Tauber-bioinfo.haifa.ac.il

Computational biology (peer-review journals): 1. Leontovich AM, Brodsky LI, Gorbalenya AE.(1990) The construction of complete local
similarity map for pairs of polymers, Biopolimery i kletka. 6(7): 14-21. Russian.
2. Nikol'skii AA, Teryokhin AT, Srebrodol'skaya YeB, Formozov NA, Paskhina NM, Brodsky LI
(1990) Correlation between the spatial structure of population and acoustic activity of Northern
Pika., Zoologischer Anzeiger, 224: 342-358.
3. Brodsky LI, Drachev AL, Tatuzov RL, Chumakov KM. (1991) GenBee: a Package of
Programs for Biopolymer Sequence Analysis, Biopolimery i kletka, 7(1): 10-14. Russian.
4. Brodsky LI, Drachev AL, Leontovich AM. (1991) A new method of multiple alignment of
biopolymer sequences, Biopolimery i kletka, 7(1): 14-22. Russian.
5. Strukova SM, Dugina TN, Kireeva EG, Brodskii LI, Kogan AE, Ashmarin IP (1991)
Regulation of thrombocyte stimulating and other activities of thrombin by modulators of the
recognition site, Vestn Akad Med Nauk SSSR 10: 28-33. Russian.
6. Zhilinskaia IN, Brodskii LI, Alekseenko LV, Kiselev OI (1991) Detection in the structure of
influenza viral proteins of sequences similar to vasoactive intestinal peptide, Biull Eksp Biol
Med. Apr; 111(4): 371-3. Russian.
7. Brodsky LI, Vassilyev AV, Kalaydzidis YL, Osipov RL, Tatuzov RL, Feranchuk SI (1992)
GeneBee: The program package for biopolymer structure analysis. DIMACS series in discrete
mathematics and computer science of American Mathematical Society, 8: 127-139
8. Leontovich AM, Brodsky LI, Gorbalenya AE (1993) Construction of the full local similarity
map for two biopolymers, Biosystems, 30(1-3): 57-63.
9. Brodsky LI, Drachev AL, Leontovich AM, Feranchuk SI (1993) A novel method of multiple
alignment of biopolymer sequences, Biosystems, 30(1-3): 65-79.
10. Kanapin A, Brodsky L, Ilyn Yu (1993) Regions of 3D similarity in potential ORF1 products
of mobile genetic elements of different classes.
Proceedings of the 1993 Miami BioTechnology Symposium, 3: 128-129
11. Brodskii LI, Ivanov VV, Kalaidzidis IaL, Leontovich AM, Nikolaev VK, Feranchuk SI,
Drachev VA (1995) GeneBee-NET: An Internet based server for biopolymer structure analysis,
Biochemistry (Moscow) 60(8): 1221-30. Russian.
12. Nikolaev VK, Leontovich AM, Drachev VA, Brodsky LI (1997) The refinement of the motif
multiple alignment by iterative dynamic programming, Biochemistry (Moscow), 62: 677-682
13. Leontovich AM, Brodsky LI, Drachev VA, Nikolaev VK (2002) Adaptive algorithm of
automated annotation, Bioinformatics,18(6): 838-44.
14. Mor O, Nativ O, Stein A, Novak L, Lehavi D, Shiboleth Y, Rozen A, Berent E, Brodsky L,
Feinstein E, Rahav A, Morag K, Rothenstein D, Persi N, Mor Y, Skaliter R, Regev A. (2003)
Molecular analysis of transitional cell carcinoma using cDNA microarray, Nature(Oncogene),
22(48): 7702-10.
15. Brodsky L, Leontovich A, Shtutman M, Feinstein E (2004) Identification and Handling of
Artifactual Gene Expression Profiles Emerging in Microarray Hybridization Experiments, Nucleic
Acid Research, 32: 4, e46, 1-12.
16. Brodsky, L., Jacob-Hirsch, J., Avivi, A., Trakhtenbrot, L., Zeligson S., Amariglio, N., Paz,
A., Korol,Band M.A.,A. Rechavi, G. Nevo, E. (2005)Evolutionary regulation of the blind
subterranean mole rat, Spalax , revealed by genome wide gene expression, PNAS, 102(47):
17047-17052
17. Sanda, C., Weitzel, P., Tsukahara, T., Schaley, J., Edenberg, H.J., Stephens, M.A.,
McClintick, J.N., Blatt, L.M., Lang Li, Brodsky L., Taylor, M.W.(2006) Differential gene induction
by type I and type II interferons and their combination, Journal of Interferon & Cytokine
Research, 26: 462-472
18. Avivi A., Brodsky L., Nevo E., Band M.R. (2006) Differential expression profiling of the
blind subterranean mole rat Spalax ehrenbergi superspecies: bio-prospecting for hypoxia
tolerance, Physiological Genomics, 27: 54-64.
