Ron Unger: List of Publications
Nov 2013
1. Articles
1. Harel, D., Unger, R. and Sussman, J.L. Beauty is in the genes of the beholder.
Tibs 124, 11(4): 155-156 (1986).
2. Unger, R., Harel, D. and Sussman, J.L. DNAMAT: an efficient graphic matrix
sequence homolgy algorithm and its application to structural analysis. Cabios
2(4): 283-289 (1986).
3. Unger, R., Harel, D., Wherland, S. and Sussman, J.L. A 3D building blocks
approach to analyzing and predicting structure of proteins. Proteins 5(4): 355373 (1989).
4. Unger, R., Harel, D., Wherland, S. and Sussman, J.L. Analysis of dihedral
angles distribution: The doublet distribution determines
conformations. Biopolymers 30(5-6): 499-508 (1990).
polypeptides
5. Moult, J. and Unger, R., An analysis of protein folding pathways. Biochemistry
30(16): 3816-3824 (1991).
6. Unger, R. and Moult, J. On the applicability of genetic algorithms to protein
folding. Proc. of the 26th Annual Hawaii International Conference on System
Sciences (HICSS), IEEE Press 715-725 (1993).
7. Unger, R. and Moult, J. Genetic algorithms for protein folding simulations.
Journal of Molecular Biology 231(1): 75-81 (1993).
8. Unger, R. and Sussman, J.L. The importance of short structural motifs in protein
structure analysis. Journal of Computer Aided Molecular Design 7: 457-472
(1993).
9. Unger, R. and Moult, J. Finding the lowest free energy conformation of a
protein is a NP-hard problem: Proof and implications. Bulletin of Mathematical
Biology 55(6): 1183-1198 (1993).
10. Unger, R. and Moult, J. A genetic algorithms for three dimensional protein
folding simulations. Proceedings of the 5th International Conference on genetic
Algorithms (ICGA-93), Morgan Kaufmann Publishers, 581-588 (1993).
11. Unger, R. and Moult, J. Effects of mutations on the performance of genetic
algorithms suitable for protein folding simulations. Computer Aided Innovation
of New materials, Elsevier Science Publishers, 1283-1287. (1993).
12. Unger, R. and Moult, J. Local interactions dominate folding in a simple protein
model. Journal of Molecular Biology 259: 988-994 (1996).
13. Kandel, D., Matias, Y., Unger, R. and Winkler, P. Shuffling biological
sequences. Discrete Applied Mathematics 71 (1-3): 171-186 (1996).
14. Bucci, E., Razynska, A., Kwansa, H., Gryczynski, Z., Collins, J.H., Fronticelli,
C., Unger, R., Braxenthaler, M., Moult, J., Ji, X. and Gilliland, G. Positive and
negative cooperativities at subsequent steps of oxygenation regulate the allosteric
behavior of multistate sebacyl-hemoglobin. Biochemistry 35: 3418-3425 (1996).
15. Braxenthaler, M., Unger, R., Auerbach, D., Given, G. and Moult, J. Chaos in
protein folding dynamics. Protein 29: 417-425 (1997).
16. Prokocimer, M., Unger, R., Rennert, H., Rotter, V. and Rennert, G. Pooled
Analysis of P53 Mutations in Hematological Malignancies: A lesson to be
learned. Human Mutations 12: 4-18 (1998).
17. Yadgari, J., Amir, A. and Unger, R. Genetic Algorithms for Protein Threading.
Proceedings of Int. Con. On Intelligent Systems for Molecular Biology. ISMB98, 193-202, AAAI Press (1998).
18. Kaffe-Abramovich, T. and Unger, R. A Simple Model for Evolution of Protein
Towards the Global Minimum of Free Energy. Folding & Design 3: 389-399,
(1998).
19. Uliel, S., Fliess, A., Amir, A. and Unger, R. A Simple Algorithm for Detecting
Circular Permutations in Proteins. Bioinformatics 15: 930-936 (1999).
