James Yorke - Publications

Affiliations: 
Physics University of Maryland, College Park, College Park, MD 
Website:
http://yorke.umd.edu/

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 6: 1. PMID 29020755 DOI: 10.1093/Gigascience/Gix072  0.36
2017 Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, ... ... Yorke JA, et al. The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3 (Bethesda, Md.). PMID 28751502 DOI: 10.1534/G3.117.300078  0.36
2017 Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience. 6: 1-4. PMID 28369353 DOI: 10.1093/Gigascience/Giw016  0.36
2017 Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research. PMID 28130360 DOI: 10.1101/Gr.213405.116  0.36
2016 Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, ... ... Yorke JA, et al. The Atlantic salmon genome provides insights into rediploidization. Nature. PMID 27088604 DOI: 10.1038/Nature17164  1
2015 Joglekar M, Feudel U, Yorke JA. Geometry of the edge of chaos in a low-dimensional turbulent shear flow model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 052903. PMID 26066225 DOI: 10.1103/Physreve.91.052903  1
2015 Joglekar M, Yorke JA. Robustness of periodic orbits in the presence of noise Nonlinearity. 28: 697-711. DOI: 10.1088/0951-7715/28/3/697  1
2015 Joglekar M, Ott E, Yorke JA. Uncertainty as to whether or not a system has a chaotic attractor Nonlinearity. 28: 3803-3820. DOI: 10.1088/0951-7715/28/11/3803  1
2014 Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, ... ... Yorke JA, et al. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct. 9: 20. PMID 25319552 DOI: 10.1186/1745-6150-9-20  0.4
2014 Joglekar M, Ott E, Yorke JA. Scaling of chaos versus periodicity: how certain is it that an attractor is chaotic? Physical Review Letters. 113: 084101. PMID 25192099 DOI: 10.1103/Physrevlett.113.084101  1
2014 Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 196: 891-909. PMID 24653211 DOI: 10.1534/Genetics.113.159996  1
2014 Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 196: 875-90. PMID 24653210 DOI: 10.1534/Genetics.113.159715  1
2014 Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, ... ... Yorke JA, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology. 15: R59. PMID 24647006 DOI: 10.1186/Gb-2014-15-3-R59  1
2013 Sander E, Yorke JA. A period-doubling cascade precedes chaos for planar maps. Chaos (Woodbury, N.Y.). 23: 033113. PMID 24089949 DOI: 10.1063/1.4813600  1
2013 Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics (Oxford, England). 29: 2669-77. PMID 23990416 DOI: 10.1093/Bioinformatics/Btt476  1
2012 Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. Plos One. 7: e42680. PMID 22880081 DOI: 10.1371/Journal.Pone.0042680  1
2012 . Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. 487: 94-8. PMID 22722851 DOI: 10.1038/Nature11041  1
2012 Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/Gr.131383.111  1
2011 Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, ... ... Yorke JA, et al. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences of the United States of America. 108: 5673-8. PMID 21282631 DOI: 10.1073/Pnas.1008617108  1
2011 Sander E, Yorke JA. Period-doubling cascades galore Ergodic Theory and Dynamical Systems. 31: 1249-1267. DOI: 10.1017/S0143385710000994  1
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Yorke JA, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475  1
