Publications

2025

2025

EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology

A. Monziani, J.P. Unfried, T. Cvetanovic and I. Ulitsky. EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology. Preprint at bioRxiv.

4

2025

Neuromuscular dysfunction in patient-derived FUSR244RR-ALS iPSC model via axonal downregulation of neuromuscular junction proteins

N. von Kuegelgen, K. Ludwik, S. Mendonsa, C. Roemer, E. Becher, L. Breimann, M. Strauch, T. Mari, S. Mongellaz, B. Zuckerman, F. Efendic, N. Grexa, A. Oliveras-Martinez, A. Woehler, M. Selbach, V. la Bella, I. Ulitsky, M. Chekulaeva. Neuromuscular dysfunction in patient-derived FUSR244RR-ALS iPSC model via axonal downregulation of neuromuscular junction proteins. Nucleic Acids Research Molecular Medicine 2(2) (2025)

2

2025

BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1

A. Monziani, R. Ben-Tov Perry, H. Hezroni, and I. Ulitsky. BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A-HDAC1. Preprint at bioRxiv.

1

2024

2024

Neurodevelopmental Disorder Caused by Deletion of CHASERR, a lncRNA Gene

V.S. Ganesh, K. Riquin,N. Chatron, K.M. Lamar,M.C. Aziz, P. Monin,M. O’Leary, J.K. Goodrich, K.V. Garimella, E. England, E. Yoon, B. Weisburd, F. Aguet, C.A. Bacino, D.R. Murdock, H. Dai, J.A. Rosenfeld,L.T Emrick, S.Ketkar,Undiagnosed Diseases Network, Y. Sarusi, D. Sanlaville, S. Kayani, B. Broadbent, B. Isidor, A. Pengam, B. Cogné, D.G. MacArthur, I. Ulitsky, G.L. Carvill,A. O’Donnell-Luria. Neurodevelopmental Disorder Caused by Deletion of CHASERR, a lncRNA Gene. New England Journal of Medicine 391(16):1511-1518 (2024).

10

2024

Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity

S. Farberov, O. Ziv, J.Y. Lau, R. Ben-Tov Perry, Y. Lubelsky, E. Miska, G. Kudla and I. Ulitsky. Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity. Nature Structural and Molecular Biology (2024)

9

2024

Systematic analysis of the target recognition and repression by the Pumilio proteins

S. Farberov and I. Ulitsky. Systematic analysis of the target recognition and repression by the Pumilio proteins. Nucleic Acids Research, In revision. bioRxiv (2024)

8

2024

ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response

L.Q.J. Lim, L. Adler, E. Hajaj, L.R. Soria, R. Ben-Tov Perry, N. Darzi, R. Brody, N. Furth, M. Lichtenstein, E. Bab-Dinitz, Z. Porat, T. Melman, A. Brandis, S. Malitsky, M. Itkin, Y. Aylon, S. Ben-Dor, I. Orr, A. Pri-Or, R. Seger, Y. Shaul, E. Ruppin, M. Oren, M. Perez, J. Meier, N. Brunetti-Pierri, E. Shema, I. Ulitsky and A. Erez. ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response. Nature Metabolism 6, 1294–1309 (2024)

8

2024

Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression

H. Dunn-Davies, T. Dudnakova, A. Nogara, J. Rodor, A.C. Thomas, E. Parish, P. Gautier, A. Meynert, I. Ulitsky, P. Madeddu, A. Caporali, A. Baker, D. Tollervey, T. Mitic. . Molecular Therapy Nucleic Acids. 35(2): 102173 (2024).

4

2023

2023

Long non-coding RNAs: Definitions, functions, challenges and recommendations.

J. Mattick, P. Amaral, P. Carninci, S. Carpenter, H. Chang, L.L. Chen, R. Chen, C. Dean, M. Dinger, K. Fitzgerald, T. Gingeras, M. Guttman, T. Hirose, M. Huarte, R. Johnson, C. Kanduri, P. Kapranov, J. Lawrence, J. Lee, J. Mendell, T. Mercer, K. Moore, S. Nakagawa, J. Rinn, D. Spector, I. Ulitsky, Y. Wan, J. Wilusz and M. Wu. Nature Reviews Molecular Cell Biology. 24(6):430-447 (2023)

7

2023

Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs.

A. Monziani and I. Ulitsky. Trends in Genetics. 39(12):908-923 (2023)

2023

CENTRE: A gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.

