John Reinitz - Publications

Affiliations: 
Stony Brook University, Stony Brook, NY, United States 
Area:
segment determination, transcriptional regulation
Website:
http://flyex.ams.sunysb.edu/

76 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
2018 Barr KA, Reinitz J. Correction: A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. Plos One. 13: e0197211. PMID 29734377 DOI: 10.1371/journal.pone.0197211  0.44
2017 Barr KA, Martinez C, Moran JR, Kim AR, Ramos AF, Reinitz J. Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation. Bmc Systems Biology. 11: 116. PMID 29187214 DOI: 10.1186/s12918-017-0485-2  0.44
2017 Barr KA, Reinitz J. A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. Plos One. 12: e0180861. PMID 28715438 DOI: 10.1371/journal.pone.0180861  0.44
2016 Bertolino E, Reinitz J, Manu. The analysis of novel distal Cebpaenhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Developmental Biology. PMID 26945717 DOI: 10.1016/j.ydbio.2016.02.030  0.76
2016 Lou Z, Reinitz J. Parallel Simulated Annealing Using an Adaptive Resampling Interval. Parallel Computing. 53: 23-31. PMID 26941469 DOI: 10.1016/j.parco.2016.02.001  1
2015 Jiang P, Ludwig MZ, Kreitman M, Reinitz J. Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. Developmental Biology. PMID 26129990 DOI: 10.1016/j.ydbio.2015.06.019  1
2015 Ramos AF, Hornos JE, Reinitz J. Gene regulation and noise reduction by coupling of stochastic processes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 020701. PMID 25768447 DOI: 10.1103/PhysRevE.91.020701  1
2014 Grigoriev D, Reinitz J, Vakulenko S, Weber A. Punctuated evolution and robustness in morphogenesis. Bio Systems. 123: 106-13. PMID 24996115 DOI: 10.1016/j.biosystems.2014.06.013  1
2014 Martinez C, Rest JS, Kim AR, Ludwig M, Kreitman M, White K, Reinitz J. Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change. Molecular Biology and Evolution. 31: 903-16. PMID 24408913 DOI: 10.1093/molbev/msu042  1
2013 Lee U, Frankenberger C, Yun J, Bevilacqua E, Caldas C, Chin SF, Rueda OM, Reinitz J, Rosner MR. A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients. Plos One. 8: e82125. PMID 24349199 DOI: 10.1371/journal.pone.0082125  1
2013 Surkova S, Myasnikova E, Kozlov KN, Pisarev A, Reinitz J, Samsonova M. Quantitative imaging of gene expression in Drosophila embryos. Cold Spring Harbor Protocols. 2013: 488-97. PMID 23734022 DOI: 10.1101/pdb.top075101  1
2013 Surkova S, Myasnikova E, Kozlov KN, Pisarev A, Reinitz J, Samsonova M. Preparation of Drosophila embryos for quantitative imaging of gene expression. Cold Spring Harbor Protocols. 2013: 533-6. PMID 23734021 DOI: 10.1101/pdb.prot075093  1
2013 Martinez CA, Barr KA, Kim AR, Reinitz J. A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design. Methods (San Diego, Calif.). 62: 91-8. PMID 23732772 DOI: 10.1016/j.ymeth.2013.05.014  1
2013 Kim AR, Martinez C, Ionides J, Ramos AF, Ludwig MZ, Ogawa N, Sharp DH, Reinitz J. Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic. Plos Genetics. 9: e1003243. PMID 23468638 DOI: 10.1371/journal.pgen.1003243  1
2013 Surkova S, Golubkova E, Manu, Panok L, Mamon L, Reinitz J, Samsonova M. Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants. Developmental Biology. 376: 99-112. PMID 23333947 DOI: 10.1016/j.ydbio.2013.01.008  1
2012 Jaeger J, Manu, Reinitz J. Drosophila blastoderm patterning. Current Opinion in Genetics & Development. 22: 533-41. PMID 23290311 DOI: 10.1016/j.gde.2012.10.005  1
2012 Kozlov K, Surkova S, Myasnikova E, Reinitz J, Samsonova M. Modeling of gap gene expression in Drosophila Kruppel mutants. Plos Computational Biology. 8: e1002635. PMID 22927803 DOI: 10.1371/journal.pcbi.1002635  1
2012 Reinitz J. Turing centenary: Pattern formation. Nature. 482: 464. PMID 22358813 DOI: 10.1038/482464a  1
2011 Gursky VV, Panok L, Myasnikova EM, Manu, Samsonova MG, Reinitz J, Samsonov AM. Mechanisms of gap gene expression canalization in the Drosophila blastoderm. Bmc Systems Biology. 5: 118. PMID 21794172 DOI: 10.1186/1752-0509-5-118  1
