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1. Hebbar S, Panzade G, Vashisht AA, Wohlschlegel JA, Veksler-Lublinsky I, Zinovyeva A (2022).  Functional identification of microRNA-centered complexes in C. elegans. Scientific Reports 12, 7133. [Link]
   
2. Duan Y, Veksler-Lublinsky I, Ambros V (2022). Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA. Cell Reports 39 (4), 110745. 
3. Ben Or G and Veksler-Lublinsky I (2021). Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. BMC Bioinformatics 22, 264.
4. Degani G, Veksler-Lublinsky I, Meerson A (2021). Markers of Genetic Variation in Blue Gourami (Trichogaster trichopterus) as a Model for Labyrinth Fish. Biology 10(3):228.
5. Vieux KF, Prothro KP, Kelley LH, Palmer C, Maine EM, Veksler-Lublinsky I, McJunkin K (2021). Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans. Nucleic Acids Research.
6. Cohen s, Rokach L, Motro Y, Moran-Gilad J, Veksler-Lublinsky I (2021). minMLST: machine learning for optimization of bacterial strain typing. Bioinformatics, 37(3), 303-311.
7. Vasquez-Rifo A*, Veksler-Lublinsky I*, Cheng Z, Ausubel FM, and Ambros V (2019). The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans. Genome Biology, 20 (1), 1-22 (* equal contribution and co-corresponding authors).
8. Li L, Veksler-Lublinsky I, Zinovyeva A (2019). HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development. PLoS Genetics. 15(10):e1008067. 
9. Jonathan Engel, Isana Veksler-Lublinsky* and Michal Ziv-Ukelson* (2019). Constrained gene block discovery and its application to prokaryotic genomes. J Comput Biol. 26(7):745-766. (*Co-corresponding Authors)
10. Eilam-Frenkel B, Naaman H, Brkic G, Veksler-Lublinsky I, Rall G, Shemer-Avni Y, Gopas J (2018). MicroRNA 146-5p, miR-let-7c-5p, miR-221 and miR-345-5p are differentially expressed in Respiratory Syncytial Virus (RSV) persistently infected HEp-2 cells.Virus Res 251:34-39.  
11. Naaman H, Rall G, Matullo C, Veksler-Lublinsky I, Shemer-Avni Y, Gopas J (2017). MiRNA-124 is a link between measles virus persistent infection and cell division of human neuroblastoma cells. PLoS One 12(10):e0187077.
12. Ren Z, Veksler-Lublinsky I, Morrissey D and Ambros V (2016). Staufen Negatively Modulates microRNA Activity in C. elegans. G3 3;6(5):1227-37.
13. Zinovyeva AY*, Veksler-Lublinsky I*, Vashisht AA, Wohlschlegel JA and Ambros V (2015). C. elegans ALG-1 antimorphic mutations uncover functions for Argonaute in microRNA guide strand selection and passenger strand disposal. Proc Natl Acad Sci USA 112(38):E5271-80 (* equal contribution).
14. Sterling CH, Veksler-Lublinsky I and Ambros V (2014). An efficient and sensitive method for preparing cDNA libraries from scarce biological samples. Nucleic Acids Res 9;43(1):e1.
15. Ward J*, Kanchagar C*, Veksler-Lublinsky I*, Lee RC*, McGill MR, Jaeschke H, Curry SC and Ambros V (2014). Circulating microRNA profiles in human patients with acetaminophen hepatotoxicity or ischemic hepatitis. Proc Natl Acad Sci USA 111(33):12169-74. (* equal contribution) 
16. Veksler-Lublinsky I, Shemer-Avni Y, Meiri E, Bentwich Z, Kedem K and Ziv-Ukelson M (2012). Finding quasi-modules of human and viral miRNAs: case study in HCMV. BMC Bioinformatics, 13:322.
17. Meshesha MK*, Veksler-Lublinsky I*, Isakov O, Reichenstein I, Shomron N, Kedem K, Ziv-Ukelson M, Bentwich Z and Shemer-Avni Y (2012). The microRNA Transcriptome of Human Cytomegalovirus (HCMV). The Open Virology Journal, 6: 38-48.   (* equal contribution) 
18. Tuller T*, Veksler-Lublinsky I*, Gazit N, Kupiec M, Ruppin E and Ziv-Ukelson M (2011). Composite effects of gene determinants on the speed and density of ribosomes. Genome Biology, 12:R110. (* equal contribution)
19. Veksler-Lublinsky I, Shemer-Avni Y, Kedem K and Ziv-Ukelson M (2010). Gene bi-targeting by viral and human miRNAs. BMC Bioinformatics, 11:249.
20. Veksler-Lublinsky I, Barash D, Avisar C, Troim E, Chew P and Kedem K (2008). FASH: A web application for nucleotides sequence search. Source Code for Biology and Medicine 3:9.
21. Cohen A, Bocobza S, Veksler  I, Gabdank I, Kedem K, Shapira M, Aharoni  A, Nudler E and Barash D (2008). Computational identification of three-way junctions in folded RNAs: A case study in Arabidopsis. In Silico Biology 8(10).
22. Veksler-Lublinsky I, Ziv-Ukelson M, Barash D and Kedem K (2007). A structure based flexible search method for ncRNA motifs. Journal of Computational Biology, 14(7): 908-926.