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John Reinitz

InstitutionUniversity of Chicago
AddressChicago IL 60637
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    My laboratory is engaged in a long term project to understand how DNA sequence specifies biological form. We are interested not only in the specification of typical form by a typical genome, but also in the effects of variability. Such variability might take the form of genetic variation in a population or intrinsic fluctuations in an individual. These problems touch on issues central to developmental and evolutionary biology, and efforts to solve them have previously led to the development of new branches of mathematics.

    We consider these issues in the specific context of segment determination in the fruit fly Drosophila melanogaster, but actively seek collaborations with investigators working on other organisms or with pure theoreticians. The starting point for our own investigations are quantitative data on gene expression, extracted from images of confocally scanned fixed or living embryos. We use this numerical information to find parameter sets for specific models of fundamental processes of gene regulation and pattern formation by means of large scale optimization procedures performed on parallel computers. These models may be specified in terms of DNA sequence or be more coarse-grained. They might take the form of a dynamical system, deterministic or stochastic, or simply be a complex but explicit mathematical function.

    Our goal is to use every tool in the toolbox—wet experiments, statistics, computational science, and mathematics—to solve a well focused scientific problem: how does a fly go from DNA sequence to a fate map of presumptive segments at single cell resolution?

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    R01OD010936     (REINITZ, JOHN B.)Jan 1, 2011 - May 31, 2024
    Physiological Model of Gene Regulation in Drosophila
    Role: Principal Investigator

    S10RR025635     (REINITZ, JOHN B.)May 20, 2010 - May 19, 2011
    Shared Equipment Grant for Purchase of a Leica TCS SP5 Confocal Microscope
    Role: Principal Investigator

    R03TW001147     (REINITZ, JOHN B.)Sep 30, 1999 - Aug 31, 2003
    Role: Principal Investigator

    R01RR007801     (REINITZ, JOHN B.)Sep 30, 1992 - Dec 31, 2013
    Physiological Model of Gene Regulation in Drosophila
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Jiang P, Kreitman M, Reinitz J. The effect of mutational robustness on the evolvability of multicellular organisms and eukaryotic cells. J Evol Biol. 2023 06; 36(6):906-924. PMID: 37256290; PMCID: PMC10315174.
      Citations:    Fields:    Translation:Cells
    2. Reinitz J, Vakulenko S, Sudakow I, Grigoriev D. Robust morphogenesis by chaotic dynamics. Sci Rep. 2023 05 09; 13(1):7482. PMID: 37160971; PMCID: PMC10170119.
      Citations:    Fields:    
    3. Liu Y, Barr K, Reinitz J. Fully interpretable deep learning model of transcriptional control. Bioinformatics. 2020 07 01; 36(Suppl_1):i499-i507. PMID: 32657418; PMCID: PMC7355248.
      Citations: 10     Fields:    
    4. Barr K, Reinitz J, Radulescu O. An in silico analysis of robust but fragile gene regulation links enhancer length to robustness. PLoS Comput Biol. 2019 11; 15(11):e1007497. PMID: 31730659; PMCID: PMC6881076.
      Citations: 3     Fields:    Translation:AnimalsCells
    5. Reinitz J, Ramos AF. Physical implications of so(2, 1) symmetry in exact solutions for a self-repressing gene. J Chem Phys. 2019 Jul 28; 151(4):041101. PMID: 31370538; PMCID: PMC6934145.
      Citations: 1     Fields:    
    6. Reinitz J, Vakulenko S, Weber A, Grigoriev D. Adaptation, fitness landscape learning and fast evolution. F1000Res. 2019; 8:358. PMID: 31656586; PMCID: PMC6798318.
      Citations: 1     Fields:    
    7. Barr KA, Reinitz J. Correction: A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. PLoS One. 2018; 13(5):e0197211. PMID: 29734377; PMCID: PMC5937780.
