Ultrafast data mining of molecular assemblies in multiplexed high-density super-resolution images.

Yandong Yin, Wei Ting Chelsea Lee, and Eli Rothenberg.

Nature Communications 2019 10(1):119.

Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes.

Hannah L Klein, Kenny K.H. Ang, Michelle R. Arkin, Emily C. Beckwitt, Yi-Hsuan Chang, Jun Fan, Youngho Kwon, Michael J. Morten, Sucheta Mukherjee, Oliver J. Pambos, Hafez el Sayyed, Elizabeth S. Thrall, João P. Vieira-da-Rocha, Quan Wang, Shuang Wang, Hsin-Yi Yeh, Julie S. Biteen, Peter Chi, Wolf-Dietrich Heyer, Achillefs N. Kapanidis, Joseph J. Loparo, Terence R. Strick, Patrick Sung, Bennett Van Houten, Hengyao Niu, and Eli Rothenberg.

Microbial Cell 2019 6(1):65-101.

 

BRCA2 controls DNA: RNA hybrid level at DSBs by mediating RNase H2 recruitment.

Giuseppina D’Alessandro, Donna Rose Whelan, Sean Michael Howard, Valerio Vitelli, Xavier Renaudin, Marek Adamowicz, Fabio Iannelli, Corey Winston Jones-Weinert, MiYoung Lee, Valentina Matti, Wei Ting C. Lee, Michael John Morten, Ashok Raraakrishnan Venkitaraman, Petr Cejka, Eli Rothenberg and Fabrizio d’Adda di Fagagna.

Nature Communications 2018 9(1):5376.

Translesion polymerase kappa-dependent DNA synthesis underlies replication fork recovery.

Peter Tonzi, Yandong Yin, Chelsea WT Lee, Eli Rothenberg, and Tony T Huang.

eLife 2018 11 13;7.

 

Novel Imaging Techniques in Cardiac Ion Channel Research.

Esperanza Agullo-Pascual, Alejandra Leo-Macias, Donna R. Whelan, Mario Delmar, and Eli Rothenberg.

In: Thomas D., Remme C. (eds) Channelopathies in Heart Disease.

Cardiac and Vascular Biology Springer, Cham (2018).

Spatiotemporal Dynamics of Homologous Recombination Repair at Single Collapsed Replication Forks.

Donna Whelan, Wei Ting Chelsea Lee, Yandong Yin, Dylan Ofri, Keria Bermudez-Hernandez, Sarah Keegan, David Fenyö
and Eli Rothenberg.

Nature Communications 2018 9(1):3882.

XLF and APLF bind to Ku80 on two remote sites to ensure DNA repair by non-homologous end-joining.

Clement Nemoz, Virginie Ropars, Philippe Frit, Amandine Gontier, Pascal Drevet, Jinchao Yu, Raphaël Guérois, Aurelien Pitois, Audrey Comte, Christine Delteil, Nadia Barboule, Pierre Legrand, Sonia Baconnais, Yandong Yin, Satish Tadi,
Emeline Barbet-Massin, Imre Berger, Eric Le Cam, Mauro Modesti, Eli Rothenberg, Patrick Calsou, and Jean-Baptiste Charbonnier.

Nature Structural and Molecular Biology 2018 (10):971-980.

 

Anosmin1 Shuttles Fgf to Facilitate Its Diffusion, Increase Its Local Concentration, and Induce Sensory Organs.

Wang J, Yin Y, Lau S, Sankaran J, Rothenberg E, Wohland T, Meier-Schellersheim M, Knaut H.

Developmental Cell 2018 09 24; 46(6):751-766.e12.

PARP1-dependent recruitment of the FBXL10-RNF68-RNF2 ubiquitin ligase to
sites of DNA damage controls H2A.Z loading.

Rona G, Roberti D, Yin Y, Pagan JK, Homer H, Sassani E, Zeke A, Busino L, Rothenberg E, Pagano M.

eLife 2018 Jul 9.

 

Mechanosensitive Gene Regulation by Myocardin-Related Transcription Factors is Required
for Cardiomyocyte Integrity in Load-Induced Ventricular Hypertrophy.

Trembley MA, Quijada P, Agullo-Pascual E, Tylock KM, Colpan M, Dirkx RA Jr, Myers JR, Mickelsen DM, de Mesy Bentley K, Rothenberg E, Moravec CS, Alexis JD, Gregorio CC, Dirksen RT, Delmar M, Small EM.