2010 Joglekar MR, Sander E, Yorke JA. Fixed points indices and period-doubling cascades Journal of Fixed Point Theory and Applications. 8: 151-176. DOI: 10.1007/S11784-010-0029-5  1
2009 Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/Gb-2009-10-4-R42  1
2009 Rapatski B, Yorke J. Modeling HIV outbreaks: the male to female prevalence ratio in the core population. Mathematical Biosciences and Engineering : Mbe. 6: 135-43. PMID 19292512 DOI: 10.3934/Mbe.2009.6.135  1
2009 Sander E, Yorke JA. A classification of explosions in dimension one Ergodic Theory and Dynamical Systems. 29: 715-731. DOI: 10.1017/S0143385708080486  1
2009 Sander E, Yorke JA. Period-doubling cascades for large perturbations of Hénon families Journal of Fixed Point Theory and Applications. 6: 153-163. DOI: 10.1007/S11784-009-0116-7  1
2008 Sindi SS, Hunt BR, Yorke JA. Duplication count distributions in DNA sequences. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 78: 061912. PMID 19256873 DOI: 10.1103/Physreve.78.061912  1
2008 Roberts M, Zimin AV, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke J. Improving Phrap-based assembly of the rat using "reliable" overlaps. Plos One. 3: e1836. PMID 18350171 DOI: 10.1371/Journal.Pone.0001836  1
2008 White JR, Roberts M, Yorke JA, Pop M. Figaro: a novel statistical method for vector sequence removal. Bioinformatics (Oxford, England). 24: 462-7. PMID 18202027 DOI: 10.1093/Bioinformatics/Btm632  1
2008 Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics (Oxford, England). 24: 42-5. PMID 18057021 DOI: 10.1093/Bioinformatics/Btm542  0.36
2008 Szunyogh I, Kostelich EJ, Gyarmati G, Kalnay E, Hunt BR, Ott E, Satterfield E, Yorke JA. A local ensemble transform Kalman filter data assimilation system for the NCEP global model Tellus, Series a: Dynamic Meteorology and Oceanography. 60: 113-130. DOI: 10.1111/J.1600-0870.2007.00274.X  1
2007 Kuhl D, Szunyogh I, Kostelich EJ, Gyarmati G, Patil DJ, Oczkowski M, Hunt BR, Kalnay E, Ott E, Yorke JA. Assessing predictability with a local ensemble Kalman filter Journal of the Atmospheric Sciences. 64: 1116-1140. DOI: 10.1175/Jas3885.1  1
2006 Rapatski BL, Suppe F, Yorke JA. Reconciling different infectivity estimates for HIV-1. Journal of Acquired Immune Deficiency Syndromes (1999). 43: 253-6. PMID 17003694 DOI: 10.1097/01.qai.0000243095.19405.5c  1
2006 Alligood KT, Sander E, Yorke JA. Crossing bifurcations and unstable dimension variability. Physical Review Letters. 96: 244103. PMID 16907246 DOI: 10.1103/Physrevlett.96.244103  1
2006 Skufca JD, Yorke JA, Eckhardt B. Edge of chaos in a parallel shear flow. Physical Review Letters. 96: 174101. PMID 16712300 DOI: 10.1103/Physrevlett.96.174101  1
2006 Danforth CM, Yorke JA. Making forecasts for chaotic physical processes. Physical Review Letters. 96: 144102. PMID 16712079 DOI: 10.1103/Physrevlett.96.144102  1
2005 Harlim J, Oczkowski M, Yorke JA, Kalnay E, Hunt BR. Convex error growth patterns in a global weather model. Physical Review Letters. 94: 228501. PMID 16090440 DOI: 10.1103/Physrevlett.94.228501  1
2005 Rapatski BL, Suppe F, Yorke JA. HIV epidemics driven by late disease stage transmission. Journal of Acquired Immune Deficiency Syndromes (1999). 38: 241-53. PMID 15735440  1