2011 Surkova SIu, Gurski? VV, Reinitz J, Samsonova MG. [Studies of stability mechanisms of early embryonal development of fruit fly Drosophila]. Ontogenez. 42: 3-19. PMID 21442898  1
2011 Surkova SY, Gurskiy VV, Reinitz J, Samsonova MG. Study of stability mechanisms of embryonic development in fruit fly Drosophila Russian Journal of Developmental Biology. 42: 1-15. DOI: 10.1134/S1062360411010115  1
2009 Vakulenko S, Manu, Reinitz J, Radulescu O. Size regulation in the segmentation of Drosophila: interacting interfaces between localized domains of gene expression ensure robust spatial patterning. Physical Review Letters. 103: 168102. PMID 19911861 DOI: 10.1103/PhysRevLett.103.168102  1
2009 Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR, Radulescu O, Vanario-Alonso CE, Sharp DH, Samsonova M, Reinitz J. Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. Plos Biology. 7: e1000049. PMID 19750121 DOI: 10.1371/journal.pbio.1000049  1
2009 Kozlov KN, Myasnikova E, Samsonova AA, Surkova S, Reinitz J, Samsonova M. GCPReg package for registration of the segmentation gene expression data in Drosophila. Fly. 3: 151-6. PMID 19550114  1
2009 Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR, Radulescu O, Vanario-Alonso CE, Sharp DH, Samsonova M, Reinitz J. Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. Plos Computational Biology. 5: e1000303. PMID 19282965 DOI: 10.1371/journal.pcbi.1000303  1
2009 Myasnikova E, Surkova S, Panok L, Samsonova M, Reinitz J. Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila. Bioinformatics (Oxford, England). 25: 346-52. PMID 19052059 DOI: 10.1093/bioinformatics/btn620  1
2009 Pisarev A, Poustelnikova E, Samsonova M, Reinitz J. FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Research. 37: D560-6. PMID 18953041 DOI: 10.1093/nar/gkn717  1
2009 Myasnikova E, Surkova S, Samsonova M, Reinitz J. Estimation of errors in gene expression data introduced by diffractive blurring of confocal images Imvip 2009 - 2009 International Machine Vision and Image Processing Conference. 53-58. DOI: 10.1109/IMVIP.2009.17  1
2008 Surkova SY, Myasnikova EM, Kozlov KN, Samsonova AA, Reinitz J, Samsonova MG. Methods for Acquisition of Quantitative Data from Confocal Images of Gene Expression in situ. Cell and Tissue Biology. 2: 200-215. PMID 19343098 DOI: 10.1134/S1990519X08020156  1
2008 Surkova S, Myasnikova E, Janssens H, Kozlov KN, Samsonova AA, Reinitz J, Samsonova M. Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. Fly. 2: 58-66. PMID 18820476  1
2008 Surkova SIu, Miasnikova EM, Kozlov KN, Samsonova AA, Reinitz J, Samsonova MG. [Methods for acquisition of quantitative from confocal images of gene expression in situ]. Tsitologiia. 50: 352-69. PMID 18664119  1
2008 Gurski? VV, Kozlov KN, Samsonov AM, Reinitz J. [A model with asymptotically stable dynamics for the network of Drosophila gap genes]. Biofizika. 53: 235-49. PMID 18543766  1
2008 Surkova S, Kosman D, Kozlov K, Manu, Myasnikova E, Samsonova AA, Spirov A, Vanario-Alonso CE, Samsonova M, Reinitz J. Characterization of the Drosophila segment determination morphome. Developmental Biology. 313: 844-62. PMID 18067886 DOI: 10.1016/j.ydbio.2007.10.037  1
2008 Surkova SY, Myasnikova EM, Reinitz J, Samsonova MG. Dynamic filtration of the expression pattern variability of Drosophila zygotic segmentation genes Biophysics. 53: 226-231. DOI: 10.1134/S0006350908030093  1
2008 Gursky VV, Kozlov KN, Samsonov AM, Reinitz J. Model with asymptotically stable dynamics for Drosophila gap gene network Biophysics. 53: 164-176. DOI: 10.1134/S0006350908020085  1
2007 Wu YF, Myasnikova E, Reinitz J. Master equation simulation analysis of immunostained Bicoid morphogen gradient. Bmc Systems Biology. 1: 52. PMID 18021413 DOI: 10.1186/1752-0509-1-52  1
2007 Reinitz J. Developmental biology: a ten per cent solution. Nature. 448: 420-1. PMID 17653180 DOI: 10.1038/448420a  1