Circulation 2018 May 1. pii.


The Ubiquitin E3/E4 Ligase UBE4A Adjusts Protein Ubiquitylation and Accumulation
at Sites of DNA Damage, Facilitating Double-Strand Break Repair.

Baranes-Bachar K, Levy-Barda A, Oehler J, Reid DA, Soria-Bretones I, Voss TC, Chung D, Park Y, Liu C, Yoon JB, Li W,
Dellaire G, Misteli T, Huertas P, Rothenberg E, Ramadan K, Ziv Y, Shiloh Y.

Molecular Cell 2018 Mar 1;69(5):866-878.


Localized Myosin II Activity Regulates Assembly and Plasticity of the Axon Initial Segment.

Berger SL, Leo-Macias A, Yuen S, Khatri L, Pfennig S, Zhang Y, Agullo-Pascual E, Caillol G, Zhu MS, Rothenberg E,
Melendez-Vasquez CV, Delmar M, Leterrier C, Salzer JL.

Neuron 2018 Feb 7;97(3):555-570.e6. 


Sodium Channel Remodeling in Subcellular Microdomains of Murine Failing Cardiomyocytes.

Rivaud MR, Agullo-Pascual E, Lin X, Leo-Macias A, Zhang M, Rothenberg E, Bezzina CR, Delmar M, Remme CA.

Journal of the American Heart Association 2017 Dec 8;6(12). 
 

A Method for Quantifying Molecular Interactions Using Stochastic Modelling
and Super-Resolution Microscopy.

Keria Bermudez-Hernandez, Sarah Keegan, Donna R. Whelan DR, Dylan A. Reid, Jennifer Zagelbaum,
Yandong Yin, Sisi Ma, Eli Rothenberg*, David Fenyö*.

Scientific Reports 7(1):14882 (2017). PMID: 29093506. 

DNA Ligase IV Guides End-Processing Choice during Nonhomologous End Joining.

Michael P. Conlin, Dylan A. Reid, George W. Small, Howard H. Chang, Go Watanabe, Michael R. Lieber,
Dale A. Ramsden*, Eli Rothenberg*.

Cell Reports 20(12):2810-2819 (2017). PMID: 28930678. 

Plakophilin-2 is required for transcription of genes that control calcium cycling
and cardiac rhythm.

M Cerrone, J Montnach, X Lin X, YT Zhao, M Zhang, E Agullo-Pascual, A Leo-Macias, FJ Alvarado, I Dolgalev,
TV Karathanos, K Malkani, CJM Van Opbergen, JJA van Bavel, HQ Yang, C Vasquez, D Tester, S Fowler, F Liang,
E Rothenberg, A Heguy, GE Morley, WA Coetzee, NA Trayanova, MJ Ackerman, TB van Veen, HH Valdivia,
M Delmar.

Nature Communications 8(1):106 (2017). PMID: 28740174.

SAMHD1 Promotes DNA End Resection to Facilitate DNA Repair by Homologous Recombination.

W Daddacha, AE Koyen, AJ Bastien, PE Head, VR Dhere, GN Nabeta, EC Connolly, E Werner, MZ Madden, MB Daly, EV Minten, DR Whelan, AJ Schlafstein, H Zhang, R Anand, C Doronio, AE Withers, C Shepard, RK Sundaram, X Deng, WS Dynan, Y Wang, RS Bindra, P Cejka, E Rothenberg, PW Doetsch, B Kim, David S Yu.

Cell Reports 20(8):1921-1935 (2017). PMID: 28834754.

Multilevel analyses of SCN5A mutations in arrhythmogenic right ventricular dysplasia/cardiomyopathy suggest non-canonicalmechanisms for disease pathogenesis.

Te Riele AS, Agullo-Pascual E, James CA, Leo-Macias A, Cerrone M, Zhang M, Lin X, Lin B, Rothenberg E, Sobreira NL, Amat-Alarcon N, Marsman RF, Murray B, Tichnell C, van der Heijden JF, Dooijes D, van Veen TA, Tandri H, Fowler SJ, Hauer RN, Tomaselli G, van den Berg MP, Taylor MR, Brun F, Sinagra G, Wilde AA,
Mestroni L, Bezzina CR, Calkins H, Peter van Tintelen J, Bu L, Delmar M, Judge DP.

Cardiovascular Research 113(1):102-111. PMID: 28069705.

Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex
is modulated by DNA end chemistry.