19. G.Peleg, G.Katzir, O.Peleg, M.Kamara, L.Brodsky, H.Hel-Or, D.Keren, and E.Nevo (2006)
Hereditary family signature of facial expression, PNAS, 103(43): 15921–15926
20. Taylor MW, Tsukahara T, Brodsky L, Schaley J, Sanda C, Stephens MJ, McClintick JN,
Edenberg HJ, Li L, Tavis JE, Howell C, Belle SH.(2007) Changes in gene expression during
pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders
pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders
from nonresponders to antiviral therapy. J Virol. 2007 Apr;81(7):3391-401
21. Katerina Selezska, Leonid Brodsky & Eviatar Nevo, (2007) Adaptive growth rates of fungi
from Aspergillus niger group from contrasting environments: Dead Sea and “Evolution Canyon”
I (Israel) under different osmostress, MYCOLOGIA BALCANICA ,4:51-60 2007
*22. Leonid I. Brodsky, Wahed Abdus, Jia Li, John E. Tavis, and Milton W. Taylor (2007) A
Novel Unsupervised Method to Identify Genes Important in the Anti-viral Response: Application
to Interferon/Ribavirin in Hepatitis C Patients, PLoS ONE 2(7): e584
23. G. Peleg, G. Katzir, O. Peleg, M. Kamara, L. Brodsky, H. Hel-Or, D. Keren, and E. Nevo
(2009) Facial expressions in various emotional states in congenitally blind and sighted subjects,
Israel Journal of Ecology & Evolution 55(1): 11-30
24. Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman AH, Raskina O (2010).
Transposable elements in a marginal plant population: temporal fluctuations provide new
insights into genome evolution of wild diploid wheat. Mobile DNA, 1:6
25. Aviv DeMorgan, Leonid Brodsky, Yefim Ronin, Eviatar Nevo, Abraham Korol, Yechezkel
Kashi (2010) Genome-wide analysis of DNA turnover and gene expression in
stationary phase Saccharomyces cerevisiae, Microbiology, doi:
10.1099/mic.0.035519-0
26. Brodsky L, Kogan S, BenJacob E, Nevo E (2010) An application of a binary search
algorithm to analysis of whole genome data, PNAS, 107(39): 16893-16898
27. Brodsky L, Moussaieff A, Shahaf N, Aharoni A, and Rogachev I (2010) Evaluation of peak
picking quality in LC-MS metabolomics data, Analytical Chemistry, 82(22):9177-9187
28. Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L,
Leshkowitz D, Galatenko V, Nikolaev V, Mugasimangalam RC , Bransburg-Zabary S, Gutnick
DL, Lancet D, Ben-Jacob E (2010) Genome sequence of the pattern forming Paenibacillus
vortex bacterium reveals potential for thriving in complex environments, BMC Genomics 2010,
11:710 doi:10.1186/1471-2164-11-710
29. Moing A, Aharoni A, Biais B, Rogachev I, Meir S, Brodsky L, Allwood JW, Erban A, Dunn
WB, Kay L, de Koning S, de Vos R, Jonker H, Mumm R, Deborde C, Maucourt M, Bernillon S,
Gibon Y, Hansen TH, Husted S, Goodacre R, Kopka J, Schjoerring J, Rolin D, Hall RD
(2011) Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental
combinatorial metabolomics, New Phytologist, 190:3, 683–696, DOI: HYPERLINK
"http://dx.doi.org/10.1111/j.1469-8137.2010.03626.x" 10.1111/j.1469-8137.2010.03626.x
30. Raskina O, Brodsky L, Belyayev A (2011) Tandem repeats on an eco geographical scale:
outcomes from the genome of Aegilops speltoides, Chromosome Research, DOI
10.1007/s10577-011-9220-9
31. A. V. Gasparian, C. A. Burkhart, A.A. Purmal, L. Brodsky, M. Pal, M. Saranadasa, D. A.
Bosykh, M Commane, O. A. Guryanova, S. Pal, A. Safina, S. Sviridov, I. E Koman, A. A.