      Citations:    Fields:    
    8. Barr KA, Martinez C, Moran JR, Kim AR, Reinitz J, Ramos AF. Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation. BMC Syst Biol. 2017 Nov 29; 11(1):116. PMID: 29187214; PMCID: PMC5708098.
      Citations: 9     Fields:    Translation:AnimalsCells
    9. Barr KA, Reinitz J. A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. PLoS One. 2017; 12(7):e0180861. PMID: 28715438; PMCID: PMC5513433.
      Citations: 6     Fields:    Translation:AnimalsCells
    10. Hope CM, Rebay I, Reinitz J. DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan. Biophys J. 2017 Jan 10; 112(1):180-192. PMID: 28076810; PMCID: PMC5232354.
      Citations: 5     Fields:    Translation:AnimalsCells
    11. Lou Z, Reinitz J. Parallel Simulated Annealing Using an Adaptive Resampling Interval. Parallel Comput. 2016 Apr 01; 53:23-31. PMID: 26941469; PMCID: PMC4770898.
      Citations: 1     
    12. Bertolino E, Reinitz J. The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Dev Biol. 2016 May 01; 413(1):128-44. PMID: 26945717; PMCID: PMC4878123.
      Citations: 8     Fields:    Translation:AnimalsCells
    13. Lee U, Skinner JJ, Reinitz J, Rosner MR, Kim EJ. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations. PLoS One. 2015; 10(7):e0132397. PMID: 26203903; PMCID: PMC4512695.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    14. Jiang P, Ludwig MZ, Kreitman M, Reinitz J. Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. Dev Biol. 2015 Sep 01; 405(1):173-81. PMID: 26129990; PMCID: PMC4529771.
      Citations: 11     Fields:    Translation:Animals
    15. Reinitz J, Ramos AF, Hornos JE. Gene regulation and noise reduction by coupling of stochastic processes. Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Feb; 91(2):020701. PMID: 25768447; PMCID: PMC4476401.
      Citations: 7     Fields:    Translation:Cells
    16. Reinitz J, Vakulenko S, Weber A, Grigoriev D. Punctuated evolution and robustness in morphogenesis. Biosystems. 2014 Sep; 123:106-13. PMID: 24996115; PMCID: PMC4283494.
      Citations: 2     Fields:    Translation:HumansAnimals
    17. 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. Mol Biol Evol. 2014 Apr; 31(4):903-16. PMID: 24408913; PMCID: PMC3969564.
      Citations: 11     Fields:    Translation:AnimalsCells
    18. 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. 2013; 8(12):e82125. PMID: 24349199; PMCID: PMC3859562.
      Citations: 26     Fields:    Translation:HumansCells
    19. Surkova S, Myasnikova E, Kozlov KN, Pisarev A, Reinitz J, Samsonova M. Quantitative imaging of gene expression in Drosophila embryos. Cold Spring Harb Protoc. 2013 Jun 01; 2013(6):488-97. PMID: 23734022.
      Citations: 1     Fields:    Translation:Animals
    20. Surkova S, Myasnikova E, Kozlov KN, Pisarev A, Reinitz J, Samsonova M. Preparation of Drosophila embryos for quantitative imaging of gene expression. Cold Spring Harb Protoc. 2013 Jun 01; 2013(6):533-6. PMID: 23734021.
      Citations:    Fields:    Translation:Animals
    21. Martinez CA, Barr KA, Kim AR, Reinitz J. A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design. Methods. 2013 Jul 15; 62(1):91-8. PMID: 23732772; PMCID: PMC3924567.
      Citations: 6     Fields:    Translation:AnimalsCells
    22. 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 Genet. 2013; 9(2):e1003243. PMID: 23468638; PMCID: PMC3585115.
      Citations: 36     Fields:    Translation:AnimalsCells
    23. Surkova S, Golubkova E, Panok L, Mamon L, Reinitz J, Samsonova M. Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants. Dev Biol. 2013 Apr 01; 376(1):99-112. PMID: 23333947.
