processing and Health Promotion. American Chemical Society, p. 111-130 20 p. (ACS Symposium Series; vol. 1089).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Processing

Health

Antioxidants

Fermentation

Bacteria

Differential analysis of lipids in xylose fermenting S. cerevisiae 424A (LNH-ST) and its ethanol resistant variant S. cerevisiae 424A (LNH-ST)-ER

Kim, J. H., Adamec, J., Mosier, N. S., Ho, N. W. Y. & Sedlak, M., Dec 1 2011, 11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings. (11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Xylose

Lipids

Ethanol

Fatty acids

Nonesterified Fatty Acids

Differential analysis of lipids in xylose fermenting S. cerevisiae 424A (LNH-ST) and its ethanol resistant variant S. cerevisiae 424A (LNH-ST)-ER

Kim, J. H., Adamec, J., Mosier, N. S., Ho, N. W. Y. & Sedlak, M., Jan 1 2011, Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting. AIChE, Vol. 2. p. 776-777 2 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Xylose

Lipids

Ethanol

Effect of furfural on xylose fermentation using saccharomyces cerevisiae 424A (LNH-ST)

Wu, C. L., Mosier, N. S., Kim, J. H., Adamec, J., Ho, N. W. Y. & Sedlak, M., Jan 1 2011, Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting. AIChE, Vol. 2. 1 p.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Furfural

Xylose

Yeast

Fermentation

19 Citations (Scopus)

Exploring the physical channel of diffusion-based molecular communication by simulation

Llatser, I., Pascual, I., Garralda, N., Cabellos-Aparicio, A., Pierobon, M., Alarcón, E. & Solé-Pareta, J., Dec 1 2011, 2011 IEEE Global Telecommunications Conference, GLOBECOM 2011. 6134028. (GLOBECOM - IEEE Global Telecommunications Conference).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Communication

Molecules

Transmitters

Modulation

3 Citations (Scopus)

Grain sorghum lipids: Extraction, characterization, and health potential

Lee, B. H., Weller, C. L., Cuppett, S. L., Carr, T. P., Walter, J., Martínez, I. & Schlegel, V. L., Jan 1 2011, Advances in Cereal Science: Implications to Food Processing and Health Promotion. American Chemical Society, p. 149-170 22 p. (ACS Symposium Series; vol. 1089).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Lipids

Health

policosanol

Unsaturated fatty acids

Phytosterols

39 Citations (Scopus)

Information capacity of diffusion-based molecular communication in nanonetworks

Pierobon, M. & Akyildiz, I. F., Aug 2 2011, 2011 Proceedings IEEE INFOCOM. p. 506-510 5 p. 5935214. (Proceedings - IEEE INFOCOM).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Channel capacity

Statistical mechanics

Molecules

Communication

Communication systems

38 Citations (Scopus)

Simulation-based evaluation of the diffusion-based physical channel in molecular nanonetworks

Garralda, N., Llatser, I., Cabellos-Aparicio, A. & Pierobon, M., Jul 26 2011, 2011 IEEE Conference on Computer Communications Workshops, INFOCOM WKSHPS 2011. p. 443-448 6 p. 5928854. (2011 IEEE Conference on Computer Communications Workshops, INFOCOM WKSHPS 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

simulation

communication

Communication

evaluation

scenario

2010

Computational simulation of the deformation of neuronal cells

Cao, G., Zhou, Y., Lee, J. S., Lim, J. Y., Ganpule, S. & Chandra, N., Dec 1 2010, ASME 2010 International Mechanical Engineering Congress and Exposition, IMECE 2010. p. 179-180 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Neurons

Finite element method

Geometry

Confocal microscopy

Computer simulation

Mechanical model of neuronal function loss

Cao, G., Zhou, Y., Lee, J. S., Lim, J. Y. & Chandra, N., Dec 1 2010, ASME 2010 International Mechanical Engineering Congress and Exposition, IMECE 2010. p. 185-186 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

21 Citations (Scopus)

Propagation models for nanocommunication networks

Akyildiz, I. F., Jornet, J. M. & Pierobon, M., Aug 12 2010, EuCAP 2010 - The 4th European Conference on Antennas and Propagation. 5505714. (EuCAP 2010 - The 4th European Conference on Antennas and Propagation).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Communication

Nanotechnology

Nanostructured materials

Electromagnetic waves

Molecules

2009

2 Citations (Scopus)

Use of average mutual information for studying changes in HIV populations

Sayood, K., Hoffman, F. & Wood, C., Jan 1 2009, Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society, p. 3861-3864 4 p. 5332579. (Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

HIV

Bioinformatics

Viruses

Population

Amino acids

2008

3 Citations (Scopus)

Characterization of DNA sequences that confer complement resistance in Leishmania chagasi

Dahlin-Laborde, R. R., Scolaro, E. J., Romine, N. M., Ramer-Tait, A., Lei, S. M. & Beetham, J. K., Jan 1 2008, Animal Biodiversity and Emerging Diseases Prediction and Prevention. Blackwell Publishing Inc., p. 347-351 5 p. (Annals of the New York Academy of Sciences; vol. 1149).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Leishmania infantum

Cosmids

DNA sequences

Serial Passage

Psychodidae

Development of fluorescent contrast agents for optical imaging of mouse disease models

Kovar, J., Simpson, M. A., Schutz-Geschwender, A., Xu, X., Volcheck, W. M., Sevickmuraca, E. & Olive, D. M., Apr 21 2008, Molecular Probes for Biomedical Applications II. 686707. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 6867).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Imaging techniques

Glucose

Animals

Molecular imaging

Pharmacokinetics

2007

AffyMiner - A tool for significant gene mining in affymetrix GeneChip microarray data

Lu, G., Nguyen, T., Xia, Y., Wang, Z. & Fromm, M., Dec 1 2007, Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07. 4076628. (Proceedings of the Annual Hawaii International Conference on System Sciences).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Microarrays

Genes

Ontology

Molecular biology

Interfaces (computer)

Discussion

Black, P. N., Bernlohr, D. A., Shi, Y., Attie, A. D., Hotamisligil, G. S., Spiegelman, B. M., Tabas, I., O'Rahilly, S., Sabin, M., Saito, M., Glass, C. K. & Daum, G., Dec 1 2007, Fatty Acids and Lipotoxicity in Obesity and Diabetes. p. 121-126 6 p. (Novartis Foundation Symposium; vol. 286).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Discussion

Spiegelman, B. M., Muoio, D. M., Black, P. N., Hotamisligil, G. S., Zhang, C. Y., Kadowaki, T., Bernlohr, D. A., Shi, Y. & Attie, A. D., Dec 1 2007, Fatty Acids and Lipotoxicity in Obesity and Diabetes. p. 38-46 9 p. (Novartis Foundation Symposium; vol. 286).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Acetyl Coenzyme A

Methane

Nickel

Acetic Acid

Carbon Monoxide

25 Citations (Scopus)

Vectorial acylation: Linking fatty acid transport and activation to metabolic trafficking

Black, P. N. & DiRusso, C. C., Dec 1 2007, Fatty Acids and Lipotoxicity in Obesity and Diabetes. p. 127-138 12 p. (Novartis Foundation Symposium; vol. 286).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Fatty Acid Transport Proteins

Acylation

Fatty Acids

Protein Isoforms

Cell Membrane