Komar, A. V. Gudkov and K. V. Gurova (2011) Curaxins: Anticancer Compounds that
Simultaneously Suppress NF-kB and Activate p53 through depletion of functional “Facilitate
Chromatin Transcription” (FACT) Complex, Science Translational Medicine, 3:(95): 95ra74
Hosid E, Brodsky L, Kalendar R, Raskina O, Belyayev A (2012) Diversity of LTR
retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops
speltoides. Genetics 190:263-274
33. Sirota-Madi A, Olender T, Helman Y, Brainis I, Finkelshtein A, Roth D, Hagai E, Leshkowitz
D, Brodsky L, Galatenko V, Nikolaev V, Gutnick DL, Lancet D, Ben-Jacob E. (2012) Genome
Sequence of the Pattern-Forming Social Bacterium Paenibacillus dendritiformis C454 Chiral
Morphotype. J Bacteriol. 194(8):2127-2128
34. Leonova K, Lipchick B, Brodsky L, Komarova E, and Gudkov A (2012) p53 as a guardian
of genomic junk: A novel role for p53 in epigenetic silencing of retroelements, Cancer
Research, 72 (8), Supplement 1, doi: 10.1158/1538-7445.AM2012-2959
35. Bolen C, Robek M, Brodsky L, Schulz V, Lim JK, Taylor M, and Kleinstein S (2013)The
Blood Transcriptional Signature of Chronic Hepatitis C Virus Is Consistent with an Ongoing
Interferon-Mediated Antiviral Response, Journal of Interferon & Cytokine Research, Vol. 33,
No. 1: 15-23
36. Leonova KI, Brodsky L, Lipchick B, Pal M, Novototskaya L, Chenchik AA, Sen GC,
Komarova EA and Gudkov AV (2013) p53 cooperates with DNA methylation and a suicidal
interferon response to maintain epigenetic silencing of repeats and non-coding RNAs, PNAS
110:22-23
37. A. Moussaieff, I. Rogachev, L. Brodsky, S. Malitsky, T. W. Toal, H. Belcher, M. Yativ, S. M.
Brady , P. N. Benfey, A. Aharoni (2013) High Resolution Metabolic Mapping of Cell Types in
Plant Roots, PNAS, 110(13):E1232-41, doi:10.1073/pnas.1302019110
38. D. Roth, A. Finkelshtein, C. Ingham, Y. Helman, A. Sirota-Madi, L. Brodsky, and E. Ben-
Jacob (2013) Identification and characterization of a highly motile and antibiotic refractory
subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex, DOI:
subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex, DOI:10.1111/1462-2920.12160 Statistics and mathematical modeling (peer-review journals): 1. Brodsky LI, Maloletkin GN, Melnikov NN (1976) The package of programs for construction of
main effects factorial designs. Sistemy i sredstva avtomatizatzii nauchnykh issledovanii,
Moscow, 112-113. Russian.
2. Brodsky LI, Brodsky VZ. (1977) Qualities of geometrical factorial designs. Moscow State
University series in regression experiments, 85-102. Russian.
3. Brodsky LI, Brodsky VZ, Maloletkin GN, Melnikov NN (1978) On the computer catalogue of
factorial designs. Voprosy kibernetiki. 47: 6-23. Russian.
4. Brodsky VZ, Brodsky LI, Smiryagina TG. On the one method of G-matrix inversion in
factorial experiments. Voprosy kibernetiki, 47: 24-29. Russian.
5. Brodsky LI (1978) The theorems on the bundles of parallel planes for linked sets of
geometrical designs. Voprosy kibernetiki, 47: 64-68. Russian.
6. Brodsky VZ, Brodsky LI, Maloletkin GN, Melnikov NN (1980) The package of programs for
design of experiments, Voprosy kibernetiki, 73; 138-157. Russian.
7. Barabasheva YuM, Brodsky LI, Budilova EV, Devyatkova GN, Nosov VN, Terehin AT (1982)
Numerical modeling of transfer processes in North Caspian ecosystem, Biologiya, 22: 137-138.
Russian.
1. Brodsky VZ, Brodsky LI, Golikova TI, Nikitina EP, Panchenko LA (1982) Tables of
experimental designs for factorial and polynomial models. Metallurgia, Moscow. 1982. Russian.
2. Brodsky LI, Golikova TI, Gorsky VG, Granovsky YuV, Dujenko VS, Maksimov VN, Mikeshina
NG, Nikitina EP, Nosov VN (1991) Design of biological and agricultural experiments. Moscow
State University, Moscow, 1991. Russian.
3. Fedorov VD, Brodsky LI, Golikova TI, Myatlev VD, Nosov VN, Terehin AT, Levich AP (1984)
Ecological and mathematical modeling of biological productivity for USSR internal seas.