Dylan A. Reid, Michael Conlin, Yandong Yin, Howard Chang, Go Watanabe, Michael Lieber*, Dale  Ramsden*,
and Eli Rothenberg*.

Nucleic Acid Research 45(4):1872-1878 (2017). PMID:27924007.

Real-time Analysis of RAG Complex Activity in V(D)J Recombination.

Jennifer Zagelbaum, Noriko Shimazaki , Zitadel Anne Esguerra , Go Watanabe , Michael R Lieber*,
and Eli Rothenberg*.

PNAS 113:11853-11858  (2016). PMID:27702897.

Probing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation.

Yandong Yin, and Eli Rothenberg.

Scientific Reports 22, 6:30819 (2016). PMID:27545293.

Single Molecule Localization Microscopy of DNA Damage Response Pathways in Cancer.

Donna R. Whelan, Yandong Yin, Keria Bermudez-Hernandez, Sarah Keegan, David Fenyö, and Eli Rothenberg.
Microscopy and Microanalysis 22, S3, 1016-1017 (2016).

 

The Tumor-Associated Variant RAD51 G151D Induces a Hyper-recombination Phenotype.

Carolyn Marsden, Ryan B. Jensen, Jennifer Zagelbaum, Eli Rothenberg, Scott W Morrical, Susan S Wallace,
and Joann B Sweasy.

PLoS Genetics 11, 12(8): e1006208 (2016). PMID:27513445.

Nanoscale Visualization of Functional Adhesion/Excitability Nodes at the Intercalated Disc.

Alejandra Leo-Macias, Esperanza Agullo-Pascual, Jose L. Sanchez-Alonso, Sarah Keegan, Xianming Lin,
Tatiana Arcos, Feng-Xia-Liang, Yuri E. Korchev, Julia Gorelik, David Fenyo, Eli Rothenberg*, and Mario Delmar*.

Nature Communications 7:10342 (2016). PMID:26787348. (*Corresponding authors)

 

TIMELESS Forms a Complex with PARP1 Distinct from Its Complex with TIPIN and
Plays a Role in the DNA Damage Response.

Lauren M. Young, Antonio Marzio, Pablo Perez-Duran, Dylan A. Reid, Daniel N. Meredith, Domenico Roberti, Ayelet Star, Eli Rothenberg, Beatrix Ueberheide, and Michele Pagano.

Cell Reports 15, S2211-1247 (2015). PMID:26456830. 

Repair of chromosomal breaks by NHEJ.

Dylan A. Reid, and Eli Rothenberg.

Oncotarget 18, 15730-1 (2015) PMID:26119149. 

 

Organization and Dynamics of the Nonhomologous End Joining Machinery During
DNA Double Strand Break Repair.

Dylan A. Reid, Sarah Keegan, Alejandra Leo-Macias, Go Watanabe, Natasha T. Strande, Howard H. Chang,
Betul Akgol Oksuz, David Fenyö, Michael Lieber, Dale Ramsden, and Eli Rothenberg.

PNAS 112, 2575-84 (2015). PMID:25941401.

Recommended by Faculty of 1000 (READ IT HERE)

 

Single-Molecule Fluorescence Imaging Techniques.

Dylan A. Reid, and Eli Rothenberg. Encyclopedia of Analytical Chemistry, eds R.A. Meyers, John Wiley: Chichester.

DOI: 10.1002/9780470027318.a9494. 17 March (2015).

 

ATR-Mediated Phosphorylation of FANCI Regulates Dormant Origin Firing
in Response to Replication Stress.

Yu-Hung Chen, Mathew JK Jones, Yandong Yin, Sarah B. Crist, Luca Colnaghi, Robert J. Sims, Eli Rothenberg, Prasad V. Jallepalli, and Tony T. Huang.

Molecular Cell 58, 323-38 (2015). PMID: 25843623.

Recommended by Faculty of 1000 (READ IT HERE)

 

Mechanistic Insight into the Interaction of BLM helicase with Intra-strand
G-quadruplex Structures.

Sujoy Chatterjee, Jennifer Zagelbaum, Pavel Savitsky, Diana Huttner, Pavel Janscak, Ian Hickson, Opher Gileadi, and Eli Rothenberg.

Nature Communications 5:5556 (2014).  

 

Super-resolution imaging reveals that loss of the C-terminus of connexin43
limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc.

