133. "Metagenomic Analyses of an Uncultured Viral Community from Human Feces", Mya Breitbart, Ian Hewson, Ben Felts, Joseph M. Mahaffy, James Nulton, Peter Salamon, and Forest Rohwer, Journal of Bacteriology,185, p. 62206223, 2003.
134. "Correlation structure of landscapes of NP-complete optimization problems at finite temperatures", Wolfgang Gehring, Peter Salamon, Roger E. Whitney and Paolo Sibani, Open Systems and Information Dynamics, 11: 177-184 (2004) (pdf).
135. "Optimal Allocation of Heat Exchanger Inventory in a Serial Type Diabatic Distillation Column", Edward Steven Jimenez, Peter Salamon, Ricardo Rivero, Consuelo Rendon, and Karl Heinz Hoffmann, Proceedings of ECOS 2004, editors R. Rivero, L. Monroy, R. Pulido, and G. Tsatsaronis, pp. 179-187 (IMP, Mexico, 2004) (pdf).
136. "Best possible probability distribution over extremal optimization ranks", F. Heilmann, K. H. Hoffmann and P. Salamon, Europhysics Letters, 66 pp. 305–310 (2004)(pdf)
137. "Optimization of a Diabatic Distillation Column with Sequential Heat Exchangers," E.S. Jimenez, P. Salamon, R. Rivero, C. Rendon, K.H. Hoffmann, M. Schaller, and B. Andresen, Ind. Eng. Chem. Res. 43, 7566-7571 (2004) (pdf).
138. "Fitness Threshold Accepting over Extremal Optimization Ranks," K.H. Hoffmann, F. Heilmann, and P. Salamon, Physical Review E, 70, 046704-1 -- 046704-6 (2004) (pdf).
139. "Modeling tubular shapes of mitochondrial membranes" A. Ponnuswamy, J. Nulton, J. Mahaffy, P. Salamon, T. Frey and A. R. C. Baljon, Physical Biology, 2 , 73-79 (2005). (pdf).
140. "Transport of O2 from arterioles," S. Bertuglia, A. Limon, B. Andresen, K.H. Hoffmann, C. Essex, and P. Salamon, Journal of Non-Equilibrium Thermodynamics, 30, pp.151-162 (2005) (pdf).
141. "PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information," F. Angly, B. Rodriguez-Brito, D. Bangor, P. McNairnie, M. Breitbart, P. Salamon, B. Felts, J. Nulton, J. Mahaffy, and F. Rohwer, BMC Bioinformatics, 6, 41 (2005). (pdf)
142. "The Structure of Marine Phage Populations" Karl Heinz Hoffmann, Beltran Rodriguez-Brito, Mya Breitbart, David Bangor, Florent Angly, Ben Felts, James Nulton, Forest Rohwer, and Peter Salamon, Proceedings of ECOS 2005, editors Signe Kjelstrup and Johan Einar Hustad (pdf).
143. "Cycling Co-Evolution Resulting from Genetic Adaptation in Two-Person Zero-Sum Games", David Salamon and Peter Salamon, Open Systems and Information Dynamics, 12, 265-271 (2005). (pdf).
144. "A Structural Diffusion Approach to Labeling Rows and Columns in an Irregular Array", P. Salamon, B. Felts, C. Hand, A. Limon, J. Rose and J. Torre-Bueno, Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, editors F. Valafar, H. Valafar, and H.R. Arabnia, CSREA Press, p. 269-273 (2005). (pdf).
145. "Labeling Rows and Columns in an Irregular Array", P. Salamon, B. Felts, C. Hand, A. Limon, J. Rose and J. Torre-Bueno, Medical Image Analysis, 10, 150-161 (2006) (pdf).
146. "Oxygen Transport from the Outer Boundary of a Pulsating Wall of an Arteriole to the Surrounding Tissue," A. Limon, S. Bertuglia, A. Nadim, and P. Salamon, Mathematics and Computers in Simulation 73, 175-182 (2006) (pdf).