20. Albeck, S., Unger, R. and Schreiber, G. Evaluation of Direct and Cooperative
Contributions towards the Strength of Buried Hydrogen Bonds and Salt Bridges.
Journal of Molecular Biology 298: 503-520, (2000).
21. Yadgari, J., Amir, A. and Unger, R. Genetic Threading. J. Constraints 6: 271292, (2001).
22. Uliel, S, Fliess, A. and Unger, R. Naturally Occurring Circular Permutations in
Proteins. Protein Engineering 14: 533-542 (2001).
23. Nudelman, G., Tennenbaum, T., Mehr, R. and Unger, R. PESI - An Intelligent
System for Prediction of Enzyme-Substrate Interactions Based on Experimental
Constraints. In Silico Biology 2:44 (2002).
24. Fliess A. Motro B. and Unger, R. Swaps in protein sequences. Proteins 48: 377387 (2002).
25. Liu, L., Liang, X.H., Uliel, S., Unger, R., Ullu, E., Michaeli, S. RNA
interference of signal-peptide-binding protein SRP54 elicits deleterious effects
and protein sorting defects in trypanosomes. Journal of Biological Chemistry
277: 47348-47357 (2002).
26. Unger, R., Uliel, S. and Havlin, S. Scaling Law in Sizes of Protein Sequence
Families: From Super-Families to Orphan Genes. Proteins 51: 569-576 (2003).
27. Horesh, Y., Amir, A., Michaeli, S. and Unger, R. A Rapid Method for Detection
of Putative RNAi Target Genes in Genomic Data. Bioinformatics 19: 1173-1180
(2003).
28. Uliel, S., Liang, X.H., Unger, R., and Michaeli, S. Small nucleolar RNAs that
guide modification in trypanosomatids: repertoire, targets, genome organization,
and unique functions. Int. J. Parasitol. 34: 445-454 (2004).
29. Liu, Q., Liang, X.H., Uliel, S., Belahcen, M., Unger, R. and Michaeli, S.
Identification and functional characterization of Lsm proteins in Tryapnosoma
brucei. J. Biol. Chem. 279:18210-18219. (2004).
30. Horesh, Y., Amir, A, Michaeli, S. and Unger R. RNAMAT: An Efficient
Method to Detect Classes of RNA Molecules and their Structural Features.
Proceedings of the 26th Annual International Conference of the IEEE
Engineering in Medicine and Biology Society. 2: 2869-2872 (2004).
31. Rozenberg, Y. and Unger R. The Made-In-Israel Bioinformatics Portal.
Briefings In Bioinformatics. 5:389-390. (2004).
SINCE LAST PROMOTION
32. Liang, X.H., Uliel, S., Barth, S. Hury, A., Doniger, T., Unger R. and Michaeli
S. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
Trypanosoma brucei reveals trypanosome-specific pattern of rRNA modification.
RNA 11(5):619-45. (2005).
33. Horesh, Y. and Unger R. A Bottom-up Clustering Algorithm to Detect ncRNA
Molecules with a Common Secondary Structure. Int. J. Bioinformatics Research
and App. IJBRA 1:294-302. (2005).
34. Unger, R. and J. Moult. Towards Computing with Proteins, Proteins, 63:53-64.
(2006).
35. Horesh Y., Mehr, R., and Unger R, Designing an A* Algorithm for Calculating
Edit Distance between Rooted-Unlabeled Trees. J. Comp. Biol. 13:1165-1176
(2006).
36. Jacob, E. and Unger R. A Tale of Two Tails: Why are terminal residues of
proteins exposed? Bioinformatics 15:e225-230. (2007).
37. Liang XH, Hury A, Hoze E, Uliel S, Myslyuk I, Apatoff A, Unger R, Michaeli
S. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
Leishmania major indicates conservation among trypanosomatids in the
repertoire and in their rRNA targets. Eukaryot Cell. 6:361-377. (2007).