2005 Szunyogh I, Kostelich EJ, Gyarmati G, Patil DJ, Hunt BR, Kalnay E, Ott E, Yorke JA. Assessing a local ensemble Kalman filter: Perfect model experiments with the National Centers For Environmental Prediction global model Tellus, Series a: Dynamic Meteorology and Oceanography. 57: 528-545. DOI: 10.3402/Tellusa.V57I4.14721  1
2004 Roberts M, Hunt BR, Yorke JA, Bolanos RA, Delcher AL. A preprocessor for shotgun assembly of large genomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 734-52. PMID 15579242 DOI: 10.1089/Cmb.2004.11.734  1
2004 Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA. Reducing storage requirements for biological sequence comparison. Bioinformatics (Oxford, England). 20: 3363-9. PMID 15256412 DOI: 10.1093/Bioinformatics/Bth408  1
2004 Ott E, Hunt BR, Szunyogh I, Zimin AV, Kostelich EJ, Corazza M, Kalnay E, Patil DJ, Yorke JA. A local ensemble Kalman filter for atmospheric data assimilation Tellus, Series a: Dynamic Meteorology and Oceanography. 56: 415-428. DOI: 10.3402/Tellusa.V56I5.14462  1
2004 Hunt BR, Kalnay E, Kostelich EJ, Ott E, Patil DJ, Sauer T, Szunyogh I, Yorke JA, Zimin AV. Four-dimensional ensemble Kalman filtering Tellus, Series a: Dynamic Meteorology and Oceanography. 56: 273-277. DOI: 10.3402/Tellusa.V56I4.14424  1
2001 Patil DJ, Hunt BR, Kalnay E, Yorke JA, Ott E. Local low dimensionality of atmospheric dynamics Physical Review Letters. 86: 5878-5881. DOI: 10.1103/PhysRevLett.86.5878  1
2000 Yuan GC, Yorke JA, Carroll TL, Ott E, Pecora LM. Testing whether two chaotic one dimensional processes are dynamically identical Physical Review Letters. 85: 4265-8. PMID 11060614 DOI: 10.1103/Physrevlett.85.4265  0.68
2000 Guharay S, Hunt BR, Yorke JA, White OR. Correlations in DNA sequences across the three domains of life Physica D: Nonlinear Phenomena. 146: 388-396. DOI: 10.1016/S0167-2789(00)00153-6  1
1995 Nusse HE, Ott E, Yorke JA. Saddle-node bifurcations on fractal basin boundaries. Physical Review Letters. 75: 2482-2485. PMID 10059323 DOI: 10.1103/Physrevlett.75.2482  0.68
1995 Kennedy JA, Yorke JA. Bizarre topology is natural in dynamical systems Bulletin of the American Mathematical Society. 32: 309-316. DOI: 10.1090/S0273-0979-1995-00599-9  1
1995 Salvino LW, Cawley R, Grebogi C, Yorke JA. Predictability in time series Physics Letters A. 209: 327-332. DOI: 10.1016/0375-9601(95)00871-3  1
1994 Kennedy JA, Yorke JA. Pseudocirclesi in dynamicals ystems Transactions of the American Mathematical Society. 343: 349-366. DOI: 10.1090/S0002-9947-1994-1187029-5  1
1993 Lai YC, Grebogi C, Yorke JA, Kan I. How often are chaotic saddles nonhyperbolic? Nonlinearity. 6: 779-797. DOI: 10.1088/0951-7715/6/5/007  1
1992 Shinbrot T, Grebogi C, Ott E, Yorke JA. Using chaos to target stationary states of flows Physics Letters A. 169: 349-354. DOI: 10.1016/0375-9601(92)90239-I  1
1991 Hunt BR, Yorke JA. Smooth dynamics on weierstrass nowhere differentiable curves Transactions of the American Mathematical Society. 325: 141-154. DOI: 10.1090/S0002-9947-1991-1040043-X  1
1991 Ding M, Grebogi C, Ott E, Yorke JA. Massive bifurcation of chaotic scattering Physics Letters A. 153: 21-26. DOI: 10.1016/0375-9601(91)90355-C  1
1990 Kostelich EJ, Yorke JA. Noise reduction: Finding the simplest dynamical system consistent with the data Physica D: Nonlinear Phenomena. 41: 183-196. DOI: 10.1016/0167-2789(90)90121-5  1
1989 Ott E, Grebogi C, Yorke JA. Theory of first order phase transitions for chaotic attractors of nonlinear dynamical systems Physics Letters A. 135: 343-348. DOI: 10.1016/0375-9601(89)90005-4  1