      Citations: 23     Fields:    Translation:Animals
    24. Jaeger J, Reinitz J. Drosophila blastoderm patterning. Curr Opin Genet Dev. 2012 Dec; 22(6):533-41. PMID: 23290311.
      Citations: 30     Fields:    Translation:Animals
    25. Kozlov K, Surkova S, Myasnikova E, Reinitz J, Samsonova M. Modeling of gap gene expression in Drosophila Kruppel mutants. PLoS Comput Biol. 2012; 8(8):e1002635. PMID: 22927803; PMCID: PMC3426564.
      Citations: 18     Fields:    Translation:Animals
    26. Reinitz J. Turing centenary: Pattern formation. Nature. 2012 Feb 22; 482(7386):464. PMID: 22358813.
      Citations: 8     Fields:    Translation:Cells
    27. Gursky VV, Panok L, Myasnikova EM, Samsonova MG, Reinitz J, Samsonov AM. Mechanisms of gap gene expression canalization in the Drosophila blastoderm. BMC Syst Biol. 2011; 5:118. PMID: 21794172; PMCID: PMC3398401.
      Citations: 19     Fields:    Translation:Animals
    28. Surkova SIu, Gurskii VV, Reinitz J, Samsonova MG. [Studies of stability mechanisms of early embryonal development of fruit fly Drosophila]. Ontogenez. 2011 Jan-Feb; 42(1):3-19. PMID: 21442898; PMCID: PMC3250312.
      Citations:    Fields:    Translation:Animals
    29. Vakulenko S, Reinitz J, Radulescu O. Size regulation in the segmentation of Drosophila: interacting interfaces between localized domains of gene expression ensure robust spatial patterning. Phys Rev Lett. 2009 Oct 16; 103(16):168102. PMID: 19911861; PMCID: PMC2977926.
      Citations: 18     Fields:    Translation:Animals
    30. 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 (Austin). 2009 Apr-Jun; 3(2):151-6. PMID: 19550114; PMCID: PMC3171190.
      Citations: 7     Fields:    Translation:Animals
    31. 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 Comput Biol. 2009 Mar; 5(3):e1000303. PMID: 19282965; PMCID: PMC2646127.
      Citations: 111     Fields:    Translation:Animals
    32. 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 Biol. 2009 Mar; 7(3):e1000049. PMID: 19750121; PMCID: PMC2653557.
      Citations: 144     Fields:    Translation:Animals
    33. 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. 2009 Feb 01; 25(3):346-52. PMID: 19052059; PMCID: PMC2639076.
      Citations: 9     Fields:    Translation:Animals
    34. Pisarev A, Poustelnikova E, Samsonova M, Reinitz J. FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Res. 2009 Jan; 37(Database issue):D560-6. PMID: 18953041; PMCID: PMC2686593.
      Citations: 58     Fields:    Translation:Animals
    35. 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 tissue biol. 2008 Apr; 2(2):200-215. PMID: 19343098; PMCID: PMC2630218.
      Citations: 7     
    36. 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 (Austin). 2008 Mar-Apr; 2(2):58-66. PMID: 18820476; PMCID: PMC2803333.
      Citations: 27     Fields:    Translation:Animals
    37. Gurskii VV, Kozlov KN, Samsonov AM, Reinitz J. [A model with asymptotically stable dynamics for the network of Drosophila gap genes]. Biofizika. 2008 Mar-Apr; 53(2):235-49. PMID: 18543766.
      Citations: 3     Fields:    Translation:Animals
    38. 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. 2008; 50(4):352-69. PMID: 18664119.
      Citations: 1     Fields:    Translation:Animals
    39. Wu YF, Myasnikova E, Reinitz J. Master equation simulation analysis of immunostained Bicoid morphogen gradient. BMC Syst Biol. 2007 Nov 16; 1:52. PMID: 18021413; PMCID: PMC2212647.
