[{"status":"public","type":"conference","conference":{"name":"ICSE: Software Engineering"},"_id":"4581","title":"Generating tests from counterexamples","author":[{"last_name":"Beyer","full_name":"Beyer, Dirk","first_name":"Dirk"},{"first_name":"Adam","last_name":"Chlipala","full_name":"Chlipala, Adam J"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger"},{"full_name":"Jhala, Ranjit","last_name":"Jhala","first_name":"Ranjit"},{"full_name":"Majumdar, Ritankar S","last_name":"Majumdar","first_name":"Ritankar"}],"publist_id":"128","extern":1,"citation":{"ieee":"D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “Generating tests from counterexamples,” presented at the ICSE: Software Engineering, 2004, pp. 326–335.","short":"D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 326–335.","ama":"Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. Generating tests from counterexamples. In: IEEE; 2004:326-335. doi:10.1109/ICSE.2004.1317455","apa":"Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Generating tests from counterexamples (pp. 326–335). Presented at the ICSE: Software Engineering, IEEE. https://doi.org/10.1109/ICSE.2004.1317455","mla":"Beyer, Dirk, et al. Generating Tests from Counterexamples. IEEE, 2004, pp. 326–35, doi:10.1109/ICSE.2004.1317455.","ista":"Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. Generating tests from counterexamples. ICSE: Software Engineering, 326–335.","chicago":"Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Generating Tests from Counterexamples,” 326–35. IEEE, 2004. https://doi.org/10.1109/ICSE.2004.1317455."},"date_updated":"2021-01-12T07:59:52Z","month":"07","quality_controlled":0,"publisher":"IEEE","abstract":[{"text":"We have extended the software model checker BLAST to automatically generate test suites that guarantee full coverage with respect to a given predicate. More precisely, given a C program and a target predicate p, BLAST determines the set L of program locations which program execution can reach with p true, and automatically generates a set of test vectors that exhibit the truth of p at all locations in L. We have used BLAST to generate test suites and to detect dead code in C programs with up to 30 K lines of code. The analysis and test vector generation is fully automatic (no user intervention) and exact (no false positives).","lang":"eng"}],"doi":"10.1109/ICSE.2004.1317455","date_published":"2004-07-26T00:00:00Z","date_created":"2018-12-11T12:09:35Z","page":"326 - 335","day":"26","year":"2004","publication_status":"published"},{"acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the ONR grant N00014-02-1-0671, and the NSF grants CCR-0132780, CCR-9988172, CCR-0225610, and CCR-0234690.","abstract":[{"lang":"eng","text":"Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a generalization of the branching-time logic Ctl which achieves robustness with respect to model perturbations by giving a quantitative interpretation to predicates and logical operators, and by discounting the importance of events according to how late they occur. In every state, the value of a formula is a real number in the interval [0,1], where 1 corresponds to truth and 0 to falsehood. The boolean operators and and or are replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over all paths from a given state, and the temporal operators and □ specify sup and inf over a given path; a new operator averages all values along a path. Furthermore, all path operators are discounted by a parameter that can be chosen to give more weight to states that are closer to the beginning of the path. We interpret the resulting logic Dctl over transition systems, Markov chains, and Markov decision processes. We present two semantics for Dctl: a path semantics, inspired by the standard interpretation of state and path formulas in CTL, and a fixpoint semantics, inspired by the μ-calculus evaluation of CTL formulas. We show that, while these semantics coincide for CTL, they differ for Dctl, and we provide model-checking algorithms for both semantics."}],"intvolume":" 2988","month":"03","alternative_title":["LNCS"],"quality_controlled":0,"publisher":"Springer","day":"18","year":"2004","publication_status":"published","date_created":"2018-12-11T12:09:50Z","volume":2988,"date_published":"2004-03-18T00:00:00Z","doi":"10.1007/978-3-540-24730-2_6","page":"77 - 92","_id":"4629","status":"public","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"type":"conference","extern":1,"date_updated":"2021-01-12T08:00:38Z","citation":{"ista":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2004. Model checking discounted temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 2988, 77–92.","chicago":"De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties,” 2988:77–92. Springer, 2004. https://doi.org/10.1007/978-3-540-24730-2_6.","apa":"De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2004). Model checking discounted temporal properties (Vol. 2988, pp. 77–92). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/978-3-540-24730-2_6","ama":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking discounted temporal properties. In: Vol 2988. Springer; 2004:77-92. doi:10.1007/978-3-540-24730-2_6","short":"L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, Springer, 2004, pp. 77–92.","ieee":"L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2004, vol. 2988, pp. 77–92.","mla":"De Alfaro, Luca, et al. Model Checking Discounted Temporal Properties. Vol. 2988, Springer, 2004, pp. 77–92, doi:10.1007/978-3-540-24730-2_6."