T. Rapakoulia, S.L. Ruiz De Vargas, P.A. Omgba, V. Laupert, I. Ulitsky and M. Vingron. Bioinformatics. 39(11):btad687

2023

The status of the human gene catalogue

P. Amaral, S. Carbonell-Sala, F.N. Vega, T. Faial, A. Frankish, T. Gingeras, R. Guigo, J.L. Harrow, A.G Hatzigeorgiou, R. Johnson, T.D. Murphy, M. Pertea, K.D. Pruitt, S. Pujar, H. Takahashi, I. Ulitsky, A. Varabyou, C.A. Wells, M. Yandell, P. Carninci and S.L. Salzberg. Nature. 622(7981):41-47 (2023)

2023

Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation

R. Ben-Tov Perry, M. Tsoory, M. Tolmasov and I. Ulitsky. Cell Reports 42(10):113168 (2023)

2023

Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma

M.I. Rosenberg, E. Greenstein, M. Buchkovich, M. Mikl, A. Peres, E. Santoni-Rugiu, D. Reshef, A. Salovin, D.L. Gibbs, M.S. Irwin, A. Naranjo, I. Ulitsky, P.A. de Alarcon, V. Weigman, G. Yaari, J.A. Panzer, N. Friedman, J. Maris. Cell Reports. 42(8):112879 (2023).

2023

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus

N. Gil, R. Ben-Tov Perry, A. Tuck, M. Buhler and I. Ulitsky. Cell Reports. 42(6):112569 (2023)

2023

Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn disease, and celiac disease.

T. Braun, K.E. Sosnovski, A. Amir, M. BenShoshan, K.L. VanDussen, R. Karns, N. Levhar, H. Abbas-Egbariya, R. Hadar, G. Efroni, D. Castel, C. Avivi, M.J. Rosen, A.M. Grifiths, T.D. Walters, D.R. Mack, B.M. Boyle, S. Asad Ali, S. R. Moore, M. Schirmer, R.J. Xavier, S. Kugathasan, A.G. Jegga, B. Weiss, C. Mayer, I. Barshack, S. Ben-Horin, I. Ulitsky, A. Beucher, J. Ferrer, J.S. Hyams, L.A. Denson, and Y. Haberman. JCI Insight. 8(14):e170181 (2023)

2023

LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways.

A. Kshirsagar, S.N. Doroshev, A. Gorelik, T. Olender, T. Sapir, D. Tsuboi, I. Rosenhek-Goldian, S. Malitsky, M. Itkin, A. Argoetti, Y. Mandel-Gutfreund, S.R. Cohen, J. Hanna, I. Ulitsky, K. Kaibuchi and O.Reiner. Nature Communications. 14(1):3293 (2023)

2023

Folylpolyglutamate synthetase mRNA G-quadruplexes regulate its cell protrusion localization and enhance cancer cell invasion upon folate repletion.

M. Stark, M. Levin, I. Ulitsky and Y. Assaraf. BMC Biology. 21(1):13 (2023)

2023

Massively parallel identification of mRNA localization elements in primary cortical neurons

S. Mendonsa*, N. von Kügelgen*, S. Dantsuji*, M. Ron*, L. Breimann, A. Baranovskii, I. Lödige, M. Kirchner, M. Fischer, N. Zerna, L. Bujanic, P. Mertins, I. Ulitsky^# and M Chekulaeva^#. Nature Neuroscience. 26(3):394-405 (2023) (* - equal contribution, # - co-corresponding authors)

2023

GATA6-AS1 regulates intestinal epithelial mitochondrial functions, and its reduced expression is linked to intestinal inflammation and less favorable disease course in ulcerative colitis (UC).

K.E. Sosnovski, T. Braun, A. Amir, D. Moshel, M. BenShoshan, K.L. VanDussen, N. Levhar, H. Abbas-Egbariya, K. Beider, R. Ben-Yishay, S. Asad Ali, S.R. Moore, S. Kugathasan, I. Abramovich, E.G. Saar, B. Weiss, I. Barshack, E. Gottlieb, T. Geiger, S. Ben-Horin, I. Ulitsky, J.S. Hyams, L.A. Denson and Y. Haberman. Journal of Crohn’s and Colitis. 17(6):960-971 (2023)

2023

miR-4734 conditionally suppresses ER stress-associated proinflammatory responses

D. Michael, E. Feldmesser, C. Gonen, N. Furth, A. Maman, O. Heyman, A. Argoetti, A. Tofield, A. Baichman-Kass, A. Ben-Dov, D. Benbenisti, N. Chen, R. Rotkopf, F. Ganci, G. Blandino, I. Ulitsky, and M. Oren, FEBS Reports. 597(9):1233-1245 (2023)

2022

2022

Cap-independent translation and a precisely localized RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response. Submitted