      Citations: 16     Fields:    Translation:Animals
    40. Surkova S, Kosman D, Kozlov K, Myasnikova E, Samsonova AA, Spirov A, Vanario-Alonso CE, Samsonova M, Reinitz J. Characterization of the Drosophila segment determination morphome. Dev Biol. 2008 Jan 15; 313(2):844-62. PMID: 18067886; PMCID: PMC2254320.
      Citations: 110     Fields:    Translation:Animals
    41. Reinitz J. Developmental biology: a ten per cent solution. Nature. 2007 Jul 26; 448(7152):420-1. PMID: 17653180.
      Citations: 17     Fields:    Translation:AnimalsCells
    42. Jaeger J, Sharp DH, Reinitz J. Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster. Mech Dev. 2007 Feb; 124(2):108-28. PMID: 17196796; PMCID: PMC1992814.
      Citations: 47     Fields:    
    43. Jaeger J, Reinitz J. On the dynamic nature of positional information. Bioessays. 2006 Nov; 28(11):1102-11. PMID: 17041900.
      Citations: 41     Fields:    Translation:Animals
    44. 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. Nat Genet. 2006 Oct; 38(10):1159-65. PMID: 16980977.
      Citations: 107     Fields:    Translation:AnimalsCells
    45. Perkins TJ, Jaeger J, Reinitz J, Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput Biol. 2006 May; 2(5):e51. PMID: 16710449; PMCID: PMC1463021.
      Citations: 76     Fields:    Translation:Animals
    46. 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. Proc Natl Acad Sci U S A. 2005 Sep 13; 102(37):13176-81. PMID: 16150708; PMCID: PMC1201621.
      Citations: 48     Fields:    Translation:AnimalsCells
    47. 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. Dev Genes Evol. 2005 Jul; 215(7):374-81. PMID: 15834586.
      Citations: 43     Fields:    Translation:Animals
    48. Myasnikova E, Samsonova M, Kosman D, Reinitz J. Removal of background signal from in situ data on the expression of segmentation genes in Drosophila. Dev Genes Evol. 2005 Jun; 215(6):320-6. PMID: 15711806.
      Citations: 28     Fields:    Translation:Animals
    49. Jaeger J, Blagov M, Kosman D, Kozlov KN, 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. 2004 Aug; 167(4):1721-37. PMID: 15342511; PMCID: PMC1471003.
      Citations: 98     Fields:    Translation:AnimalsCells
    50. Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, Kozlov KN, Myasnikova E, Vanario-Alonso CE, Samsonova M, Sharp DH, Reinitz J. Dynamic control of positional information in the early Drosophila embryo. Nature. 2004 Jul 15; 430(6997):368-71. PMID: 15254541.
      Citations: 241     Fields:    Translation:AnimalsCells
    51. Poustelnikova E, Pisarev A, Blagov M, Samsonova M, Reinitz J. A database for management of gene expression data in situ. Bioinformatics. 2004 Sep 22; 20(14):2212-21. PMID: 15059825.
      Citations: 55     Fields:    Translation:Animals
    52. Holloway DM, Reinitz J, Spirov A, Vanario-Alonso CE. Sharp borders from fuzzy gradients. Trends Genet. 2002 Aug; 18(8):385-7. PMID: 12142000.
      Citations: 4     Fields:    Translation:Animals
    53. Aizenberg I, Myasnikova E, Samsonova M, Reinitz J. Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method. Math Biosci. 2002 Mar; 176(1):145-59. PMID: 11867088.
      Citations: 1     Fields:    Translation:Animals
    54. 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. 2002; 18 Suppl 1:S87-95. PMID: 12169535.
      Citations: 6     Fields:    Translation:Animals
    55. Kozlov K, Myasnikova E, Pisarev A, Samsonova M, Reinitz J, Kozlov K, Myasnikova E, Pisarev 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 Biol. 2002; 2(2):125-41. PMID: 12066837.