},"title":"Model checking discounted temporal properties","publist_id":"79","author":[{"full_name":"de Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"last_name":"Faella","full_name":"Faella, Marco","first_name":"Marco"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar S","last_name":"Majumdar"},{"full_name":"Stoelinga, Mariëlle","last_name":"Stoelinga","first_name":"Mariëlle"}]},{"month":"06","intvolume":" 14","quality_controlled":"1","publisher":"Elsevier","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid."}],"date_published":"2004-06-22T00:00:00Z","issue":"12","doi":"10.1016/j.cub.2004.06.027","volume":14,"date_created":"2019-03-21T09:42:01Z","page":"1105-1111","day":"22","publication":"Current Biology","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0960-9822"]},"publication_status":"published","year":"2004","status":"public","type":"journal_article","_id":"6155","title":"Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior","author":[{"last_name":"Cheung","full_name":"Cheung, Benny H.H","first_name":"Benny H.H"},{"full_name":"Arellano-Carbajal, Fausto","last_name":"Arellano-Carbajal","first_name":"Fausto"},{"first_name":"Irene","last_name":"Rybicki","full_name":"Rybicki, Irene"},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"external_id":{"pmid":["15203005"]},"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology, vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:10.1016/j.cub.2004.06.027.","apa":"Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., & de Bono, M. (2004). Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.027","ama":"Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 2004;14(12):1105-1111. doi:10.1016/j.cub.2004.06.027","ieee":"B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior,” Current Biology, vol. 14, no. 12. Elsevier, pp. 1105–1111, 2004.","short":"B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology 14 (2004) 1105–1111.","chicago":"Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.027.","ista":"Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 14(12), 1105–1111."},"date_updated":"2021-01-12T08:06:25Z"},{"title":"Fuel cell modeling and simulations","author":[{"last_name":"Mantzaras","full_name":"Mantzaras, John","first_name":"John"},{"last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Felix N.","last_name":"Büchi","full_name":"Büchi, Felix N."},{"first_name":"Markus","last_name":"Roos","full_name":"Roos, Markus"},{"full_name":"Brandstätter, Wilhelm","last_name":"Brandstätter","first_name":"Wilhelm"},{"first_name":"Michel","last_name":"Prestat","full_name":"Prestat, Michel"},{"full_name":"Gauckler, Ludwig J.","last_name":"Gauckler","first_name":"Ludwig J."},{"full_name":"Andreaus, Bernhard","last_name":"Andreaus","first_name":"Bernhard"},{"first_name":"Faegheh","full_name":"Hajbolouri, Faegheh","last_name":"Hajbolouri"},{"last_name":"Senn","full_name":"Senn, Stephan M.","first_name":"Stephan M."},{"last_name":"Poulikakos","full_name":"Poulikakos, Dimos","first_name":"Dimos"},{"first_name":"Andreas K.","last_name":"Chaniotis","full_name":"Chaniotis, Andreas K."},{"first_name":"Diego","last_name":"Larrain","full_name":"Larrain, Diego"},{"first_name":"Nordahl","full_name":"Autissier, Nordahl","last_name":"Autissier"},{"first_name":"François","full_name":"Maréchal, François","last_name":"Maréchal"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos, Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International Journal for Chemistry. Swiss Chemical Society, 2004. https://doi.org/10.2533/000942904777677029.","ista":"Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M, Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 58(12), 857–868.","mla":"Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International Journal for Chemistry, vol. 58, no. 12, Swiss Chemical Society, 2004, pp. 857–68, doi:10.2533/000942904777677029.","short":"J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M. Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos, A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal for Chemistry 58 (2004) 857–868.","ieee":"J. Mantzaras et al., “Fuel cell modeling and simulations,” CHIMIA International Journal for Chemistry, vol. 58, no. 12. Swiss Chemical Society, pp. 857–868, 2004.","apa":"Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W., Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. Swiss Chemical Society. https://doi.org/10.2533/000942904777677029","ama":"Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 2004;58(12):857-868. doi:10.2533/000942904777677029"},"date_updated":"2021-01-12T08:13:09Z","status":"public","article_type":"original","type":"journal_article","_id":"7334","volume":58,"date_published":"2004-12-01T00:00:00Z","doi":"10.2533/000942904777677029","issue":"12","date_created":"2020-01-15T12:24:23Z","page":"857-868","day":"01","language":[{"iso":"eng"}],"publication":"CHIMIA International Journal for Chemistry","publication_identifier":{"issn":["0009-4293"]},"publication_status":"published","year":"2004","month":"12","intvolume":" 58","quality_controlled":"1","publisher":"Swiss Chemical Society","oa_version":"None","abstract":[{"text":"Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. ","lang":"eng"}]},{"title":"Modular stack-internal air humidification concept-verification in a 1 kW stack","article_processing_charge":"No","author":[{"full_name":"Santis, M.","last_name":"Santis","first_name":"M."