B. Slobodin, U. Sehrawat, A. Lev, D. Hayat, B. Zuckerman, D. Fraticelli, A. Ogran, A. Ben-Shmuel, E. Bar-David, H. Levy, I. Ulitsky and R. Dikstein, Aug 2022, Nucleic Acids Research. 14, 50, p. 8080-8092

2022

OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency

L. Bernard, A. Dubois, V. Heurtier, V. Fischer, I. Gonzalez, A. Chervova, A. Tachtsidi, N. Gil, N. Owens, S. Vanormael-Pournin, J.C.R. Silva, I. Ulitsky, M. Cohen-Tannoudji and P. Navarro, Jul 2022, Nucleic Acids Rearch. 13, 50, p. 7367-7379

2022

Substoichiometric action of long noncoding RNAs

J.P. Unfried and I. Ulitsky, May 2022, Nature Cell Biology. 5, 24, p. 608-615

2022

Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs

M. Ron and I. Ulitsky, May 2022, Nature Communications. 1, 13, p. 2481

2022

Unique features of transcription termination and initiation at closely spaced tandem human genes

N. Nissani and I. Ulitsky, Apr 2022, Molecular Systems Biology. 4, 18, p. e10682

2022

Social fear-linked transcriptomics and chromatin alterations - Septal lncRNA Meg3 is involved in social fear in mice

M. Royer, B. Pai, R. Menon, A. Bludau, K. Gryksa, R. Ben-Tov Perry, I. Ulitsky, G. Meister and I. Neumann, Mar 2022, Molecular Psychiatry.

2022

Nucleoporin-93 reveals a common feature of aggressive breast cancers: robust nucleocytoplasmic transport of transcription factors

N. B. Nataraj, A. Noronha, J.S. Lee, S. Ghosh, H. R. M. Raju, A. Sekar, B. Zuckerman, M. Lindzen, E. Tarcitano, S. Srivastava, M. Selitrennik, I. Livneh, D. Drago-Garcia, O. Rueda, C. Caldas, S. Lev, T. Geiger, A. Ciechanover, I. Ulitsky, R. Seger, E. Ruppin and Y. Yarden, Feb 2022, Cell Reports. 8, 38, p. 110418

2022

Discovering functional motifs in long noncoding RNAs

C.J. Ross and I. Ulitsky, Jan 2022, WIREs RNA. p. e1708

2021

2021

Therapy based on functional RNA elements

R. Ben-Tov Perry and I. Ulitsky, Aug 2021, Science. 373, 6555, p. 623-624

2021

Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage

N. Degani, Y. Lubelsky, R. Ben-Tov Perry, E. Ainbinder and I. Ulitsky, Jul 2021, PLoS Genetics. 17, 7, p. e1009681

2021

SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis

Y. Finkel, A. Gluck, R. Winkler, A. Nachshon, R. Winkler, T. Fisher, B. Rozman, O. Mizrahi, Y. Lubelsky, B. Zuckerman, B. Slobodin, Y. Yahalom-Ronen, H. Tamir, I. Ulitsky, T. Israely, N. Paran, M. Schwartz and N. Stern-Ginossar, Jun 2021, Nature. 594, 7862, p. 240-245

2021

The sequence-binding-function axes of an RNA nuclear enrichment element

Y. Lubelsky, B. Zuckerman and I. Ulitsky, May 2021, The EMBO Journal. 40:e106357

2021

The GUL-1 protein binds multiple RNAs involved in cell wall remodeling and affects the MAK-1 pathway in Neurospora crassa.

I. Herold, A. Zolti, M. Garduno-Rosales, Z. Wang, F. Lopez-Giraldez, R. Mouriño-Pérez, J. Townsend, I. Ulitsky and O. Yarden, May 2021, Frontiers in Fungal Biology, section Fungal Physiology and Metabolism.

2021

The evolutionarily conserved long non-coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms

R. L. Mather, A. Parolia, E. Venalainen, S.C. Cho, S. Carson, D.R. Carles, I. Alborelli, D. Lin, E. Jachetti, M.P. Colombo, H. Xue, P. Pucci, X. Ci, C. Hawkes, H. Pandha, I. Ulitsky, C.N. Marconett, L. Quagliata, W. Jiang, I. Romero, Y. Wang and F. Crea, Apr 2021, Molecular Oncology.