      Citations: 7     Fields:    Translation:AnimalsCells
    56. Wu X, Vasisht V, Kosman D, Reinitz J, Small S, Wu X, Vasisht V, Kosman D, Reinitz J, Small S. Thoracic patterning by the Drosophila gap gene hunchback. Dev Biol. 2001 Sep 01; 237(1):79-92. PMID: 11518507.
      Citations: 22     Fields:    Translation:Animals
    57. Gursky VV, Reinitz J, Samsonov AM. How gap genes make their domains: An analytical study based on data driven approximations. Chaos. 2001 Mar; 11(1):132-141. PMID: 12779448.
      Citations: 2     Fields:    
    58. Myasnikova E, Samsonova A, Kozlov K, Samsonova M, Reinitz J. Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics. 2001 Jan; 17(1):3-12. PMID: 11222257.
      Citations: 43     Fields:    Translation:Animals
    59. Spirov AV, Bowler T, Reinitz J. HOX Pro: a specialized database for clusters and networks of homeobox genes. Nucleic Acids Res. 2000 Jan 01; 28(1):337-40. PMID: 10592267; PMCID: PMC102436.
      Citations: 6     Fields:    Translation:AnimalsCells
    60. 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. 1999 Mar; 126(6):1201-10. PMID: 10021339.
      Citations: 33     Fields:    Translation:AnimalsCells
    61. Myasnikova EM, Kosman D, Reinitz J, Samsonova MG. Spatio-temporal registration of the expression patterns of Drosophila segmentation genes. Proc Int Conf Intell Syst Mol Biol. 1999; 195-201. PMID: 10786302.
      Citations: 1     Fields:    Translation:AnimalsCells
    62. Kosman D, Small S, Reinitz J. Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins. Dev Genes Evol. 1998 Jul; 208(5):290-4. PMID: 9683745.
      Citations: 111     Fields:    Translation:Animals
    63. Sharp DH, Reinitz J. Prediction of mutant expression patterns using gene circuits. Biosystems. 1998 Jun-Jul; 47(1-2):79-90. PMID: 9715752.
      Citations: 15     Fields:    
    64. Reinitz J, Kosman D, Vanario-Alonso CE, Sharp DH. Stripe forming architecture of the gap gene system. Dev Genet. 1998; 23(1):11-27. PMID: 9706690.
      Citations: 15     Fields:    Translation:Animals
    65. Kosman D, Reinitz J, Sharp DH. Automated assay of gene expression at cellular resolution. Pac Symp Biocomput. 1998; 6-17. PMID: 9697167.
      Citations: 4     Fields:    Translation:AnimalsCells
    66. Reinitz J, Mjolsness E, Sharp DH. Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback. J Exp Zool. 1995 Jan 01; 271(1):47-56. PMID: 7852948.
      Citations: 47     Fields:    Translation:Animals
    67. Reinitz J, Sharp DH. Mechanism of eve stripe formation. Mech Dev. 1995 Jan; 49(1-2):133-58. PMID: 7748785.
      Citations: 74     Fields:    Translation:AnimalsCells
    68. Wright LW, Lichter JB, Reinitz J, Shifman MA, Kidd KK, Miller PL. Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty. Comput Appl Biosci. 1994 Jul; 10(4):435-42. PMID: 7804876.
      Citations: 1     Fields:    
    69. Mjolsness E, Sharp DH, Reinitz J. A connectionist model of development. J Theor Biol. 1991 Oct 21; 152(4):429-53. PMID: 1758194.
      Citations: 101     Fields:    Translation:Animals
    70. Reinitz J, Vaisnys JR. Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity. J Theor Biol. 1990 Aug 09; 145(3):295-318. PMID: 2146446.
      Citations: 24     Fields:    Translation:Cells
    71. Reinitz J, Levine M. Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila. Dev Biol. 1990 Jul; 140(1):57-72. PMID: 1972684.
      Citations: 39     Fields:    Translation:AnimalsCells
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