2007 Jaeger J, Sharp DH, Reinitz J. Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster. Mechanisms of Development. 124: 108-28. PMID 17196796 DOI: 10.1016/j.mod.2006.11.001  1
2006 Jaeger J, Reinitz J. On the dynamic nature of positional information. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 28: 1102-11. PMID 17041900 DOI: 10.1002/bies.20494  1
2006 Janssens H, Hou S, Jaeger J, Kim AR, Myasnikova E, Sharp D, Reinitz J. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nature Genetics. 38: 1159-65. PMID 16980977 DOI: 10.1038/ng1886  1
2006 Perkins TJ, Jaeger J, Reinitz J, Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. Plos Computational Biology. 2: e51. PMID 16710449 DOI: 10.1371/journal.pcbi.0020051  1
2006 Gursky VV, Kozlov KN, Samsonov AM, Reinitz J. Cell divisions as a mechanism for selection in stable steady states of multi-stationary gene circuits Physica D: Nonlinear Phenomena. 218: 70-76. DOI: 10.1016/j.physd.2006.04.009  1
2005 Lebrecht D, Foehr M, Smith E, Lopes FJ, Vanario-Alonso CE, Reinitz J, Burz DS, Hanes SD. Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 102: 13176-81. PMID 16150708 DOI: 10.1073/pnas.0506462102  1
2005 Janssens H, Kosman D, Vanario-Alonso CE, Jaeger J, Samsonova M, Reinitz J. A high-throughput method for quantifying gene expression data from early Drosophila embryos. Development Genes and Evolution. 215: 374-81. PMID 15834586 DOI: 10.1007/s00427-005-0484-y  1
2005 Myasnikova E, Samsonova M, Kosman D, Reinitz J. Removal of background signal from in situ data on the expression of segmentation genes in Drosophila. Development Genes and Evolution. 215: 320-6. PMID 15711806 DOI: 10.1007/s00427-005-0472-2  1
2004 Jaeger J, Blagov M, Kosman D, Kozlov KN, Manu, Myasnikova E, Surkova S, Vanario-Alonso CE, Samsonova M, Sharp DH, Reinitz J. Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics. 167: 1721-37. PMID 15342511 DOI: 10.1534/genetics.104.027334  1
2004 Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov KN, Manu, Myasnikova E, Vanario-Alonso CE, Samsonova M, Sharp DH, Reinitz J. Dynamic control of positional information in the early Drosophila embryo. Nature. 430: 368-71. PMID 15254541 DOI: 10.1038/nature02678  1
2004 Poustelnikova E, Pisarev A, Blagov M, Samsonova M, Reinitz J. A database for management of gene expression data in situ. Bioinformatics (Oxford, England). 20: 2212-21. PMID 15059825 DOI: 10.1093/bioinformatics/bth222  1
2004 Gursky VV, Jaeger J, Kozlov KN, Reinitz J, Samsonov AM. Pattern formation and nuclear divisions are uncoupled in drosophila segmentation: Comparison of spatially discrete and continuous models Physica D: Nonlinear Phenomena. 197: 286-302. DOI: 10.1016/j.physd.2004.07.003  1
2002 Myasnikova E, Samsonova A, Samsonova M, Reinitz J. Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns. Bioinformatics (Oxford, England). 18: S87-95. PMID 12169535  1
2002 Holloway DM, Reinitz J, Spirov A, Vanario-Alonso CE. Sharp borders from fuzzy gradients. Trends in Genetics : Tig. 18: 385-7. PMID 12142000 DOI: 10.1016/S0168-9525(02)02724-5  1
2002 Kozlov K, Myasnikova E, Pisareva A, Samsonova M, Reinitz J. A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ. In Silico Biology. 2: 125-41. PMID 12066837  1
2002 Aizenberg I, Myasnikova E, Samsonova M, Reinitz J. Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method. Mathematical Biosciences. 176: 145-59. PMID 11867088 DOI: 10.1016/S0025-5564(01)00104-3  1
2002 Aizenberg I, Butakoff C, Myasnikova E, Samsonova M, Reinitz J. Classification of the images of gene expression patterns using neural network based on multi-valued neurons with the minimal number of inputs Proceedings of Spie - the International Society For Optical Engineering. 4668: 10-19. DOI: 10.1117/12.461675  1
2002 Spirov AV, Kazansky AB, Timakin DL, Reinitz J. Reconstruction of the dynamics of Drosophila genes expression from sets of images sharing a common pattern Real-Time Imaging. 8: 507-518.  1
2002 Hofestädt R, Kolchanov N, Reinitz J. Information and simulation systems for the analysis of gene regulation and metabolic pathways In Silico Biology. 2: 35-36.  1