2021

MIR503HG loss promotes endothelial-to-mesenchymal transition in vascular disease

J. Monteiro, J. Rodor, A. Caudrillier, J.P. Scanlon, A.M. Spiroski, T. Dudnakova, B. Pflüger-Müller, A. Shmakova, A. von Kriegsheim, L., R.S. Taylor, J.R. Wilson-Kanamori, S.H. Chen, K. Stewart, A. Thomson, T. Mitić, J.D. McClure, J. Iyinikkel, P.W. Hadoke, L. Denby, A.C. Bradshaw, O. Caruso, N.W. Morrell, J.C. Kovacic, I. Ulitsky, N. Henderson, A. Caporali, M.S. Leisegang, R.P. Brandes and A.H. Baker. , Mar 2021, Circulation Research. 8, 128, p. 1173-1190

2021

Novel transcript discovery expands the repertoire of pathologically-associated, long non-coding RNAs in vascular smooth muscle cells

M. Bennett, I. Ulitsky, I. Alloza, K. Vandenbroeck, V. Miscianinov, A.D. Mahmoud, M. Ballantyne, J. Rodor and A.H. Baker, Feb 2021, International Journal of Molecular Science. 3, 22, p. 1484

2020

2020

Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences

C.J. Ross, A. Rom, A. Spinrad, D. Gelbard Solodkin, N. Degani and I. Ulitsky, Dec 2020, Genome Biology. 1, 22, p. 29

2020

SCIRT lncRNA restrains tumorigenesis by controlling transcriptional programs of tumor initiating cells

S. Zagorac, A.de Giorgio, M. Kalisz, A.Dabrowska, M. Kalisz, N. Casas-Vila, P. Cathcart, A. Yiu, S. Ottaviani, N. Degani, Y. Lombardo, A. Tweedie, T. Nissan, K.W. Vance, I. Ulitsky, J. Stebbing and L. Castellano. Nov 2020, Cancer Research. 3, 81, p. 580-593

2020

Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus

H. Hezroni, R. Ben-Tov Perry, N. Gil, N. Degani and I. Ulitsky, Sep 2020, EMBO Reports. 11, 21, p. e51264,

2020

Identification and characterization of key long non-coding RNAs in the auditory system

T. Koffler-Brill, S. Taiber, A. Anaya, M. Bordeynik-Cohen, E. Rosen, L. Kolla, M.W. Kelley, I. Ulitsky and K.B. Avraham, Sep 2020, RNA Biology. Nov 1, p. 1-10

2020

Functional annotation of human long noncoding RNAs via molecular phenotyping

J.A. Ramilowski, C.W. Yip, S. Agrawal, J.C. Chang, Y. Ciani, I.V. Kulakovskiy, M. Mendez, J.L.C. Ooi, J.F. Ouyang, N. Parkinson, A. Petri, L. Roos, J. Severin, K. Yasuzawa, I. Abugessaisa, A. Akalin, I.V. Antonov, E. Arner, A. Bonetti, H. Bono, B. Borsari, F. Brombacher, C.J.F. Cameron, C. Vittorio Cannistraci, R. Cardenas, M. Cardon, H. Chang, J. Dostie, L. Ducoli, A. Favorov, A. Fort, D. Garrido, N. Gil, J. Gimenez, R. Guler, L. Handoko, J. Harshbarger, A. Hasegawa, Y. Hasegawa, K. Hashimoto, N. Hayatsu, P. Heutink, T. Hirose, E.L. Imada, M. Itoh, B. Kaczkowski, A. Kanhere, E. Kawabata, H. Kawaji, T. Kawashima, S.T. Kelly, M. Kojima, N. Kondo, H. Koseki, T. Kouno, A. Kratz, M. Kurowska-Stolarska, A. Tae Jun Kwon, J. Leek, A. Lennartsson, M. Lizio, F. López-Redondo, J. Luginbühl, S. Maeda, V.J. Makeev, L. Marchionni, Y.A. Medvedeva, A. Minoda, F. Müller, M. Muñoz-Aguirre, M. Murata, H. Nishiyori, K.R. Nitta, S. Noguchi, Y. Noro, R. Nurtdinov, Y. Okazaki, V. Orlando, D. Paquette, C.J.C. Parr, O.J.L. Rackham, P. Rizzu, D. Fernando Sánchez Martinez, A. Sandelin, P. Sanjana, C.A.M. Semple, Y. Shibayama, D.M. Sivaraman, T. Suzuki, S.C. Szumowski, M. Tagami, M.S. Taylor, C. Terao, M. Thodberg, S. Thongjuea, V. Tripathi, I. Ulitsky, R. Verardo, I.E. Vorontsov, C. Yamamoto, R.S. Young39, J.K. Baillie, A.R.R. Forrest, R. Guigó, M.M. Hoffman, C.C. Hon, T. Kasukawa, S. Kauppinen, J. Kere, B. Lenhard, C. Schneider, H. Suzuki, K. Yagi, M.J.L. de Hoon, J.W. Shin and P. Carninci, Jul 2020, Genome Research. 30(7):1060-1072

2020

Gene architecture and sequence composition underpin selective dependency of long RNAs on components of the nuclear export pathway

B. Zuckerman, M. Ron, M. Mikl, E. Segal and I. Ulitsky, Jun 2020, Molecular Cell. 79, 2, p. 251-267.e6

2020

Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels.