Esperanza Agullo-Pascual, Xianming Lin, Alejandra Leo-Macias, Mingliang Zhang, Feng-Xia Liang, Zhen Li,
Anna Pfenniger, Indra Lübkemeier, Sarah Keegan, David Fenyö, Klaus Willecke, Eli Rothenberg,
and Mario Delmar.

Cardiovascular Research 104(2):371-81 (2014). 

 

Missense Mutations in Plakophilin-2 Cause Sodium Current Deficit
and Associate with a Brugada Syndrome Phenotype.

Marina Cerrone, Xianming Lin, Mingliang Zhang, Esperanza Agullo-Pascual, Anna Pfenniger, Halina Chkourko Gusky, Valeria Novelli, Changsung Kim, Tiara Tirasawasdichai, Daniel P. Judge, Eli Rothenberg, Huei-Sheng Vincent Chen, Carlo Napolitano, Silvia Priori, and Mario Delmar.

Circulation 129(10):1092-103 (2014).

 

FBH1 disrupts RAD51 filaments in vitro and modulates homologous recombination
in mammalian cells.

Jitka Simandlova, Jennifer Zagelbaum, Miranda J. Payne, Wai Kit Chu, Igor Shevelev, Katsuhiro Hanada,
Sujoy Chatterjee, Dylan A. Reid, Ying Liu, Pavel Janscak*, Eli Rothenberg*, and Ian D. Hickson*.

Journal of Biological Chemistry 288, 34168-34180 (2013).

 

Inhibitors of SCF-Skp2/Cks1 E3ligase block estrogen-induced growth stimulation
and degradation of nuclear p27kip1: therapeutic potential for endometrial cancer.

Savvas C Pavlides, Kuang-Tzu Huang, Dylan A. Reid, Lily Wu, Stephanie V Blank, Khushbakhat Mittal,
Paraskevi Briasouli, Eli Rothenberg*, Bo Rueda*, Timothy Cardozo*, and Leslie I Gold*.

Endocrinology 11, 4030–4045 (2013).

 

Super-resolution fluorescence microscopy of the cardiac connexome reveals
plakophilin-2 inside the connexin43 plaque.

Esperanza Agullo-Pascual, Dylan A Reid, Sarah Keegan, Manavjeet Sidhu, David Fenyö*, Eli Rothenberg*,
and Mario Delmar*.

Cardiovascular Research 100, 231–240 (2013). 

 

Changes in Psp protein binding partners, localization and behavior upon activation
of the Yersinia enterocolitica phage shock protein response.

Saori Yamaguchi, Dylan A. Reid, Eli Rothenberg*, and Andrew Darwin*.

Molecular Microbiology 87, 656-671 (2013).

 

Interaction of bacteriophage λ with its E. coli receptor, LamB.

Sujoy Chatterjee, and Eli Rothenberg.

Viruses 4, 3162-3178 (2012).

 

Heterogeneity of ATP-Sensitive K+ Channels in Cardiac Myocytes: Enrichment
at the Intercalated Disk.

M Hong, Li Bao, Esperanza Agullo-Pascual, E Kefaloyianni, Halina Chkouro, M Foster, E Taskin, M Zhandre,
Dylan A Reid, 
Eli Rothenberg, Mario Delmar, and William A Coetzee.

Journal of Biological Chemistry 49, 41258-67 (2012).

 

Remodeling of mechanical junctions and of microtubule-associated proteins
accompany cardiac Connexin43 lateralization.

Halina Chkourko, Guadalipe Guerrero-Serna, Xianming Lin, Nedal Darwish, Joshua Pohlmann, Keith Cook, Jeffrey Martens, Eli Rothenberg, Hassan Musa, and Mario Delmar.

Heart Rhythm 9, 1133-1140 (2012).

 

Single-molecule-based super-resolution images in the presence of multiple fluorophores.

Paul Simonson, Eli Rothenberg, and Paul Selvin.

Nano Letters 11, 5090-6 (2011). 

 

Two-Photon 3D FIONA of Aqueous Individual Quantum Dots.

Ruobing Zhang*, Eli Rothenberg*, Gilbert Fruhwirth, Paul Simonson, Fangfu Ye, Ido Golding, Tony Ng,
Ward Lopes, and Paul Selvin.

Nano Letters 10, 4074-8 (2011).

 

Single-Virus Tracking Reveals a Spatial Receptor-Dependent Search Mechanism.

Eli Rothenberg*, Leonardo A. Sepulveda, Samuel O. Skinner, Lanying Zeng, Paul R.  Selvin, and Ido Golding.
Biophysical Journal 100, 2875-82 (2011).