},{"full_name":"Schmid, D.","last_name":"Schmid","first_name":"D."},{"last_name":"Ruge","full_name":"Ruge, M.","first_name":"M."},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"first_name":"F.N.","full_name":"Büchi, F.N.","last_name":"Büchi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"short":"M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4 (2004) 214–218.","ieee":"M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular stack-internal air humidification concept-verification in a 1 kW stack,” Fuel Cells, vol. 4, no. 3. Wiley, pp. 214–218, 2004.","ama":"Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 2004;4(3):214-218. doi:10.1002/fuce.200400028","apa":"Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., & Büchi, F. N. (2004). Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. Wiley. https://doi.org/10.1002/fuce.200400028","mla":"Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” Fuel Cells, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:10.1002/fuce.200400028.","ista":"Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218.","chicago":"Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N. Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” Fuel Cells. Wiley, 2004. https://doi.org/10.1002/fuce.200400028."},"date_updated":"2021-01-12T08:13:08Z","status":"public","article_type":"original","type":"journal_article","_id":"7333","date_created":"2020-01-15T12:24:14Z","date_published":"2004-08-01T00:00:00Z","issue":"3","doi":"10.1002/fuce.200400028","volume":4,"page":"214-218","publication":"Fuel Cells","language":[{"iso":"eng"}],"day":"01","year":"2004","publication_status":"published","publication_identifier":{"issn":["1615-6846","1615-6854"]},"intvolume":" 4","month":"08","publisher":"Wiley","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system."}]},{"publication_status":"published","year":"2004","publication":"Protein Science","day":"01","page":"884 - 892","date_created":"2018-12-11T11:48:55Z","doi":"10.1110/ps.03465504","date_published":"2004-04-01T00:00:00Z","issue":"4","volume":13,"abstract":[{"lang":"eng","text":"We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites."}],"acknowledgement":"We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport.","publisher":"Wiley-Blackwell","quality_controlled":0,"intvolume":" 13","month":"04","citation":{"mla":"Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:10.1110/ps.03465504.","short":"A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.","ieee":"A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” Protein Science, vol. 13, no. 4. Wiley-Blackwell, pp. 884–892, 2004.","ama":"Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 2004;13(4):884-892. doi:10.1110/ps.03465504","apa":"Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. Wiley-Blackwell. https://doi.org/10.1110/ps.03465504","chicago":"Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” Protein Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504.","ista":"Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892."},"date_updated":"2021-01-12T08:20:22Z","extern":1,"author":[{"last_name":"Panchenko","full_name":"Panchenko, Anna R","first_name":"Anna"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"first_name":"Stephen","last_name":"Bryant","full_name":"Bryant, Stephen H"}],"publist_id":"6786","title":"Prediction of functional sites by analysis of sequence and structure conservation","_id":"864","type":"journal_article","status":"public"},{"publist_id":"6780","author":[{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"},{"full_name":"Ogurtsov, Aleksey Yu","last_name":"Ogurtsov","first_name":"Aleksey"},{"last_name":"Kondrashov","full_name":"Kondrashov, Alexey S","first_name":"Alexey"}],"title":"Bioinformatical assay of human gene morbidity","citation":{"chicago":"Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University Press, 2004. https://doi.org/10.1093/nar/gkh330.","ista":"Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.","mla":"Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:10.1093/nar/gkh330.","apa":"Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkh330","ama":"Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330","ieee":"F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737."},"date_updated":"2021-01-12T08:20:37Z","extern":1,"type":"journal_article","status":"public","_id":"870","page":"1731 - 1737","date_created":"2018-12-11T11:48:56Z","volume":32,"doi":"10.1093/nar/gkh330","issue":"5","date_published":"2004-01-01T00:00:00Z","year":"2004","publication_status":"published","publication":"Nucleic Acids Research","day":"01","publisher":"Oxford University Press","quality_controlled":0,"intvolume":" 32","month":"01","abstract":[{"text":"Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates.","lang":"eng"}]},{"abstract":[{"text":"The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis.","lang":"eng"}],"intvolume":" 20","month":"07","quality_controlled":0,"publisher":"Elsevier","publication":"Trends in Genetics","day":"01","publication_status":"published","year":"2004","date_created":"2018-12-11T11:48:58Z","doi":"10.1016/j.tig.2004.05.001","date_published":"2004-07-01T00:00:00Z","volume":20,"issue":"7","page":"287 - 291","_id":"875","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T08:20:54Z","citation":{"ista":"Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291.","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001.","ama":"Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001","apa":"Kondrashov, F., & Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001","short":"F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.","ieee":"F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” Trends in Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.","mla":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001."