B. Slobodin, A. Bahat, U. Sehrawat, S. Becker-Herman, B. Zuckerman, A.N. Weiss, R. Han, R. Elkon, R. Agami, I. Ulitsky, I. Shachar, R. Dikstein., Apr 2020, Molecular Cell. 78, 3, p. 434-444.e5

2020

A guide to naming human non‐coding RNA genes

R.L. Seal, L.L. Chen, S. Griffiths‐Jones, T.M. Lowe, M.B. Mathews, D. O'Reilly, A.J. Pierce, P.F. Stadler, I. Ulitsky, S.L. Wolin and E.A. Bruford. A guide to naming human non‐coding RNA genes. , Mar 2020, The EMBO Journal. 39, 6, p. e103777

2020

Regulation of gene expression by cis-acting long noncoding RNAs

N. Gil and I. Ulitsky, Feb 2020, Nature Reviews Genetics. 21, 2, p. 102-117

2020

A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism

M. Pradas-Juni, N. R. Hansmeier, J.C. Link, E. Schmidt, B.D. Larsen, P. Klemm, N. Meola, H. Topel, R. Loureiro, I. Dhaouadi, C.A. Kiefer, R. Schwarzer, S. Khani, M. Oliverio, M. Awazawa, P. Frommolt, J. Heeren, L. Scheja, M. Heine, C. Dieterich, H. Büning, L. Yang, H. Cao, D. F. De Jesus, R.N. Kulkarni, Branko Zevnik, S.E. Tröder, U. Knippschild, P.A. Edwards, R.G. Lee, M. Yamamoto, I. Ulitsky, E. Fernandez-Rebollo, T.Q. de Aguiar Vallim and J.W. Kornfeld, Jan 2020, Nature Communications. 11, p. 644

2020

Long Noncoding RNAs in Development and Regeneration of the Neural Lineage

H. Hezroni, R. Ben Tov Perry and I. Ulitsky, Jan 2020, Cold Spring Harbor Symposia on Quantitative Biology. 84:165-177

2019

2019

Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program

L. Geirsdottir, E. David, H. Keren-Shaul, A. Weiner, S.C. Bohlen, J. Neuber, A. Balic, A. Giladi, F. Sheban, C.A. Dutertre, C. Pfeifle, F. Peri, A. Raffo-Romero, J. Vizioli, K. Matiasek, C. Scheiwe, S. Meckel, K. Mätz-Rensing, F. van der Meer, F. R. Thormodsson, C. Stadelmann, N. Zilkha, T. Kimchi, F. Ginhoux, I. Ulitsky, D. Erny, I. Amit and M. Prinz. , Dec 2019, Cell. 179, 7, p. 1609-1622

2019

In-Cell Identification and Measurement of RNA-Protein Interactions

A. Graindorge, I. Pinheiro, A. Mallory , P. Tsvetkov , N. Gil, C. Carolis, F. Buchholz, I. Ulitsky, E. Heard, M. Taipale and A. Shkumatava, Nov 2019, Nature Communications. 10, 1, p. 5317

2019

Regulation of CHD2 expression by the Chaserr long noncoding RNA is essential for viability

A. Rom, L. Melamed, N. Gil, M. Goldrich, R. Kadir, M. Golan, I. Biton, R. Ben-Tov Perry and I. Ulitsky. , Nov 2019, Nature Communications. 10, 1, p. 5092

2019

Endothelial Function and Dysfunction in the Cardiovascular System: The Long Non Coding Road

J.P. Monteiro, M. Bennett, J. Rodor, A. Caudrillier, I. Ulitsky, and A.H. Baker., Oct 2019, Cardiovascular Research. 115, 12, p. 1692-1704

2019

The Human- and Smooth Muscle Cell-Enriched lncRNA SMILR Promotes Proliferation by Regulating Mitotic CENPF mRNA and Drives Cell-Cycle Progression Which Can Be Targeted

49. A.D. Mahmoud, M.D. Ballantyne, V. Miscianinov, K. Pinel, J. Hung, J. Scanlon, J. Iyinikkel, J. Kaczynski, A.S. Tavares, A.C. Bradshaw, N.L. Mills, D.E. Newby, A. Caporali, G. W. Gould, S.J. George, I. Ulitsky, J.C. Slumier, J. Rodor and A.H. Baker., Jul 2019, Circulation Research. 125, 5, p. 525-551

2019

The EXPANDER integrated platform for transcriptome analysis.