2001 Gursky VV, Reinitz J, Samsonov AM. How gap genes make their domains: An analytical study based on data driven approximations. Chaos (Woodbury, N.Y.). 11: 132-141. PMID 12779448 DOI: 10.1063/1.1349890  1
2001 Wu X, Vasisht V, Kosman D, Reinitz J, Small S. Thoracic patterning by the Drosophila gap gene hunchback. Developmental Biology. 237: 79-92. PMID 11518507 DOI: 10.1006/dbio.2001.0355  1
2001 Myasnikova E, Samsonova A, Kozlov K, Samsonova M, Reinitz J. Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics (Oxford, England). 17: 3-12. PMID 11222257  1
2001 Aizenberg I, Myasnikova E, Samsonova M, Reinitz J. Application of the neural networks based on multi-valued neurons to classification of the images of gene expression patterns Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2206: 291-304.  1
2000 Spirov AV, Bowler T, Reinitz J. HOX Pro: a specialized database for clusters and networks of homeobox genes. Nucleic Acids Research. 28: 337-40. PMID 10592267  1
2000 Kozlov K, Myasnikova E, Samsonova M, Reinitz J, Kosman D. Fast redundant dyadic wavelet transform in application to spatial registration of the expression patterns of drosophila segmentation genes Proceedings - International Conference On Pattern Recognition. 15: 459-462.  1
1999 Myasnikova EM, Kosman D, Reinitz J, Samsonova MG. Spatio-temporal registration of the expression patterns of Drosophila segmentation genes. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 195-201. PMID 10786302  1
1999 Hewitt GF, Strunk BS, Margulies C, Priputin T, Wang XD, Amey R, Pabst BA, Kosman D, Reinitz J, Arnosti DN. Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. Development (Cambridge, England). 126: 1201-10. PMID 10021339  1
1999 Chu KW, Deng Y, Reinitz J. Parallel Simulated Annealing by Mixing of States Journal of Computational Physics. 148: 646-662. DOI: 10.1006/jcph.1998.6134  1
1998 Sharp DH, Reinitz J. Prediction of mutant expression patterns using gene circuits. Bio Systems. 47: 79-90. PMID 9715752 DOI: 10.1016/S0303-2647(98)00014-8  1
1998 Reinitz J, Kosman D, Vanario-Alonso CE, Sharp DH. Stripe forming architecture of the gap gene system. Developmental Genetics. 23: 11-27. PMID 9706690 DOI: 10.1002/(SICI)1520-6408(1998)23:1<11::AID-DVG2>3.0.CO;2-9  1
1998 Kosman D, Reinitz J, Sharp DH. Automated assay of gene expression at cellular resolution. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 6-17. PMID 9697167  1
1998 Kosman D, Small S, Reinitz J. Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins. Development Genes and Evolution. 208: 290-4. PMID 9683745 DOI: 10.1007/s004270050184  1
1995 Reinitz J, Mjolsness E, Sharp DH. Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback. The Journal of Experimental Zoology. 271: 47-56. PMID 7852948 DOI: 10.1002/jez.1402710106  1
1995 Reinitz J, Sharp DH. Mechanism of eve stripe formation. Mechanisms of Development. 49: 133-58. PMID 7748785 DOI: 10.1016/0925-4773(94)00310-J  1
1994 Wright LW, Lichter JB, Reinitz J, Shifman MA, Kidd KK, Miller PL. Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty. Computer Applications in the Biosciences : Cabios. 10: 435-42. PMID 7804876 DOI: 10.1093/bioinformatics/10.4.435  1
1993 Sharp DH, Reinitz J, Mjolsness E. Multiscale modeling of developmental processes Open Systems & Information Dynamics. 2: 67-76. DOI: 10.1007/BF02228972  1
1991 Mjolsness E, Sharp DH, Reinitz J. A connectionist model of development. Journal of Theoretical Biology. 152: 429-53. PMID 1758194 DOI: 10.1016/S0022-5193(05)80391-1  1
1990 Reinitz J, Vaisnys JR. Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity. Journal of Theoretical Biology. 145: 295-318. PMID 2146446 DOI: 10.1016/S0022-5193(05)80111-0  1
1990 Reinitz J, Levine M. Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila. Developmental Biology. 140: 57-72. PMID 1972684 DOI: 10.1016/0012-1606(90)90053-L  1
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