},"title":"A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications","author":[{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene V"}],"publist_id":"6775"},{"intvolume":" 36","month":"11","quality_controlled":0,"publisher":"Nature Publishing Group","acknowledgement":"We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp, S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were supported by a grant from the US National Institutes of Health to S. Nuzhdin, and A.D.K. is a Howard Hughes","abstract":[{"text":"The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges.","lang":"eng"}],"date_created":"2018-12-11T11:49:02Z","volume":36,"date_published":"2004-11-01T00:00:00Z","issue":"11","doi":"10.1038/ng1451","page":"1207 - 1212","publication":"Nature Genetics","day":"01","year":"2004","publication_status":"published","status":"public","type":"journal_article","_id":"889","title":"Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs","publist_id":"6759","author":[{"full_name":"Kern, Andrew D","last_name":"Kern","first_name":"Andrew"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"extern":1,"date_updated":"2021-01-12T08:21:17Z","citation":{"mla":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.","short":"A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.","ieee":"A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004.","ama":"Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212. doi:10.1038/ng1451","apa":"Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng1451","chicago":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing Group, 2004. https://doi.org/10.1038/ng1451.","ista":"Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212."}},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"13","publication":"Current Biology","year":"2004","doi":"10.1016/j.cub.2004.06.055","date_published":"2004-07-13T00:00:00Z","date_created":"2021-06-07T10:33:00Z","page":"1214-1220","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.055.","ista":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220.","mla":"Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055.","apa":"Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., & Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055","ama":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055","ieee":"D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.","short":"D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220."},"title":"Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats","author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Xiaofeng","last_name":"Cao","full_name":"Cao, Xiaofeng"},{"full_name":"Johansen, Lisa K.","last_name":"Johansen","first_name":"Lisa K."},{"first_name":"Zhixin","last_name":"Xie","full_name":"Xie, Zhixin"},{"first_name":"James C.","full_name":"Carrington, James C.","last_name":"Carrington"},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."}],"external_id":{"pmid":["15242620 "]},"article_processing_charge":"No","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene \"trigger\" and any other homologous DNA sequences--\"targets\". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production."}],"month":"07","intvolume":" 14","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2004.06.055","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"publication_status":"published","volume":14,"issue":"13","_id":"9493","status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-12-14T08:52:00Z","department":[{"_id":"DaZi"}]},{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"year":"2004","day":"24","publication":"PLoS Biology","page":"0642-0652","date_published":"2004-02-24T00:00:00Z","doi":"10.1371/journal.pbio.0020104","date_created":"2021-06-07T14:12:08Z","citation":{"ista":"Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2(5), 0642–0652.","chicago":"Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104.","ama":"Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104","apa":"Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0020104","short":"Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.","ieee":"Z. Xie et al., “Genetic and functional diversification of small RNA pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004.","mla":"Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS Biology, vol. 2, no. 5, Public Library of Science, 2004, pp. 0642–52, doi:10.1371/journal.pbio.0020104."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Xie","full_name":"Xie, Zhixin","first_name":"Zhixin"},{"first_name":"Lisa K.","last_name":"Johansen","full_name":"Johansen, Lisa K."