T.A. Hait, A. Maron-Katz, D. Sagir, D. Amar, I. Ulitsky, C. Linhart, R. Sharan, Y. Shiloh, R. Elkon and R. Shamir, Jun 2019, Journal of Molecular Biology. 431, 13, p. 2398-2406

2019

Aging Well With Norad

F. Carvalhal Marques and I. Ulitsky, Apr 2019, eLife. 8, p. e45974

2019

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

C. Ciolli Mattioli, A. Rom, V. Franke, K. Imami, G. Tane, M. Terne; A. Woehler, A. Akalin, I. Ulitsky and M. Chekulaeva. , Mar 2019, Nucleic Acids Research. 47, 5, p. 2560-2573

2019

Predictive models of subcellular localization of long RNAs

B. Zuckerman and I. Ulitsky, Feb 2019, RNA. 25, 5, p. 557-572

2018

2018

Acid-induced downregulation of ASS1 contributes to the maintenance of intracellular pH in cancer.

A. Silberman, O. Goldman, O. Boukobza Assayag, A. Jacob, S. Limanovich, L. Adler, J.S. Lee, R. Keshet, A. Sarver, J. Frug, N. Stettner, S. Galai, E. Persi, K. Bahar Halpern, Y. Zaltsman-Amir, B. Pode-Shakked, R. Eilam, Y. Anikster, S.C.S. Nagamani, I. Ulitsky, E. Ruppin and A. Erez, Dec 2018, Cancer Research. 79 (3): 518–533

2018

Regulation of Neuroregeneration by Long Noncoding RNAs

R. Ben-Tov Perry, H. Hezroni, M.J. Goldrich and I. Ulitsky, Oct 2018, Molecular Cell. 72, 3, p. 553-567.E5

2018

Predicting microRNA targeting efficacy in Drosophila

V. Agarwal, A.O. Subtelny, O. Thiru, I. Ulitsky and D.P. Bartel, Sep 2018, Genome Biology. 19, 1, p. 19(1):152

2018

Production of spliced long noncoding RNAs specifies regions with increased enhancer activity

N. Gil and I. Ulitsky, Jun 2018, Cell Systems. 7, 5, p. 537-547

2018

Altered p53 functionality in cancer-associated fibroblasts contributes to their cancer-supporting features.

S. Arandkar, N. Furth, Y. Elisha, N.B. Nataraj, H. van der Kuip, Y. Yarden, W. Aulitzky, I. Ulitsky, B. Geiger and M. Oren, Jun 2018, PNAS. 115, 25, p. 6410-6415

2018

Interactions between short and long noncoding RNAs

Ulitsky, I, May 2018, FEBS Letters. 592: 2874-2883

2018

Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies

Z. Haimon, A. Volasky, J. Orthgiess, S. Boura-Halfon, D. Varol, A. Shemer, S. Yona, B. Zuckerman, E. David, L. Chappell-Maor, I. Bechmann, M. Gericke, I. Ulitsky and S. Jung, 2018, Nature Immunology. 19, 6, p. 636-644

2018

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

Y. Lubelsky and I. Ulitsky, Mar 2018, Nature. 555, 7694, p. 107-111

2018

SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA

A. Tichon, R. Ben-Tov Perry, L. Stojic and I. Ulitsky, Jan 2018, Genes & Development. 32, 1, p. 70-78

2017

2017

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes

H. Hezroni, R. Ben-Tov Perry, Z. Meir, G. Housman, Y. Lubelsky and I. Ulitsky, I, Feb 2017, Genome Biology. 18, p. 162

2017

The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence elemen

O. Marín-Béjar, A.M. Mas, J. González, D. Martinez, A. Athie, X. Morales, M.Galduroz, I. Raimondi, E. Grossi, S. Guo, A. Rouzaut, I. Ulitsky and M. Huarte, Feb 2017, Genome Biology. 18, 1, p. 202

2017

Analysis of blood-based gene expression in idiopathic Parkinson disease.

R. Shamir, C. Klein, D. Amar, E.J. Vollstedt, M. Bonin, M. Usenovic, Y.C. Wong, A. Maver, S. Poths, H. Safer, J.C. Corvol, S. Lesage, O. Lavi, G. Deuschl, G. Kuhlenbaeumer, H. Pawlack, I. Ulitsky, M. Kasten, O. Riess, A. Brice, B. Peterlin and D. Krainc, Feb 2017, Neurology. 89, 16, p. 1676-1683

2017

Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress

A. Tamarkin-Ben-Harush, J.J. Vasseur, F. Debart, I. Ulitsky and R. Dikstein, Feb 2017, eLife. 6,

2017

Efficient and Accurate Translation Initiation Directed by TISU Involves RPS3 and RPS10e Binding and Differential Eukaryotic Initiation Factor 1A Regulation