Recommended by Faculty of 1000  (READ IT HERE)

 

Single Molecule FRET Analysis of Helicase functions.

Eli Rothenberg* and Taekjip Ha.

Methods in Molecular Biology 587, 29-43 (2010). 

 

Human Rad52 Binds and wraps Single-Stranded DNA and Mediates Annealing
Via Two hRad52-ssDNA Complexes.

Jill M. Grimme, M. Honda, Rebecca Wright, Y. Okuno, Eli Rothenberg, Alex V. Mazin, Taekjip Ha, and Maria Spies.
Nucleic Acid Research 38, 2917-30 (2010).

 

Human Rad52-mediated homology search and annealing occurs by
continuous interactions between overlapping nucleoprotein complexes.

Eli Rothenberg, Jill Wiedman-Grimme, Maria Spies, and Taekjip Ha.

PNAS 205, 20274–20279 (2008).

 

MCM fork substrate specificity involves dynamic interaction with the 5’ tail.

Eli Rothenberg, Michael A. Trakselis, Stephen D. Bell, and Taekjip Ha.

Journal of Biological Chemistry 282, 34229-34234 (2007). 

 

Seeded Growth of InP and InAs Quantum Rods Using Indium Acetate and Myristic Acid.

Itzhak Shweky, Assaf Aharoni, Taleb Mokari, Eli Rothenberg, Moshe Nadler, Inna Popov, and Uri Banin.

Materials Science and Engineering C 26, 788-794 (2006).

 

Electric Field Induced Switching of the Fluorescence of Single Semiconductor Quantum Rods.

Eli Rothenberg, Miri Kazes, Ehud Shaviv, and Uri Banin.

Nano Letters 5, 1581-1586 (2005).

 

Synthesis of InP and InAs quantum rods using Induim Acetate and Myristic acid.

Itzhak Shweky, Assaf Aharoni, Taleb Mokari, Moshe Nadler, Eli Rothenberg, Inna Popov, and Uri Banin.

Materials Research Society Symposium Proceedings Vol. 848, FF8.3.1 (2005). 

 

Electronic Level Structure and Single Electron Tunneling Effects in CdSe Quantum Rods.

Eli Rothenberg, Taleb Mokari, Miri Kazes, Uri Banin, David Katz, Dov Steiner, and Oded Millo.

Israel Journal of Chemistry 44, 391-400 (2004).

 

Direct observation of highly polarized non-linear absorption dipole
of single semiconductor quantum rods.

Eli Rothenberg, Yuval Ebenstein, Miri Kazes, and Uri Banin.

Materials Research Society Symposium Proceedings Vol. 818, M6.5.1 (2004).

 

Selective Growth of Metal Tips onto Semiconductor Quantum Rods and Tetrapods.

Taleb Mokari, Eli Rothenberg, Inna Popov, Ronny Costi, and Uri Banin.

Science 304, 1787-1790 (2004). 

 

Two-Photon Fluorescence Microscopy of Single Semiconductor Quantum Rods:
Direct Observation of Highly Polarized Nonlinear Absorption Dipole.

Eli Rothenberg, Yuval Ebenstein, Miri Kazes, and Uri Banin.

Journal of Physical Chemistry B. 108, 2797-2800 (2004).

 

Charging and quantum size effects in tunnelling and optical spectroscopy of CdSe nanorods.

Oded Millo, David Katz, Dov Steiner, Eli Rothenberg, Taleb Mokari, Miri Kazes, and Uri Banin.

Nanotechnology 15, R1-R6 (2004).

 

Size and shape dependent level structure in CdSe quantum rods.

Eli Rothenberg, Taleb Mokari, Uri Banin, David Katz, Tommer Wizansky, and Oded Millo.

Materials Research Society Symposium Proceedings Vol. 737, E17.1.1 (2002).

 

Synthesis and size dependent properties of semiconductor quantum rods with cubic lattice.

Shihai Kan, Taleb Mokari, Eli Rothenberg, and Uri Banin.

Nature Materials 2, 155-158 (2003).

 

Size-Dependent Tunneling and Optical Spectroscopy of CdSe Quantum Rods.

David Katz*, Tommer Wizansky, Oded Millo, Eli Rothenberg*, Taleb Mokari, and Uri Banin.

Physical Review Letters 89, 086801-1 - 086801-4 (2002).

 

Publications

©Eli Rothenberg 2013