},{"first_name":"Adam M.","full_name":"Gustafson, Adam M.","last_name":"Gustafson"},{"full_name":"Kasschau, Kristin D.","last_name":"Kasschau","first_name":"Kristin D."},{"last_name":"Lellis","full_name":"Lellis, Andrew D. ","first_name":"Andrew D. "},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"first_name":"Steven E.","full_name":"Jacobsen, Steven E.","last_name":"Jacobsen"},{"first_name":"James C.","full_name":"Carrington, James C.","last_name":"Carrington"}],"external_id":{"pmid":["15024409"]},"article_processing_charge":"No","title":"Genetic and functional diversification of small RNA pathways in plants","abstract":[{"text":"Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pbio.0020104"}],"month":"02","intvolume":" 2","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":2,"issue":"5","_id":"9517","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-12-14T08:43:57Z","extern":"1","department":[{"_id":"DaZi"}]},{"intvolume":" 5","month":"11","main_file_link":[{"url":"https://doi.org/10.1186/gb-2004-5-12-249","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it."}],"issue":"12","volume":5,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"status":"public","type":"journal_article","article_type":"review","_id":"9511","department":[{"_id":"DaZi"}],"extern":"1","date_updated":"2021-12-14T08:44:24Z","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_created":"2021-06-07T12:58:06Z","doi":"10.1186/gb-2004-5-12-249","date_published":"2004-11-16T00:00:00Z","publication":"Genome Biology","day":"16","year":"2004","article_number":"249","title":"Silencing of transposons in plant genomes: kick them when they're down","article_processing_charge":"No","external_id":{"pmid":["15575975"]},"author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 2004;5(12). doi:10.1186/gb-2004-5-12-249","apa":"Zilberman, D., & Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. Springer Nature. https://doi.org/10.1186/gb-2004-5-12-249","short":"D. Zilberman, S. Henikoff, Genome Biology 5 (2004).","ieee":"D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” Genome Biology, vol. 5, no. 12. Springer Nature, 2004.","mla":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” Genome Biology, vol. 5, no. 12, 249, Springer Nature, 2004, doi:10.1186/gb-2004-5-12-249.","ista":"Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” Genome Biology. Springer Nature, 2004. https://doi.org/10.1186/gb-2004-5-12-249."}},{"_id":"8517","type":"journal_article","article_type":"original","keyword":["Applied Mathematics","General Mathematics"],"status":"public","date_updated":"2021-01-12T08:19:50Z","citation":{"ista":"Dolgopyat D, Kaloshin V, Koralov L. 2004. A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. 57(9), 1127–1158.","chicago":"Dolgopyat, Dmitry, Vadim Kaloshin, and Leonid Koralov. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” Communications on Pure and Applied Mathematics. Wiley, 2004. https://doi.org/10.1002/cpa.20032.","short":"D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied Mathematics 57 (2004) 1127–1158.","ieee":"D. Dolgopyat, V. Kaloshin, and L. Koralov, “A limit shape theorem for periodic stochastic dispersion,” Communications on Pure and Applied Mathematics, vol. 57, no. 9. Wiley, pp. 1127–1158, 2004.","apa":"Dolgopyat, D., Kaloshin, V., & Koralov, L. (2004). A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.20032","ama":"Dolgopyat D, Kaloshin V, Koralov L. A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. 2004;57(9):1127-1158. doi:10.1002/cpa.20032","mla":"Dolgopyat, Dmitry, et al. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” Communications on Pure and Applied Mathematics, vol. 57, no. 9, Wiley, 2004, pp. 1127–58, doi:10.1002/cpa.20032."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"first_name":"Dmitry","last_name":"Dolgopyat","full_name":"Dolgopyat, Dmitry"},{"last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Koralov","full_name":"Koralov, Leonid","first_name":"Leonid"}],"title":"A limit shape theorem for periodic stochastic dispersion","abstract":[{"lang":"eng","text":"We consider the evolution of a connected set on the plane carried by a space periodic incompressible stochastic flow. While for almost every realization of the stochastic flow at time t most of the particles are at a distance of order equation image away from the origin, there is a measure zero set of points that escape to infinity at the linear rate. We study the set of points visited by the original set by time t and show that such a set, when scaled down by the factor of t, has a limiting nonrandom shape."}],"oa_version":"None","quality_controlled":"1","publisher":"Wiley","intvolume":" 57","month":"09","year":"2004","publication_status":"published","publication_identifier":{"issn":["0010-3640","1097-0312"]},"publication":"Communications on Pure and Applied Mathematics","language":[{"iso":"eng"}],"day":"01","page":"1127-1158","date_created":"2020-09-18T10:49:12Z","date_published":"2004-09-01T00:00:00Z","doi":"10.1002/cpa.20032","issue":"9","volume":57},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Koralov, Leonid, et al. “Sample Path Properties of the Stochastic Flows.” The Annals of Probability, vol. 32, no. 1A, Institute of Mathematical Statistics, 2004, pp. 1–27, doi:10.1214/aop/1078415827.","ieee":"L. Koralov, V. Kaloshin, and D. Dolgopyat, “Sample path properties of the stochastic flows,” The Annals of Probability, vol. 32, no. 1A. Institute of Mathematical Statistics, pp. 1–27, 2004.","short":"L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004) 1–27.","apa":"Koralov, L., Kaloshin, V., & Dolgopyat, D. (2004). Sample path properties of the stochastic flows. The Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/aop/1078415827","ama":"Koralov L, Kaloshin V, Dolgopyat D. Sample path properties of the stochastic flows. The Annals of Probability. 