147. "Thermodynamics for Systems Biology", Peter Salamon, Anna Salamon, and Andrzej K. Konopka, in Systems Biology, ed. A.K. Konopka, (CRC, New York, 2006). (pdf)
148. "The mathematical structure of thermodynamics for systems biologists", Peter Salamon, Andrzej K. Konopka, James Nulton, and Bjarne Andresen, in Systems Biology, ed. A.K. Konopka, (CRC, New York, 2006). (pdf)
149. "The Marine Viromes of Four Oceanic Regions," F. Angly, B. Felts, M. Breitbart, P. Salamon, R. Edwards, C. Carlson, A. Chan, M. Haynes, S. Kelley, H. Liu, J. Mahaffy, J. Mueller, J. Nulton, R. Olson, R. Parsons, S. Rayhawk, C. Suttle, F. Rohwer, PLoS BIOLOGY, 4, e368 (2006) (pdf).
150. "Membrane Remodeling and Diffusion of Cytochrome C from a Geometrically Idealized Mitochondrial Crista," J.C. Manor, T. Frey, A. Baljon, J. Mahaffy J. Nulton, and P. Salamon in Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology, H.R. Arabnia & H. Valafar editors, (CSREA Press, USA 2006).
151. "Power law rank-abundance relationships in marine phage populations," Karl Heinz Hoffmann, Beltran Rodriguez-Brito, Mya Breitbart, David Bangor, Florent Angly, Ben Felts, James Nulton, Forest Rohwer, and Peter Salamon, FEMS Microbiology Letters, 273, 224-228 (2007). (pdf)
152. "Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi, and viruses in soil," N. Fierer, M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R.A. Edwards, B. Felts, S. Rayhawk, R. Knight, F. Rohwer, R.B. Jackson, Applied and Environmental Microbiology 73, 7059-7066 (2007). (pdf)
153. "Direct measurements of heat output by marine microbial and phage communities," E. Djamali, P. Turner, J. Nulton, F. Rohwer, and P. Salamon CSRCR2008-18. (pdf)
154. "The Poverty of Growth with Interdependent Utility Functions," Komlos, John and Salamon, Peter, Journal of Socio-Economics, 37, 2242-2247 (2008) (pdf).
155. “An Interlacing Theorem for Markov Chains,” Robert Grone, Karl Heinz Hoffmann and Peter Salamon, Journal of Physics A: Mathematical and Theoretical, 41, 212002 (2008) (iop).
156. “Viral Diversity and Dynamics in an Infant’s Gut,” M. Breitbart, M. Haynes, S. Kelley, F. Angly, R. A. Edwards, B. Felts, J.M. Mahaffy, J. Mueller, J. Nulton, S. Rayhawk, B. Rodriguez-Brito, P. Salamon, F. Rohwer, Research in Microbiology, 159, 367-373 (2008). (pdf).
157. "Interactions between branched DNAs and peptide inhibitors of DNA repair", Kevin V. Kepple, Namita Patel, Peter Salamon and Anca M. Segall, doi:10.1093/nar/gkn512 (2008); Nucleic Acids Res. (html/pdf).
158. "Apparatus and method for labeling rows and columns in an irregular array", Jose De La Torre-Bueno and Peter Salamon, U.S. Patent number 7,457,481 (2008).
159. "Maximum Work in Minimum Time from a Conservative Quantum System", P.Salamon, K.H. Hoffmann, Y. Rezek, and R. Kosloff, Phys. Chem. Chem. Phys., 11, 1027–1032 (2009) (pdf).
160. "The Quantum Refrigerator: The quest for absolute zero", Yair Rezek, Peter Salamon, Karl Heinz Hoffmann, and Ronnie Kosloff, Europhysics Letters, 85, 30008 (2009) (pdf).
161. “Bounding the Lumping Error in Markov Chain Dynamics,” Karl Heinz Hoffmann and Peter Salamon, Applied Mathematics Letters, 22, 1471-1475 (2009). (pdf)
162. "Mitochondrial stereology from the statistics of sections", D.C. Flynn, J.D. Nulton, P. Salamon, T.G. Frey, A. Rabinovitch, and A.R.C. Baljon, Image Analysis and Stereology, 28, 11-22 (2009). (pdf).