O. Haimov, H. Sinvani, F. Martin, I. Ulitsky, R. Emmanuel, A. Tamarkin-Ben-Harush, A. Vardy and R. Dikstein, Feb 2017, Molecular and Cellular Biology. 37

2017

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems

K. Ushakov, T. Koffler-Brill, A. Rom, K. Perl, I. Ulitsky and K.B. Avraham, KB, Feb 2017, Scientific Reports. 7

2016

2016

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

G. Housman and I. Ulitsky, Feb 2016, BBA - Gene Regulatory Mechanisms. 1859, p. 31-40

2016

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

A. Tichon, N. Gil, Y. Lubelsky, T. Havkin Solomon, D. Lemze, S. Itzkovitz, N. Stern-Ginossar and I. Ulitsky, Feb 2016, Nature communications. 7

2016

LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer

A. Sas-Chen, M.R. Aure, L. Leibovich, … , I. Ulitsky, S. Diederichs, S. Wiemann, Z. Yakhini, V.N. Kristensen, A.L. Børresen-Dale and Y. Yarden, Feb 2016, EMBO Molecular Medicine. 8,

2016

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

Ulitsky, I, Feb 2016, Nature Reviews Genetics. 17, p. 601-614

2016

The functions of long noncoding RNAs in development and stem cells

R Ben-Tov Perry and I. Ulitsky, Feb 2016, Development. 143, p. 3882-3894

2015

2015

Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis

S. Rabinovich, L. Adler, K. Yizhak, A. Sarver, A. Silberman, S. Agron, N. Stettner, Q. Sun, A. Brandis, D. Helbling, S. Korman, S. Itzkovitz, D. Dimmock, I. Ulitsky, S.C.S Nagamani, E. Ruppin and A. Erez, Feb 2015, Nature. 527, p. 379

2015

Nuclear Retention of mRNA in Mammalian Tissues

K. Bahar-Halpern, I. Caspi, D. Lemze, M. Levy, S. Landen, E. Elinav, I. Ulitsky and S. Itzkovitz, Feb 2015, Cell Reports. 13, p. 2653-2662

2015

Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor

Y. Enuka, M. Lauriola, M.E. Feldman, A. Sas-Chen, I. Ulitsky and Y. Yarden, Feb 2015, Nucleic Acids Research. 44, p. 1370-1383

2015

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

H. Hezroni, D. Koppstein, M.G. Schwartz, A. Avrutin, D.P. Bartel and I. Ulitsky, Feb 2015, Cell Reports. 11, p. 1110-1122

2015

Recurrent inactivating RASA2 mutations in melanoma

R. Arafeh, N. Qutob, R. Emmanuel, … , I. Ulitsky, G.J. Mann, R.A. Scolyer, N.K. Hayward and Y. Samuels, Feb 2015, Nature Genetics. 47, p. 1408

2013

2013

lincRNAs: Genomics, Evolution, and Mechanisms

I. Ulitsky and D.P. Bartel, Feb 2013, Cell. 154, p. 26-46

2013

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

V.C. Auyeung, I. Ulitsky, S.E. McGeary and D.P. Bartel, Feb 2013, Cell. 152, p. 844-858

2012

2012

Extensive alternative polyadenylation during zebrafish development

I. Ulitsky, A. Shkumatava, C. Jan, A.O. Subtelny, D. Koppstein, H. Sive and D.P. Bartel, Feb 2012, Genome Research. 22, p. 2054-2066

2011

2011

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

I. Ulitsky*, A. Shkumatava*, C. Jan, H. Sive and D.P. Bartel, DP, Feb 2011, Cell. 147, p. 1537-1550

2011

A Point Mutation in Translation Initiation Factor eIF2B Leads to Function- and Time-Specific Changes in Brain Gene Expression

L. Marom, I. Ulitsky, Y. Cabilly, R. Shamir and O. Elroy-Stein, Feb 2011, PLoS One. 6,

2011

Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear

T. Elkan-Miller, I. Ulitsky, R. Hertzano, A. Rudnicki, A.A. Dror, D.R. Lenz, R. Elkon, M. Irmler, J. Beckers, R. Shamir and K.B. Avraham, Feb 2011, PLoS One. 6,

2011

Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture

L.C. Laurent, I. Ulitsky, I. Slavin, H. Tran, A. Schork, R. Morey, C. Lynch, J.V. Harness, S. Lee, M.J. Barrero, S. Ku, M. Martynova, R. Semechkin, V. Galat, J. Gottesfeld, J.C. Izpisua Belmonte, C. Murry, H.S. Keirstead, H.S. Park, U. Schmidt, A.L. Laslett, F.J. Muller, C.M. Nievergelt, R. Shamir and J.F. Loring, Feb 2011, Cell Stem Cell. 8, p. 106-118