2004;32(1A):1-27. doi:10.1214/aop/1078415827","chicago":"Koralov, Leonid, Vadim Kaloshin, and Dmitry Dolgopyat. “Sample Path Properties of the Stochastic Flows.” The Annals of Probability. Institute of Mathematical Statistics, 2004. https://doi.org/10.1214/aop/1078415827.","ista":"Koralov L, Kaloshin V, Dolgopyat D. 2004. Sample path properties of the stochastic flows. The Annals of Probability. 32(1A), 1–27."},"date_updated":"2021-01-12T08:19:50Z","title":"Sample path properties of the stochastic flows","article_processing_charge":"No","author":[{"full_name":"Koralov, Leonid","last_name":"Koralov","first_name":"Leonid"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"first_name":"Dmitry","full_name":"Dolgopyat, Dmitry","last_name":"Dolgopyat"}],"_id":"8518","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication":"The Annals of Probability","day":"04","publication_status":"published","year":"2004","publication_identifier":{"issn":["0091-1798"]},"date_created":"2020-09-18T10:49:19Z","doi":"10.1214/aop/1078415827","volume":32,"issue":"1A","date_published":"2004-03-04T00:00:00Z","page":"1-27","oa_version":"None","intvolume":" 32","month":"03","quality_controlled":"1","publisher":"Institute of Mathematical Statistics"},{"_id":"898","status":"public","type":"journal_article","extern":1,"date_updated":"2021-01-12T08:21:37Z","citation":{"ama":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 2004;429(6991):558-562. doi:10.1038/nature02601","apa":"Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., & Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02601","short":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.","ieee":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” Nature, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004.","mla":"Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601.","ista":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562.","chicago":"Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02601."},"title":"Positive selection at sites of multiple amino acid replacements since rat-mouse divergence","publist_id":"6746","author":[{"first_name":"Georgii","full_name":"Bazykin, Georgii A","last_name":"Bazykin"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"},{"first_name":"Aleksey","last_name":"Ogurtsov","full_name":"Ogurtsov, Aleksey Yu"},{"full_name":"Sunyaev, Shamil R","last_name":"Sunyaev","first_name":"Shamil"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"}],"acknowledgement":"We thank N. Bierne for a number of suggestions. G.A.B. was supported by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation.","abstract":[{"lang":"eng","text":"New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement."}],"intvolume":" 429","month":"06","quality_controlled":0,"publisher":"Nature Publishing Group","publication":"Nature","day":"03","year":"2004","publication_status":"published","date_created":"2018-12-11T11:49:05Z","doi":"10.1038/nature02601","volume":429,"date_published":"2004-06-03T00:00:00Z","issue":"6991","page":"558 - 562"},{"abstract":[{"text":"We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.","lang":"eng"}],"acknowledgement":"We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada.\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.","publisher":"Cold Spring Harbor Laboratory Press","quality_controlled":0,"month":"05","intvolume":" 14","year":"2004","publication_status":"published","day":"01","publication":"Genome Research","page":"802 - 811","issue":"5","date_published":"2004-05-01T00:00:00Z","volume":14,"doi":"10.1101/gr.2195604","date_created":"2018-12-11T11:49:06Z","_id":"902","type":"journal_article","status":"public","citation":{"short":"C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.","ieee":"C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.","apa":"Castillo Davis, C., Kondrashov, F., Hartl, D., & Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.2195604","ama":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 2004;14(5):802-811. doi:10.1101/gr.2195604","mla":"Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004, pp. 802–11, doi:10.1101/gr.2195604.","ista":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.","chicago":"Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” Genome Research. Cold Spring Harbor Laboratory Press, 2004. https://doi.org/10.1101/gr.2195604."