163. "Deviations from ultrametricity in phage protein distances", Chad Wagner, Anna Salamon, Robert A. Edwards, Forest Rohwer and Peter Salamon, Open Systems and Information Dynamics, 16, 75-84 (2009). (pdf)
164. "Review of Entropy and the Time Evolution of Macroscopic Systems, by W. Grandy", P. Salamon, Physics Today, November 2009. (pdf)
165. "Viral and microbial community dynamics in four aquatic environments", B. Rodriguez-Brito, L. Li, L. Wegley, M. Furlan, F. Angly, M. Breitbart, J. Buchanan, C. Desnues, E. Dinsdale, R.A. Edwards, B Felts, M. Haynes, H. Liu, D. Lipson, J. Mahaffy, A. B. Martin-Cuadrado, A. Mira, J. Nulton, L. Pasic´, S. Rayhawk, J. Rodriguez-Mueller, F. Rodriguez-Valera, P. Salamon, S. Srinagesh, T.F. Thingstad, T. Tran, R.V. Thurber, D Willner, M. Youle and F.L. Rohwer, ISME Journal, 4, 739-751 (2010). (pdf)
166. "Economic implications of software minds", Steven Kaas, Steve Rayhawk, Anna Salamon, Peter Salamon, pages 431-438 in Proceedings of ECAP 10, VIII European Conference of Computing and Philosophy, Klaus Mainzer editor, ISBN 978-3-86853-546-4, Verlag Dr. Hut, Munchen 2010. (pdf)
167. "Tensile Forces and Shape Entropy Explain Observed Crista Structure in Mitochondria", M. Ghochani, J. D. Nulton, P. Salamon, T. G. Frey, A. Rabinovitch, and A. R. C. Baljon, Biophysical Journal, 99, 3244–3254 (2010). (pdf)
168."Optimal Control of the Parametric Oscillator", B. Andresen, K. H. Hoffmann, J. Nulton, A. Tsirlin, P. Salamon, European Journal of Physics 32, 827-843 (2011). (pdf)
169. "Accuracy of coarse grained Markovian dynamics", K. H. Hoffmann and P. Salamon, Physica A, 390, 3086-3094 (2011). (pdf)
170. "Potent antimicrobial small molecules screened as inhibitors of tyrosine recombinases and Holliday junction-resolving enzymes", M.C. Rideout, J.L. Boldt, G. Vahi-Ferguson, P. Salamon, A. Nefzi, J.M. Ostresh, M. Giulianotti, C. Pinilla, A.M. Segall, Molecular Diversity, DOI: 10.1007/s11030-011-9333-2 (2011). (pdf)
171. "Change of State Variables in the Problems of Parametric Control of Oscillators", A.M. Tsirlin, P. Salamon, and K.H. Hoffmann, Automation and Remote Control, 72, 1627-1638 (2011). (pdf)
172. "Time-optimal controls for frictionless cooling in harmonic traps", K. H. Hoffmann, P. Salamon, Y. Rezek and R. Kosloff, Europhysics Letters 96, 60015 (2011). (pdf)
173. "Optimal control in a quantum cooling problem", P. Salamon, K. H. Hoffmann, and A. Tsirlin, Applied Mathematics Letters, doi:10.1016/j.aml.2011.11.020 (2011). (pdf)
174. "Controllability on relaxation-free subspaces: On the relationship between adiabatic population transfer and optimal control", H. Yuan, C.P. Koch, P. Salamon and D.J. Tannor, Physical Review A 85, 033417 (2012). (pdf)
175. "Heat output by marine microbial and viral communities", E. Djamali, J. Nulton, P. Turner, F. Rohwer and P. Salamon, J. Non-Equilibrium Thermodynamics, DOI: 101515/jnetdy-2011-0235 (2012). (pdf)
176. "Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins," Victor Seguritan, Nelson Alves Jr., Michael Arnoult, Amy Raymond, Don Lorimer, Alex B. Burgin Jr., Peter Salamon, Anca M. Segall. PLoS Comput Biol 8(8): e1002657. doi:10.1371/journal.pcbi.1002657 (2012). (open access)
177. "Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score," T. McDole, J. Nulton, K.L. Barott, B. Felts, C. Hand, M. Hatay, H. Lee, M.O. Nadon, B. Nosrat, P. Salamon, B. Bailey, S.A. Sandin, B. Vargas-Angel, M. Youle, B.J. Zgliczynski, R.E. Brainard, F. Rohwer, PLoS ONE 7(9): e43233. doi:10.1371/journal.pone.0043233 (2012). (open access)