Moscow State University, Moscow, Russian.
4. Barabasheva YuM, Brodsky LI, Golikova TI, Devyatkova GN, Nosov VN, Panchenko LA.
(1988) Numerical and statistical modeling of North Caspian sea ecosystem. Biologiya okeana,
33-40. Russian.
Conference presentations and technical reports: 1. Vassilyev AD, Osipov YuS, Brodskiy LI, Drachev AL, Leontovich AM, Tatuzov RL, Adzhubei
AA. (1990)Sequence analysis of biopolymers by parallel computations, Proceedings of the
International Conference on modelling and computer methods in molecular biology and
genetics,
Novosibirsk, 1990.
2. Brodsky LI, Drachev VA, Feranchuk SI, Levin IV, Nikolaev VK, Osipov YuS. User
customized genetic database screening on the server.
ADBIS'96 Proceedings on Advances in Databases and Information System. 1996; 58-60.
3. S. Rashi-Elkeles, A. Regev, R. Elkon, R. Sharan, N. Zak, L. Brodsky, A. Kamsler, A.
Leontovitch, N. Weisman, D. Leshkovitz, O. Mor, A. Barzilai, E. Feinstein, R. Shamir, Y. Shiloh,
A. Bar-Shira Constitutive Response to Genotoxic Stress in Atm-Deficient Thymus and
Cerebellum,
Technical report, Tel Aviv University, 2000.
4. Brodsky L, Kositzky M, Leontovich A, Kalaidzidis Y, Shtutman M, Feinstein E. Gene
Expression Analysis Tools. Weizmann Institute of Science, AIBS'02 conference. 2002 (poster)
5. Brodsky L, Shtutman M, Leontovich A, Feinstein E. Detections of genes with "non-
biological" expression profiles. Technion, AIBS'03 conference, 2003 (poster)
6. L. Brodsky, Weining Song, A. Bolshoy, E. Trifonov, E. Nevo
6. L. Brodsky, Weining Song, A. Bolshoy, E. Trifonov, E. Nevo
The correction of massive artifacts in microarray data,
Hebrew University, IBS2004 conference, 2004 (poster)
7. M. R. Band, L. Brodsky, A. Joel, E. Nevo, A. Avivi, Comparative Gene Expression Between
Rat and Subterranean Blind Mole Rat of the Spalax ehrenbergi Superspecies Under Hypoxic
Conditions, Plant and Animal Genome XIII Conference, San Diego, California January 2005
(poster)
8. L. Brodsky, A. D. Makowsky, and N. Ben-Tal, Detection of Functional Regions in Proteins by
“Linearized” Representation of Three Dimensional Structures, Ben-Gurion University, Israel,
IBS2005 conference, 2005 (poster)
9. A. Avivi, L. Brodsky, E. Nevo, M.R. Band,
Differential Expression Profiling Of The Blind Subterranean Mole Rat Spalax ehrenbergi
Superspecies, Bio-Prospecting For Hypoxia Tolerance, Plant and Animal Genome XIV
Conference, San Diego, California January 2006
10. L.I.Brodsky and M.W.Taylor, Linkage of Viral Titer to Gene Expression in Hepatitis C
Patients Treated with Interferon/Ribavirin, International meeting of the interferon and cytokine
societies, Vienna, 2006 (poster)
11. L.I.Brodsky and M.W.Taylor, Linkage of Viral Titer to Gene Expressionin Hepatitis C
Patients: An unsupervised method, Bar-Ilan University, Israel, IBS06 Conference, 2006 (poster)
12. Krugman, T., Z. Peleg, Y. Saranga, B. Chalhoub, V. Chague, S. Balzergue, L. Brodsky,
A.B. Korol, E. Nevo and T. Fahima. Identification of potential candidate genes for drought
resistance in wild emmer wheat by microarray analysis. (Abstract). The Aaronsohn–ITMI
International Conference. 16-20 April, 2007, Tiberias on the Sea of Galilee, Israel.