2011

SPIKE: a database of highly curated human signaling pathways

A. Paz, Z. Brownstein, Y. Ber, S. Bialik, E. David, D. Sagir, I. Ulitsky, R. Elkon, A. Kimchi, K.B. Avraham, Y. Shiloh, R. Shamir, Feb 2011, Nucleic Acids Research. 39, p. D793-D799

2010

2010

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

I. Ulitsky, A. Krishnamurthy, R.M. Karp and R. Shamir, Feb 2010, PLoS One. 5,

2010

Towards computational prediction of microRNA function and activity

I. Ulitsky, L.C. Laurent and R. Shamir, Feb 2010, Nucleic Acids Research. 38

2010

A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking

P.S. Aguilar, F. Fröhlich, M. Rehman, M. Shales, I. Ulitsky, A. Olivera-Couto, H. Braberg, R. Shamir, P. Walter, M. Mann, C.S. Ejsing, N.J. Krogan and T.C. Walther. A, Feb 2010, Nature Structural & Molecular Biology. 17, p. 901-U175

2010

Propagation of human embryonic and induced pluripotent stem cells in an indirect co-culture system

S. Abraham, S.D. Sheridan, L.C. Laurent, K. Albert, C. Stubban, I. Ulitsky, B. Miller, J.F. Loring and R.R. Rao, Feb 2010, Biochemical and Biophysical Research Communications. 393, p. 211-216

2010

Different sets of QTLs influence fitness variation in yeast

G.H. Romano, Y. Gurevich, O. Lavi, I. Ulitsky, R. Shamir and M. Kupiec, Feb 2010, Molecular Systems Biology. 6,

2010

Expander: from expression microarrays to networks and functions

I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh and R. Shamir, Feb 2010, Nature Protocols. 5, p. 303-322

2010

Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences

Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir, Feb 2010, RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, PROCEEDINGS. 6044, p. 578-579

2009

2009

Towards accurate imputation of quantitative genetic interactions

I. Ulitsky, N.J. Krogan and R. Shamir, Feb 2009, Genome Biology. 10,

2009

Identifying functional modules using expression profiles and confidence-scored protein interactions

I. Ulitsky and R. Shamir, Feb 2009, Bioinformatics. 25, p. 1158-1164

2009

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir, Feb 2009, Nucleic Acids Research. 37, p. 1566-1579

2008

2008

Regulatory networks define phenotypic classes of human stem cell lines

F.J. Mueller, D. Kostka, L. Laurent, I. Ulitsky, R. Williams, C. Lu, I.H. Park, M.S. Rao, R. Shamir, P.H. Schwartz, N.O. Schmidt and J.F. Loring, Feb 2008, Nature. 455, p. 401-U55

2008

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

I. Ulitsky, T. Shlomi, M. Kupiec and R. Shamir, Feb 2008, Molecular Systems Biology. 4,

2008

Comprehensive MicroRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence

L.C. Laurent, J. Chen, I. Ulitsky, F.J Mueller, C. Lu, R. Shamir, J.B. Fan and J.F. Loring, Feb 2008, Stem Cells. 26, p. 1506-1516

2008

SPIKE - a database, visualization and analysis tool of cellular signaling pathways

R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, M. Weisz, N. Orlev, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh and R. Shamir, Feb 2008, BMC Bioinformatics. 9,

2008

MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data

I. Ulitsky, I. Gat-Viks and R. Shamir, Feb 2008, Genome Biology. 9,

2008

Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles

I. Ulitsky, R.M. Karp and R. Shamir, Feb 2008, RECOMB PROCEEDINGS. 4955, p. 347-359

2007

2007

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks

I. Ulitsky and R. Shamir, Feb 2007, Molecular Systems Biology. 3,

2007

Network-based prediction of protein function

R. Sharan, I. Ulitsky and R. Shamir, Feb 2007, Molecular Systems Biology. 3,

2007

Identification of functional modules using network topology and high-throughput data

I. Ulitsky and R. Shamir, Feb 2007, BMC Systems Biology. 1,

2006

2006

The average common substring approach to phylogenomic reconstruction

I. Ulitsky, D. Burstein, T. Tuller and B. Chor, Feb 2006, Journal of Computational Biology. 13, p. 336-350

2005

2005

Information theoretic approaches to whole genome phylogenies

D. Burstein, I. Ulitsky, T. Tuller and B. Chor, Feb 2005, RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, PROCEEDINGS. 3500, p. 283-295