38. Jacob, E., Horovitz A, Unger R. Different mechanistic requirements for
prokaryotic and eukaryotic chaperonins: a lattice study. Bioinformatics 23:i240248 (2007).
39. Horesh Y, Doniger T, Michaeli S, Unger R. RNAspa: a shortest path approach
for comparative prediction of the secondary structure of ncRNA molecules.
BMC Bioinformatics. 8:366 (2007).
40. Noivirt O, Unger R, Horovitz A Low folding propensity and high translation
efficiency distinguish in vivo substrates of GroEL from other E. coli proteins.
Bioinformatics 23:3276-3279. (2007)
41. Barth S, Shalem B, Hury A, Tkacz ID, Xue-hai L, Uliel S, Myslyuk I, Doniger
T, Salmon-Divon M, Unger R, Michaeli S. Elucidating the role of C/D snoRNA
in rRNA processing and modification in Trypanosoma brucei. Eukaryot Cell.
7:86-101. (2008).
42. Ashkenazy H, Unger R, Kliger Y. Optimal data collection for correlated mutation
analysis, Proteins 74:545-555. (2008).
43. Barak M, Zuckerman NS, Edelman H, Unger R, Mehr R. IgTree: creating
Immunoglobulin variable region gene lineage trees. J Immunol Methods. 338:67-74.
(2008).
44. Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S, Unger R.
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding
RNA in trypanosomatid genomes. BMC Bioinformatics. 9:471 (2008).
45. Noivirt-Brik O, Unger R, Horovitz A. Analysing the origin of long-range interactions
in proteins using lattice models. BMC Struct Biol. 9:4. (2009)
46. Shalom R, Avigal M, Unger R. A Conflict Based SAW Method for Constraint
Satisfaction. Proceedings of the IEEE Congress on Evolutionary Computation IEEE
CEC 2009:373-380 (2009).
47. Horesh Y, Wexler Y, Lebenthal I, Ziv-Ukelson M, Unger R. RNAslider: a faster
engine for consecutive windows folding and its application to the analysis of genomic
folding asymmetry. BMC Bioinformatics 10:76. (2009)
48. Doniger T, Michaeli S, Unger R. Families of H/ACA ncRNA molecules in
trypanosomatids. RNA Biol. 6(4). (2009). ()
49. ,Noivirt-Brik O, Horovitz A, Unger R. Trade-off between Positive and Negative
Design of Protein Stability: From
PLoS Comput Biol 5:e1000592 (2009).
Lattice
Models
to
Real
Proteins.
50. Yomtovian I, Teerakulkittipong N, Lee B, Moult J, Unger R. Composition Bias
and the Origin of ORFan Genes. Bioinformatics, 26:996-999. (2010).
51. Yehoshua R, Avigal M, Unger R Analysis of the Effects of Lifetime Learning on
Population Fitness using Vose Model. Proceedings of the Genetic and
Evolutionary Computation Conference, GECCO-2010, 681-688 (2010).
52. Malnick SD, Bar-Ilan A, Goland S, Somin M, Doniger T, Basevitz A, Unger R.
Perimyocarditis following streptococcal group A infection: from clinical cases to
bioinformatics analysis. Eur J Intern Med. 21:354-356. (2010).
53. Lebenthal I, Unger R Computational evidence for functionality of noncoding mouse
transcripts. Genomics. 96:10-16. (2010).
54. Doniger T, Katz R, Wachtel C, Michaeli S, Unger R. A comparative genomewide study of ncRNAs in trypanosomatids, BMC Genomics, 11:615 (2010).
55. Shahmoon A, Abraham Y, Limon O, Bitton L, Frydman A, Unger R, Zalevsky Z.
All-optical nano modulator, sensor, wavelength converter, logic gate, and flip flop
based on a manipulated gold nanoparticle. Journal of Nanophotonics, 4, (2010).