178. "Time optimal Processes for Interacting Spin Systems," F. Boldt, K.H. Hoffmann, P. Salamon, R. Kosloff, to appear, Europhysics Letters, 99 (4) 40002 (2012). (pdf)
179. "Evaluating Chronic Cystic Fibrosis Severity using Artificial Neural Networks," Jackson Redfield, Duane Palmer, Douglas J. Conrad, and Peter Salamon. Proceedings of ICIA '12, International Conference on Artificial Intelligence, Las Vegas 2012. (pdf)
180. "Evaluating Spirometric Trends in Cystic Fibrosis Patients," Sara Zarei, Mohamed Abouali, Ali Mirtar, Jackson Redfield, Duane Palmer, Douglas J. Conrad, and Peter Salamon. Proceedings of BIOCOMP’12, International Conference on Bioinformatics and Computational Biology, Las Vegas 2012. (pdf)
181. "Reference-independent comparative metagenomics using cross-assembly: crAss," Bas E. Dutilh; Robert Schmieder; Jim Nulton; Ben Felts; Peter Salamon; Robert A. Edwards; John L. Mokili, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts613 (pdf)
182. “Mucus Distribution Model in a Lung with Cystic Fibrosis,” Sara Zarei, Ali Mirtar, Forest Rohwer, Douglas J. Conrad, Rebecca J. Theilmann, and Peter Salamon, Computational and Mathematical Methods in Medicine,vol. 2012, Article ID 970809, 8 pages, 2012. doi:10.1155/2012/970809 (pdf)
183. "Cystic Fibrosis Therapy: A Community Ecology Perspective," Douglas Conrad, Matthew Haynes, Peter Salamon, Paul B. Rainey, Merry Youle, and Forest Rohwer. Am. J. Respir. Cell Mol. Biol. October 2012 doi: 10.1165/rcmb.2012-0059PS. (pdf)
184. "Applying Shannon's information theory to bacterial and phage genomes and metagenomes," Sajia Akhter, Barbara A. Bailey, Peter Salamon, Ramy K. Aziz and Robert A. Edwards. Scientific Reports, 3, Article number: 1033 doi:10.1038/srep01033 (2013). (pdf)
185. "Modeling the airflow in a lung with cystic fibrosis," Sara Zarei, Ali Mirtar, Bjarne Andresen and Peter Salamon. J. of Non-Equilibrium Thermodynamics, DOI 10.1515/jnetdy-2012-0019 (2013). (pdf)
186. "Casimir companion: An invariant of motion for Hamiltonian systems," Frank Boldt, James D Nulton, Bjarne Andresen, Peter Salamon, and Karl Heinz Hoffmann. Physical Review A, 87, 22116, (2013). (pdf)
187. "Optimal control of a collection of harmonic oscillators," Karl Heinz Hoffmann, Bjarne Andresen, and Peter Salamon. Physical Review E, 87, 062106, (2013). (pdf)
188. "Bacteriophage adhering to mucus provide a non-host-derived immunity," Jeremy J. Barr, Rita Auro, Mike Furlan, Katrine L. Whiteson, Marcella L. Erb, Joe Pogliano, Aleksandr Stotland, Roland Wolkowicz, Andrew S. Cutting, Kelly S. Doran, Peter Salamon, Merry Youle, and Forest Rohwer. Proceedings of the National Academy of Sciences, 110, 10771-10776 (2013). (pdf)
189. "Observation time scale, free energy landscapes, and molecular symmetry" David Wales and Peter Salamon. Proceedings of the National Academy of Sciences, 111, 617-622 (2014). (pdf)
190. "Free Energies of Staging a Scenario and Perpetual Motion Machines of the Third Kind" P. Salamon, B. Andresen, K.H. Hoffmann, J.D. Nulton, A.M. Segall, F.L. Rohwer. Advances in Chemical Physics, 157. (pdf)
191. "The Upper Respiratory Tract as a Microbial Source for Pulmonary Infections in Cystic Fibrosis. Parallels from Island Biogeography" Katrine L Whiteson, Barbara Bailey, Megan Bergkessel, Douglas Conrad, Laurence Delhaes, Ben Felts, J Kirk Harris, Ryan Hunter, Yan Wei Lim, Heather Maughan, Robert Quinn, Peter Salamon, James Sullivan, Brandie D Wagner, Paul B Rainey. American journal of respiratory and critical care medicine, 89, 1309-1315 (2014).