13. Brodsky L., Kossover O., BenJacob E., Korol A., and Nevo E.,
Genome Transcription Divergent Patterns Of Ricotia Lunaria On Opposite Slopes Of
"Evolution Canyon" Revealed By Tiling Array Hybridizations, Plant & Animal Genomes
Conference (PAG-XVI poster), San Diego, January, 2008
14. Brodsky L.I., Divergent patterns Of Ricotia Lunaria on opposite slopes Of "Evolution
Canyon" revealed by full genome (tiling) array hybridizations, Lecture on the 5th Congress of
FASEB (ILANIT), Eilat, Israel, 2008, January 28-31
15. Brodsky Leonid, Rogachev Ilana, Venger Ilya, Malitsky Sergey and Aharoni Asaph,
MetaboStat: post ion-identification analysis of LC/GC-MS data, IsrAnalitica2009 conference,
Tel Aviv, January 2009 (the poster Third award)
16. Brodsky Leonid, BenTal Nir, BenJacob Eshel, and Nevo Eviatar An application of “divide-
and-conquer” algorithm to analysis of whole genome tiling array data, Israel, Weizmann
Institute of Science, IBS09 Conference, 2009 (poster)
17. Brodsky Leonid, Analysis and integration of whole genome data, lecture at the Workshop
on Mechanisms Controlling Flower Development, PARADOR DE AiguaBLAVA, GIRONA;
SPAIN, 8-12 June 2009
18. Brodsky Leonid, BenTal Nir, Kogan Simon, BenJacob Eshel, and Nevo Eviatar An
application of the binary search like algorithm to analysis of whole genome regulation, Lecture
on the 1st Workshop of EU COST Action TD0801 “Statistical challenges on the 1000 euro
genome sequences in plants”, Barcelona, Spain, 4-5 October 2009
19. Brodsky Leonid, Rogachev Ilana, and Aharoni Asaph, Advanced quality control and
analysis of LC-MS metabolomics data, Research Workshop of the Israel Science Foundation
“Metabolism, Metabolomics and Metabolic Engeneering in Plants”, Ein-Gedi, Israel, 1-4
November 2009
20. Ilana Rogachev, Leonid Brodsky, Arieh Moussaieff, Liron Feldberg, Sergey Malitsky and
Asaph Aharoni RECENT DEVELOPMENTS IN PLANT METABOLOMICS, Keynote Lecture:
IsrAnalytica2010, the 13th Annual Meeting of the Israel Analytical Chemistry Society, January
19-20, 2010
21. Brodsky L, Moussaieff A, Aharoni A, and Rogachev I, Normalization and Quality Control of
LC-MS Metabolomics Data, The 13th Israeli Bioinformatics Symposium, April 6, 2010 (poster)
22. Brodsky L, Moussaieff A, Aharoni A, and Rogachev I, Normalization and Quality Control of
LC-MS Metabolomics Data, The 2nd Workshop of EU COST Action TD0801, May 20 & 21,
2010 (poster and lecture)
23. Rogachev I, Meir I, Brodsky L, Moing A, and Aharoni A, LC-MS-based Metabolomics
Analysis of Semi-polar Compounds in Diverse Melon Fruit Species and Layers, The 1st Middle
Eastern and Mediterranean Sea Region Countries Mass Spectrometry Workshop, Weizmann
Institute of Science, October 17-22, 2010 (poster)
24. Brodsky L, Rogachev I, and Aharoni A, Replicate based QC and Normalization of LC-MS
Metabolomics Data, The 1st Middle Eastern and Mediterranean Sea Region Countries Mass
Spectrometry Workshop, Weizmann Institute of Science, October 17-22, 2010 (poster)
25. Brodsky L, Network of mutual regulations for flowering time genes, SysFlo/Bloomnet
25. Brodsky L, Network of mutual regulations for flowering time genes, SysFlo/Bloomnet
conference,Max-Plant Institute, Berlin, Germany, February 8-10, 2011 (lecture)
26. Brodsky L, Aharoni A, BenJacob E, Nevo E, Korol A, Bi-clustering genome-wide
association analysis of phenotypes, 3nd Workshop of EU COST Action TD0801 “Statistical
challenges on the 1000 euro genome sequences in plants”, Toulouse, France, 14-15 April,
2011
27. Mamrut S, Harony H, Brodsky L, Wagner S, DNA Methylation is Directly Involved in the
Transcription Regulation of the Oxytocin Receptor Gene, 9th World Congress on
Neurohypophysial Hormones (WCNH 2011), Northeastern University, Boston, USA, July 27-30,
2011 (poster)
28. Brodsky L. A binary search (BS) approach to segmentation of a signal profile: applications
to the whole genome analysis, quality control in metabolomics, and genome wide SNP/traits
associations, Invited lecture at University Of California (San Francisco, USA), Department of
Microbiology and Immunology, October 13, 2011
29. Brodsky L. Landscape segmentation and omics data integration, Invited lecture at
Brandeis university (Boston, USA), Department of Biology, October 18, 2011

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