1988 Hammel SM, Yorke JA, Grebogi C. Numerical orbits of chaotic processes represent true orbits Bulletin of the American Mathematical Society. 19: 465-469. DOI: 10.1090/S0273-0979-1988-15701-1  1
1987 Grebogi C, Ott E, Yorke JA. Chaos, strange attractors, and fractal basin boundaries in nonlinear dynamics. Science (New York, N.Y.). 238: 632-8. PMID 17816542 DOI: 10.1126/Science.238.4827.632  0.68
1987 Grebogi C, Ott E, Yorke JA. Basin boundary metamorphoses: Changes in accessible boundary orbits Nuclear Physics B (Proceedings Supplements). 2: 281-300. DOI: 10.1016/0920-5632(87)90024-7  1
1987 Varosi F, Grebogi C, Yorke JA. Simplicial approximation of Poincaré maps of differential equations Physics Letters A. 124: 59-64. DOI: 10.1016/0375-9601(87)90372-0  1
1987 Grebogi C, Kostelich E, Ott E, Yorke JA. Multi-dimensioned intertwined basin boundaries: Basin structure of the kicked double rotor Physica D: Nonlinear Phenomena. 25: 347-360. DOI: 10.1016/0167-2789(87)90108-4  1
1987 Kostelich EJ, Yorke JA. Lorenz cross sections of the chaotic attractor of the double rotor Physica D: Nonlinear Phenomena. 24: 263-278. DOI: 10.1016/0167-2789(87)90079-0  1
1986 Grebogi C, Kostelich E, Ott E, Yorke JA. Multi-dimensioned intertwined basin boundaries and the kicked double rotor Physics Letters A. 118: 448-452. DOI: 10.1016/0375-9601(86)90749-8  1
1985 Grebogi C, Ott E, Yorke JA. Super persistent chaotic transients Ergodic Theory and Dynamical Systems. 5: 341-372. DOI: 10.1017/S014338570000300X  0.68
1985 Grebogi C, McDonald SW, Ott E, Yorke JA. Exterior dimension of fat fractals Physics Letters A. 110: 1-4. DOI: 10.1016/0375-9601(85)90220-8  1
1984 Grebogi C, Ott E, Pelikan S, Yorke JA. Strange attractors that are not chaotic Physica D: Nonlinear Phenomena. 13: 261-268. DOI: 10.1016/0167-2789(84)90282-3  1
1984 Hunt BR, Yorke JA. When all solutions of x′ = -∑ qi(t) x(t - Ti(t)) oscillate Journal of Differential Equations. 53: 139-145. DOI: 10.1016/0022-0396(84)90036-6  1
1983 Grebogi C, Ott E, Yorke JA. Are three-frequency quasiperiodic orbits to be expected in typical nonlinear dynamical systems? Physical Review Letters. 51: 339-342. DOI: 10.1103/Physrevlett.51.339  1
1983 Grebogi C, Ott E, Yorke JA. Fractal basin boundaries, long-lived chaotic transients, and unstable-unstable pair bifurcation Physical Review Letters. 50: 935-938. DOI: 10.1103/Physrevlett.50.935  1
1983 Grebogi C, McDonald SW, Ott E, Yorke JA. Final state sensitivity: An obstruction to predictability Physics Letters A. 99: 415-418. DOI: 10.1016/0375-9601(83)90945-3  1
1983 Grebogi C, Ott E, Yorke JA. Crises, sudden changes in chaotic attractors, and transient chaos Physica D: Nonlinear Phenomena. 7: 181-200. DOI: 10.1016/0167-2789(83)90126-4  1
1982 Grebogi C, Ott E, Yorke JA. Chaotic attractors in crisis Physical Review Letters. 48: 1507-1510. DOI: 10.1103/Physrevlett.48.1507  1
1982 Li TY, Misiurewicz M, Pianigiani G, Yorke JA. No division implies chaos Transactions of the American Mathematical Society. 273: 191-199. DOI: 10.1090/S0002-9947-1982-0664037-3  1
1972 Grossman SE, Yorke JA. Asymptotic behavior and exponential stability criteria for differential delay equations Journal of Differential Equations. 12: 236-255. DOI: 10.1016/0022-0396(72)90031-9  1
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