},"date_updated":"2021-01-12T08:21:47Z","extern":1,"author":[{"first_name":"Cristian","full_name":"Castillo-Davis, Cristian I","last_name":"Castillo Davis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov"},{"last_name":"Hartl","full_name":"Hartl, Daniel L","first_name":"Daniel"},{"first_name":"Rob","last_name":"Kulathinal","full_name":"Kulathinal, Rob J"}],"publist_id":"6750","title":"The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint"},{"volume":303,"issue":"5662","publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 303","month":"02","pmid":1,"oa_version":"None","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T09:13:53Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Multidisciplinary"],"status":"public","_id":"9454","page":"1336","date_created":"2021-06-04T11:12:35Z","date_published":"2004-02-27T00:00:00Z","doi":"10.1126/science.1095989","year":"2004","publication":"Science","day":"27","publisher":"American Association for the Advancement of Science","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["14988555"]},"author":[{"first_name":"Simon W.-L.","last_name":"Chan","full_name":"Chan, Simon W.-L."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Xie","full_name":"Xie, Zhixin","first_name":" Zhixin"},{"full_name":"Johansen, Lisa K.","last_name":"Johansen","first_name":" Lisa K."},{"last_name":"Carrington","full_name":"Carrington, James C.","first_name":"James C."},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."}],"title":"RNA silencing genes control de novo DNA methylation","citation":{"ista":"Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336.","chicago":"Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” Science. American Association for the Advancement of Science, 2004. https://doi.org/10.1126/science.1095989.","short":"S.W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.","ieee":"S. W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004.","apa":"Chan, S. W.-L., Zilberman, D., Xie, Zhixin, Johansen, Lisa K., Carrington, J. C., & Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1095989","ama":"Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336. doi:10.1126/science.1095989","mla":"Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.” Science, vol. 303, no. 5662, American Association for the Advancement of Science, 2004, p. 1336, doi:10.1126/science.1095989."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"issue":"2","volume":15,"publication_status":"published","publication_identifier":{"issn":["1042-5179"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 15","abstract":[{"lang":"eng","text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs."}],"oa_version":"None","pmid":1,"department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:58:29Z","extern":"1","type":"journal_article","article_type":"original","keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"status":"public","_id":"12203","page":"153-158","date_created":"2023-01-16T09:24:50Z","doi":"10.1080/10425170410001667348","date_published":"2004-01-01T00:00:00Z","year":"2004","publication":"DNA Sequence","quality_controlled":"1","publisher":"Informa UK Limited","acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","external_id":{"pmid":["15352294"]},"article_processing_charge":"No","author":[{"last_name":"Liao","full_name":"Liao, Zhihua","first_name":"Zhihua"},{"full_name":"Chen, Min","last_name":"Chen","first_name":"Min"},{"first_name":"Yifu","last_name":"Gong","full_name":"Gong, Yifu"},{"first_name":"Liang","full_name":"Guo, Liang","last_name":"Guo"},{"first_name":"Qiumin","last_name":"Tan","full_name":"Tan, Qiumin"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"},{"first_name":"Xiaofen","last_name":"Sun","full_name":"Sun, Xiaofen"},{"last_name":"Tan","full_name":"Tan, Feng","first_name":"Feng"},{"first_name":"Kexuan","full_name":"Tang, Kexuan","last_name":"Tang"}],"title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","citation":{"mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” DNA Sequence, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:10.1080/10425170410001667348.","short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.","ieee":"Z. Liao et al., “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” DNA Sequence, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 2004;15(2):153-158. doi:10.1080/10425170410001667348","apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. Informa UK Limited. https://doi.org/10.1080/10425170410001667348","chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” DNA Sequence. Informa UK Limited, 2004. https://doi.org/10.1080/10425170410001667348.","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":3,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"intvolume":" 3","month":"09","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"Micropatterning of surfaces with several chemicals at different spatial locations usually requires multiple stamping and registration steps. Here, we describe an experimental method based on reaction–diffusion phenomena that allows for simultaneous micropatterning of a substrate with several coloured chemicals. In this method, called wet stamping (WETS), aqueous solutions of two or more inorganic salts are delivered onto a film of dry, ionically doped gelatin from an agarose stamp patterned in bas relief. Once in conformal contact, these salts diffuse into the gelatin, where they react to give deeply coloured precipitates. Separation of colours in the plane of the surface is the consequence of the differences in the diffusion coefficients, the solubility products, and the amounts of different salts delivered from the stamp, and is faithfully reproduced by a theoretical model based on a system of reaction–diffusion partial differential equations. The multicolour micropatterns are useful as non-binary optical elements, and could potentially form the basis of new applications in microseparations and in controlled delivery."