Publications:

2019

Approaches for Studying Ribosome Specialization.

Emmott E, Jovanovic M, Slavov N. Trends Biochem Sci. 2019 Feb 18. pii: S0968-0004(19)30017-9.

Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate


Cheng Z, Mugler CF, Keskin A, Hodapp S, Chan LY, Weis K, Mertins P, Regev A, Jovanovic M, Brar GA. Molecular Cell, 2019 Jan 3; 73(1):36-47.

2018

Precise Post-translational Tuning Occurs for Most Protein Complex Components during Meiosis

Eisenberg AR, Andrea Higdon A, Keskin A, Hodapp S, Jovanovic M, Brar GA. Cell Reports, 2018 Dec 26; 25(13): 3603-3617

Ribosome Stoichiometry: From Form to Function. 


Emmott E, Jovanovic M, Slavov N. Trends Biochem Sci. 2018 Nov 22. pii: S0968-0004(18)30219-6.

Global Proteome Remodeling during ER Stress Involves Hac1-Driven Expression of Long Undecoded Transcript Isoforms.

Van Dalfsen KM, Hodapp S, Keskin A, Otto GM, Berdan CA, Higdon A, Cheunkarndee T, Nomura DK, Jovanovic M, Brar GA. Dev Cell. 2018 Jul 16;46(2):219-235.e8. doi: 10.1016/j.devcel.2018.06.016.

Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus

Quinodoz SA, Ollikainen N, Tabak B, Palla Ali, Schmidt JM, Detmar E, Lai M, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Cell. 2018 Jun 4. pii:S0092-8674(18)30636-6.

Alternative 3' UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments.

Tushev G, Glock C, Heumüller M, Biever A, Jovanovic M, Schuman EM. Neuron. 2018 May 2;98(3):495-511.

Electrophilic properties of itaconate and derivatives regulate the IκBζ-ATF3 inflammatory axis.

Bambouskova M, Gorvel L, Lampropoulou V, Sergushichev A, Loginicheva E, Johnson K, Korenfeld D, Mathyer ME, Kim H, Huang LH, Duncan D, Bregman H, Keskin A, Santeford A, Apte RS, Sehgal R, Johnson B, Amarasinghe GK, Soares MP, Satoh T, Akira S, Hai T, de Guzman Strong C, Auclair K, Roddy TP, Biller SA, Jovanovic M, Klechevsky E, Stewart KM, Randolph GJ, Artyomov MN. Nature. 2018 Apr;556(7702):501-504.

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis.

Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schütz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, Sankaran VG. Cell. 2018 Mar 22;173(1):90-103.e19.

Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis.

Cheng Z, Otto GM, Powers EN, Keskin A, Mertins P, Carr SA, Jovanovic M#, Brar GA# . Cell. 2018 Feb 22;172(5):910-923.e16. doi: 10.1016/j.cell.2018.01.035. (#corresponding authors)

2015

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic M*, Rooney M*, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez E, Fields A, Schwartz S, Raychowdhury R, Mumbach M, Eisenhaure T, Rabani M, Gennert D, Delorey T, Lu D, Weissman J, Carr SA, Hacohen N, Regev A. Science. 2015 Mar 6;347(6226):1259038. (*contributed equally)

A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation

Fields AP*, Rodriguez EH*, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, and Weissman JS. Molecular Cell, 2015 Dec 3;60(5):816-27. (*contributed equally)

A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks

Parnas O*, Jovanovic M*, Eisenhaure T*, Herbst R, Dixit A, Ye CJ, Przybylski D, Platt R, Tirosh I, Sanjana N, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A. Cell. 2015 Jul 30;162(3):675-86. (*contributed equally)

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.

Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Götze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner M. Genome Research. 2015 Jul 31.

2014

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A. Cell, 2014 Dec 18;159(7):1698-710. pdf (read here)

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling.

Platt RJ*, Chen S*, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F. Cell. 2014 Oct 9;159(2):440-55. (*contributed equally)

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA. 


Schwartz S*, Bernstein DA*, Mumbach MR*, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. Cell. 2014 Sep 25;159(1):148-62. (*contributed equally)

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5' Sites.

Schwartz S*, Mumbach MR*, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Cell Reports. 2014 Jul 10;8(1): 284-96. (*contributed equally)

2013

High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.

Schwartz S*, Agarwala SD*, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A. Cell. 2013 Dec 5;155(6):1409-21. (*contributed equally)

2012

RIP‑chip‑SRM - a New Combinatorial Large‑Scale Approach Identifies a Set of Translationally Regulated bantam/miR‑58 Targets in C. elegans

Jovanovic M, Reiter L*, Clark A*, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm L, Kaufman E, Wollscheid B, Simard M, Miska M, Aebersold R, Gerber A, Hengartner MO. Genome Research. 2012 Jul;22(7):1360-71. (*contributed equally)

2010 and earlier

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans

Jovanovic M*, Reiter L*, Picotti P, Lange V, Bogan E, Hurschler B, Blenkiron C, Lehrbach NJ, Ding XC, Weiss M, Schrimpf SP, Miska E, Grosshans H, Aebersold R, Hengartner MO. Nature Methods. October;7, 837-842 (2010). (*contributed equally)

Protein identification false discovery rates for very large proteomics datasets generated by tandem mass spectrometry.

Reiter L*, Claassen M*, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R. Molecular Cellular Proteomics. November;8(11):2405-17 (2009). (*contributed equally)

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases.

Tan CS*, Bodenmiller B*, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R. Science Signaling. July 28;2(81):ra39 (2009). (*contributed equally)

Comparative functional analysis of the C. elegans and Drosophila melanogaster proteomes.

Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malström J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO.PLoS Biology. March 3;7(3):e48 (2009).

PhosphoPep - a Database of Protein Phosphorylation Sites for Systems Level Research in Model Organisms. 


Bodenmiller B*, Campbell D*, Gerrits B*, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R. Nature Biotechnology. December;26(12):1339-40 (2008). (*contributed equally)

Design of a biological half adder.

Terzer M*, Jovanovic M*, Choutko A*, Nikolayeva O*, Korn A*, Brockhoff D*, Zurcher F, Friedmann M, Schutz R, Zitzler E, Stelling J, Panke S. IET Synthetic Biology. June;1(1-2):53-8 (2007). (*contributed equally)

Aminophospholipid translocase TAT-1 promotes phosphatidylserine exposure during C. elegans apoptosis. 


Zullig S, Neukomm LJ*, Jovanovic M*, Charette SJ, Lyssenko NN, Halleck MS, Reutelingsperger CP, Schlegel RA, Hengartner MO. Current Biology. June 5;17(11):994-9 (2007). (*contributed equally)

miRNAs and apoptosis: RNAs to die for.

Jovanovic M, Hengartner MO. 
Oncogene. October 9;25(46):6176-87. Review (2006).