In June 2005, Jon Widom gave a lecture on DNA flexibility at the 14th Conversation here in Albany (1). On June 14-18th of this year, he was in Albany again; this time to give a lecture (3) on a genomic code for nucleosome positioning from Archaebacteria to Man for the 17th Conversation. In 2009, during the 16th Conversation, he was also part of a poster presentation entitled “Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals” (2). In addition to providing the two lectures and publishing three abstracts in JBSD (1-3), Jon also impacted other members of the Albany community. Several friends of JBSD and the Albany Conversation have followed the research of Jon, and have also published in JBSD. JBSD has published 10 abstracts (4-13), which cite Jon’s published papers. In addition, JBSD has published 14 full-length research articles (14-27) dealing with nucleosome positioning, and all 14 of these papers refer to the work of Jon Widom. In view of this relationship with Jon, obviously JBSD has a responsibility and obligation to publish an In Memoriam on Jon Widom to acknowledge and mourn the loss to our community.

The news of Jon’s loss came as a shock to me. Nevertheless, as soon as I heard it from Maxim Frank-Kamenetskii on the evening of July 18th, I discussed what we should do with Maxim and Ed Trifonov. The next day, after obtaining clearance from his colleagues in Northwestern, I informed the members of our community across the globe. Sergei Mirkin agreed to write a short biography of Jon, and Ed Trifonov and Victor Zhurkin agreed to review Jon’s scientific contributions and their impact. These appear on the following pages.

Best wishes to Jon’s family and friends in these sad times, and may his soul rest in peace.

References

1. J. Widom. DNA Flexibility. J Biomol Struct Dyn 22(6), 787-788 (2005).
2. Y. Field, N. Kaplan, Y. Fondufe-Mittendorf, I. K. Moore, E. Sharon, Y. Lubling, P. Mieczkowski, J. D. Lieb, J. Widom, and E. Segal. Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals. J Biomol Struct Dyn 26(6), 919-919 (2009).
3. J. Widom. A Genomic Code for Nucleosome Positioning from Archaebacteria to Man. J Biomol Struct Dyn 28(6), 1111-1111 (2011).
4. Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii. Cyclization of Short DNA Fragments and Bending Fluctuations of the Double Helix. J Biomol Struct Dyn 22(6), 784-784 (2005).
5. L. Czapla and W. K. Olson. Sequence-dependent Cyclization of Short DNA Sequences. J Biomol Struct Dyn 22(6), 840-840 (2005).
6. E. Bishop and T. D. Tullius. Prediction of Nucleosome Positioning Using a Support Vector Machine. J Biomol Struct Dyn 24(6), 624-624 (2007).
7. D. Wang, F. Cui, and V. B. Zhurkin. The ‘Kink-and-Slide’ Folding of DNA in Nucleosome is Facilitated by Asymmetric Interactions of the Histone Arginines in the Minor Groove. J Biomol Struct Dyn 24(6), 627-627 (2007).
8. F. Cui and V. B. Zhurkin. Chicken and Yeast Nucleosomal DNA Sequences Differ at the Ends: A Possible Relation to the Linker Histone Binding. J Biomol Struct Dyn 24(6), 626-627 (2007).
9. C. Jiang and B. F. Pugh. Identification and Nomenclature of the Consensus Nucleosomes Across the Yeast Genome. J Biomol Struct Dyn 26(6), 922-922 (2009).
10. F. Cui, D. Wang, and V. B. Zhurkin. AT-rich Fragments at the Nucleosome Ends May be Related to Linker Histone Binding: Implications for Nucleosome Positioning. J Biomol Struct Dyn 26(6), 915-915 (2009).
11. D. Wang, N. B. Ulyanov, and V. B. Zhurkin. Sequence Dependence of the ‘Kink-and-Slide’ Deformations of DNA in Nucleosome. All-atom Simulations of DNA Nonharmonic Behavior. J Biomol Struct Dyn 26(6), 924-925 (2009).
12. V. B. Zhurkin, F. Cui, and D. Wang. DNA Mechanics, Nucleosome Positioning and p53-DNA Recognition. J Biomol Struct Dyn 28(6), 1158-1159 (2011).
13. F. Cui, H. A. Cole, D. J. Clark, and V. B. Zhurkin. Yeast Nucleosomes Mapped with High Resolution by Paired-end Sequencing Exhibit Strong Positioning Patterns. J Biomol Struct Dyn 28(6), 1160-1161 (2011).
14. A. Travers, E. Hiriart, M. Churcher, M. Caserta, and E. Di Mauro. The DNA sequence-dependence of nucleosome positioning in vivo and in vitro. J Biomol Struct Dyn 27(6), 713-724 (2010).
15. F. Xu and W. K. Olson. DNA Architecture, Deformability, and Nucleosome Positioning. J Biomol Struct Dyn 27(6), 725-739 (2010).
16. E. N. Trifonov. Nucleosome positioning by sequence, state of the art and apparent finale. J Biomol Struct Dyn 27(6), 741-746 (2010).
17. P. De Santis, S. Morosetti, and A. Scipioni. Prediction of Nucleosome Positioning in Genomes: Limits and Perspectives of Physical and Bioinformatic Approaches. J Biomol Struct Dyn 27(6), 747-764 (2010).
18. G. A. Babbitt, M. Y. Tolstorukov, and Y. Kim. The Molecular Evolution of Nucleosome Positioning Through Sequence-Dependent Deformation of the DNA Polymer. J Biomol Struct Dyn 27(6), 765-780 (2010)
19. D. J. Clark. Nucleosome Positioning, Nucleosome Spacing and the Nucleosome Code. J Biomol Struct Dyn 27(6), 781-793 (2010).
20. S. M. Johnson. Painting a perspective on the landscape of nucleosome positioning. J Biomol Struct Dyn 27(6), 795-802 (2010).
21. G. Arya, A. Maitra, and S. A. Grigoryev. A Structural Perspective on the Where, How, Why, and What of Nucleosome Positioning. J Biomol Struct Dyn 27(6), 803-820 (2010).
22. F. Cui and V. B. Zhurkin. Structure-based Analysis of DNA Sequence Patterns Guiding Nucleosome Positioning in vitro. J Biomol Struct Dyn 27(6), 821-841 (2010).
23. D. Wang, N. B. Ulyanov, and V. B. Zhurkin. Sequence-dependent Kink-and-Slide Deformations of Nucleosomal DNA Facilitated by Histone Arginines Bound in the Minor Groove. J Biomol Struct Dyn 27(6), 843-859 (2010).
24. Y. V. Sereda and T. C. Bishop. Evaluation of Elastic Rod Models with Long Range Interactions for Predicting Nucleosome Stability. J Biomol Struct Dyn 27(6), 867-887 (2010).
25. I. Gabdank, D. Barash, and E. N. Trifonov. Nucleosome DNA Bendability Matrix (C. elegans). J Biomol Struct Dyn 26(4), 403-411 (2009)
26. I. Gabdank, D. Barash, and E. N. Trifonov. Single-base Resolution Nucleosome Mapping on DNA Sequences. J Biomol Struct Dyn 28(1), 107-121 (2010).
27. F. Salih, B. Salih, and E. N. Trifonov. Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elgans. J Biomol Struct Dyn 26(3), 273-282 (2008).