}],"extern":"1","date_updated":"2023-08-08T12:42:51Z","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science","General Chemistry"],"status":"public","type":"journal_article","article_type":"original","_id":"13435","date_created":"2023-08-01T10:39:23Z","doi":"10.1038/nmat1231","date_published":"2004-09-19T00:00:00Z","page":"729-735","publication":"Nature Materials","day":"19","year":"2004","quality_controlled":"1","publisher":"Springer Nature","title":"Multicolour micropatterning of thin films of dry gels","external_id":{"pmid":["15378052"]},"article_processing_charge":"No","author":[{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"},{"first_name":"Marcin","full_name":"Fialkowski, Marcin","last_name":"Fialkowski"},{"first_name":"Igor T.","last_name":"Bensemann","full_name":"Bensemann, Igor T."},{"full_name":"Bitner, Agnieszka","last_name":"Bitner","first_name":"Agnieszka"},{"first_name":"C. J.","last_name":"Campbell","full_name":"Campbell, C. J."},{"first_name":"Kyle","last_name":"Bishop","full_name":"Bishop, Kyle"},{"first_name":"Stoyan","full_name":"Smoukov, Stoyan","last_name":"Smoukov"},{"full_name":"Grzybowski, Bartosz A.","last_name":"Grzybowski","first_name":"Bartosz A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Klajn, Rafal, et al. “Multicolour Micropatterning of Thin Films of Dry Gels.” Nature Materials, vol. 3, Springer Nature, 2004, pp. 729–35, doi:10.1038/nmat1231.","apa":"Klajn, R., Fialkowski, M., Bensemann, I. T., Bitner, A., Campbell, C. J., Bishop, K., … Grzybowski, B. A. (2004). Multicolour micropatterning of thin films of dry gels. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat1231","ama":"Klajn R, Fialkowski M, Bensemann IT, et al. Multicolour micropatterning of thin films of dry gels. Nature Materials. 2004;3:729-735. doi:10.1038/nmat1231","ieee":"R. Klajn et al., “Multicolour micropatterning of thin films of dry gels,” Nature Materials, vol. 3. Springer Nature, pp. 729–735, 2004.","short":"R. Klajn, M. Fialkowski, I.T. Bensemann, A. Bitner, C.J. Campbell, K. Bishop, S. Smoukov, B.A. Grzybowski, Nature Materials 3 (2004) 729–735.","chicago":"Klajn, Rafal, Marcin Fialkowski, Igor T. Bensemann, Agnieszka Bitner, C. J. Campbell, Kyle Bishop, Stoyan Smoukov, and Bartosz A. Grzybowski. “Multicolour Micropatterning of Thin Films of Dry Gels.” Nature Materials. Springer Nature, 2004. https://doi.org/10.1038/nmat1231.","ista":"Klajn R, Fialkowski M, Bensemann IT, Bitner A, Campbell CJ, Bishop K, Smoukov S, Grzybowski BA. 2004. Multicolour micropatterning of thin films of dry gels. Nature Materials. 3, 729–735."}},{"date_created":"2023-08-01T10:39:09Z","date_published":"2004-11-14T00:00:00Z","doi":"10.1002/adma.200400383","page":"1912-1917","publication":"Advanced Materials","day":"14","year":"2004","publisher":"Wiley","quality_controlled":"1","title":"Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts","article_processing_charge":"No","author":[{"full_name":"Campbell, C. J.","last_name":"Campbell","first_name":"C. J."},{"first_name":"M.","full_name":"Fialkowski, M.","last_name":"Fialkowski"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"first_name":"I. T.","full_name":"Bensemann, I. T.","last_name":"Bensemann"},{"full_name":"Grzybowski, B. A.","last_name":"Grzybowski","first_name":"B. A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. 2004;16(21):1912-1917. doi:10.1002/adma.200400383","apa":"Campbell, C. J., Fialkowski, M., Klajn, R., Bensemann, I. T., & Grzybowski, B. A. (2004). Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. Wiley. https://doi.org/10.1002/adma.200400383","short":"C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski, Advanced Materials 16 (2004) 1912–1917.","ieee":"C. J. Campbell, M. Fialkowski, R. Klajn, I. T. Bensemann, and B. A. Grzybowski, “Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts,” Advanced Materials, vol. 16, no. 21. Wiley, pp. 1912–1917, 2004.","mla":"Campbell, C. J., et al. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” Advanced Materials, vol. 16, no. 21, Wiley, 2004, pp. 1912–17, doi:10.1002/adma.200400383.","ista":"Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. 2004. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. 16(21), 1912–1917.","chicago":"Campbell, C. J., M. Fialkowski, Rafal Klajn, I. T. Bensemann, and B. A. Grzybowski. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” Advanced Materials. Wiley, 2004. https://doi.org/10.1002/adma.200400383."},"volume":16,"issue":"21","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"intvolume":" 16","month":"11","scopus_import":"1","oa_version":"None","abstract":[{"text":"Thin films of ionically doped gelatin have been color-patterned with submicrometer precision using the wet-stamping technique. Inorganic salts are delivered onto the gelatin surface from an agarose stamp, and diffuse into the gelatine layer, producting deeply colored precipitates. Reaction fronts originating from different features of the stamp cease within < 1 μm of each other, leaving sharp, transparent regions in between.","lang":"eng"}],"extern":"1","date_updated":"2023-08-08T12:41:23Z","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"status":"public","type":"journal_article","article_type":"original","_id":"13434"}]