56. Barak M, Eilat G, Unger R, Mehr R. Factors important in evolutionary shaping of
immunoglobulin gene loci. Immunome Research 6:13 (2010).
57. Ashkenazy H, Unger R Kliger Y. Hidden conformations in protein structures,
Bioinformatics, 27:1941-1947 (2011).
58. Michaeli S, Doniger T, Gupta SK, Wurtzel O, Romano M, Visnovezky D, Sorek
R, Unger R, Ullu E. RNA-seq analysis of small RNPs in Trypanosoma brucei
reveals a rich repertoire of non-coding RNAs. Nucleic Acids Res. 40:1282-1298
(2012).
59. Azia A, Unger R, Horovitz A. What distinguishes GroEL substrates from other
Escherichia coli proteins? FEBS J. 279:543-550. (2012)
60. Feiglin A, Moult J, Lee B, Ofran Y, Unger R.. Neighbor overlap is enriched in
the yeast interaction network: analysis and implications. PLoS One. 7:e39662.
(2012)
61. Feiglin A, Buchnick A, Sarusi A, Fisher J, Unger R, Ofran Y. Static network
structure can be used to model the phenotypic effects of perturbations in
regulatory networks. Bioinformatics 28:2811-2818. (2012).
62. Noivirt, O, Hazan G, Unger, R, Ofran, Y, Non local residue-residue contacts in
proteins are more conserved than local ones. Bioinformatics 29:331-337. (2013)
63. Azia A, Uversky V.N, Horovitz A, Unger R, The effects of mutations on protein
function: a comparative study of three databases of mutations in humans, Israel
Journal of Chemistry 53:217-226 (2013).
64. Solomon O, Oren, S, Safran M, Deshet-Unger N, Akiva P, Jakob-Hirsch J,
Cesarkas K, Kabesa R, Amariglio N, Unger R, Rechavi G, Eyal E. Global
regulation of alternative splicing by adenosine deaminase acting on RNA
(ADAR). RNA 19:591-604 (2013).
65. Gupta SK, Kolet L, Doniger T, Biswas VK, Unger R, Tzfati Y, Michaeli S. The
Trypanosoma brucei Telomerase RNA (TER) homologue binds core proteins of
the C/D snoRNA family. FEBS Lett, 587:1399-1404. (2013)
66. Jacob E, Unger R, Horovitz A. N-terminal domains in two-domain proteins are
biased to be shorter and predicted to fold faster than their C-terminal counterparts.
Cell reports, 3: 1051-1056. (2013)
67. Shouval R, Bondi O, Mishan H, Shimoni A, Unger R, Nagler A. Application of
machine learning algorithms for clinical predictive modeling: a data-mining
approach in SCT. Bone Marrow Transplant. In press (2013)
2. Text books
68. Unger R, Becker S, Nir A. Bioinformatics: Analysis of Sequences and Genomes
(Learning guide in Hebrew), Open University Press. ISBN 978-695-06-1059-3 (2010).
69. Lamm E and Unger R. Biological Computation. Chapman & Hall/CRC, ISBN 978-14200-8795-6 (2011).
3.
Chapters in books
70. Unger, R. Short structural motifs: Definition, identification and applications, pp.
339-352. In: Protein Structure Determination, Editors: Merz, K. and Le Grand, S.
Birkhauser Publishers (1994).
71. Harel, D., Unger, R. and Sussman, J.L. Beauty is in the genes of the beholder: A
golden tribute to a golden anniversary. In: DNA at 50: The Secret of Life, Editor:
Balaban, M. Faircount Publishers, London. (2003).
72. Unger, R. The genetic algorithm approach to protein structure prediction. In:
Structure & Bonding Vol 110: Applications of Evolutionary Computation in
Chemistry. Editor: Johnston R, Springer-Verlag (2004).
73. Unger, R. Role of Building Blocks in Protein Structure Analysis and Prediction.
In: Bioinformatics. Editor: Seckbach, J. Kluwer, The Netherlands (2005).