bibliography.bib

@phdthesis{ZoritaET,
    title    = {Space-frequency coded OFDM for underwater acoustic communications},
    school   = {Northeastern University, Massachusetts Institute of Technology, Universitat Politecnica de Catalunya},
    author   = {Zorita, Eduard},
    year     = {2012},
}

@phdthesis{ZoritaEE,
    title    = {Statistical models for genome sequence mapping},
    school   = {Universitat Politecnica de Catalunya, Centre de Regulacio Genomica},
    author   = {Zorita, Eduard},
    year     = {2016},
}

@Article{Lucic2019,
author={Lucic, Bojana
and Chen, Heng-Chang
and Kuzman, Maja
and Zorita, Eduard
and Wegner, Julia
and Minneker, Vera
and Wang, Wei
and Fronza, Raffaele
and Laufs, Stefanie
and Schmidt, Manfred
and Stadhouders, Ralph
and Roukos, Vassilis
and Vlahovicek, Kristian
and Filion, Guillaume J.
and Lusic, Marina},
title={Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration},
journal={Nature Communications},
year={2019},
month={Sep},
day={06},
volume={10},
number={1},
pages={4059},
abstract={HIV-1 recurrently targets active genes and integrates in the proximity of the nuclear pore compartment in CD4+ T cells. However, the genomic features of these genes and the relevance of their transcriptional activity for HIV-1 integration have so far remained unclear. Here we show that recurrently targeted genes are proximal to super-enhancer genomic elements and that they cluster in specific spatial compartments of the T cell nucleus. We further show that these gene clusters acquire their location during the activation of T cells. The clustering of these genes along with their transcriptional activity are the major determinants of HIV-1 integration in T cells. Our results provide evidence of the relevance of the spatial compartmentalization of the genome for HIV-1 integration, thus further strengthening the role of nuclear architecture in viral infection.},
issn={2041-1723},
doi={10.1038/s41467-019-12046-3},
url={https://doi.org/10.1038/s41467-019-12046-3}
}

@article {Filion619155,
	author = {Filion, Guillaume J. and Cortini, Ruggero and Zorita, Eduard},
	title = {Calibrating seed-based alignment heuristics with Sesame},
	elocation-id = {619155},
	year = {2019},
	doi = {10.1101/619155},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {The increasing throughput of DNA sequencing technologies creates a need for faster algorithms. The fate of most reads is to be mapped to a reference sequence, typically a genome. Modern mappers rely on heuristics to gain speed at a reasonable cost for accuracy. In the seeding heuristic, short matches between the reads and the genome are used to narrow the search to a set of candidate locations. Several seeding variants used in modern mappers show good empirical performance but they are difficult to calibrate or to optimize for lack of theoretical results. Here we develop a theory to estimate the probability that the correct location of a read is filtered out during seeding, resulting in mapping errors. We describe the properties of simple exact seeds, skip-seeds and MEM seeds (Maximal Exact Match seeds). The main innovation of this work is to use concepts from analytic combinatorics to represent reads as abstract sequences, and to specify their generative function to estimate the probabilities of interest. We provide several algorithms, which combined together give a workable solution for the problem of calibrating seeding heuristics for short reads. We also provide a C implementation of these algorithms in a library called Sesame. These results can improve current mapping algorithms and lay the foundation of a general strategy to tackle sequence alignment problems. The Sesame library is open source and available for download at https://github.com/gui11aume/sesame.},
	URL = {https://www.biorxiv.org/content/early/2019/12/12/619155},
	eprint = {https://www.biorxiv.org/content/early/2019/12/12/619155.full.pdf},
	journal = {bioRxiv}
}

@article{Abner17012018,
author = {Abner, Erik and Stoszko, Mateusz and Zeng, Lei and Chen, Heng-Chang and Izquierdo-Bouldstridge, Andrea and Konuma, Tsuyoshi and Zorita, Eduard and Fanunza, Elisa and Zhang, Qiang and Mahmoudi, Tokameh and Zhou, Ming-Ming and Filion, Guillaume J. and Jordan, Albert}, 
title = {A new quinoline BRD4 inhibitor targets a distinct latent HIV-1 reservoir for re-activation from other ‘shock’ drugs},
year = {2018}, 
doi = {10.1128/JVI.02056-17}, 
abstract ={Upon HIV-1 infection, a reservoir of latently infected resting T cells prevents the eradication of the virus from patients. To achieve complete depletion, the existing virus-suppressing antiretroviral therapy must be combined with drugs that reactivate the dormant viruses. We previously described a novel chemical scaffold compound, MMQO (8-methoxy-6-methylquinolin-4-ol) that is able to reactivate viral transcription in several models of HIV latency including J-Lat cells through an unknown mechanism. MMQO potentiates the activity of known latency-reversing agents (LRAs) or ‘shock’ drugs such as PKC agonists or HDAC inhibitors. Here we demonstrate that MMQO activates HIV-1 independently of the Tat transactivator. Gene expression microarrays in Jurkat cells indicated that MMQO treatment results in robust immunosuppression, diminishes expression of c-Myc, and causes the dysregulation of acetylation sensitive genes. These hallmarks indicated that MMQO mimics acetylated lysines of core histones and might function as a bromodomain and extraterminal domain protein family inhibitor (BETi). MMQO functionally mimics the effects of JQ1, a well-known BETi. We confirmed that MMQO interacts with the BET family protein BRD4. Utilizing MMQO and JQ1, we demonstrate how the inhibition of BRD4 targets a distinct subset of latently integrated barcoded proviruses from those targeted by HDAC inhibitors or PKC pathway agonists. Thus, the quinoline-based compound MMQO represents a new class of the BET bromodomain inhibitors, which due to its minimalistic structure holds promise for further optimization for increased affinity and specificity for distinct bromodomain family members and could potentially be of use against a variety of diseases, including HIV.IMPORTANCE The tentative “shock and kill” therapy aims to eradicate the latent functional proportion of HIV-1 proviruses in a patient. Yet to this day, clinical studies investigating the “shocking” element of this strategy have proven it to be considerably more difficult than anticipated. While the proportion of intracellular viral RNA production and general plasma viral load have been shown to increase upon a “shock” regimen, the global viral reservoir remains unaffected, highlighting both the inefficiency of the treatments used and the gap in our understanding of viral reactivation in vivo.Utilizing a new BRD4 inhibitor and barcoded HIV-1 minigenomes, we demonstrate that PKC pathway activators, HDAC and bromodomain inhibitors all target different subsets of proviral integrations. Considering the fundamental differences of these compounds and the synergies displayed between them, we propose that the field should concentrate on investigating the development of combinatory “shock” cocktail therapies for an improved reservoir reactivation.}, 
URL = {http://jvi.asm.org/content/early/2018/01/11/JVI.02056-17.abstract}, 
eprint = {http://jvi.asm.org/content/early/2018/01/11/JVI.02056-17.full.pdf+html}, 
journal = {Journal of Virology} 
}

@article{BHIVE-protocol,
author = {Chen Heng‐Chang and Zorita Eduard and Filion Guillaume J.},
title = {Using Barcoded HIV Ensembles (B‐HIVE) for Single Provirus Transcriptomics},
journal = {Current Protocols in Molecular Biology},
volume = {122},
number = {1},
pages = {e56},
year = {2018},
keywords = {B‐HIVE, HIV, latency, molecular barcodes, single‐provirus expression},
doi = {10.1002/cpmb.56},
url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpmb.56},
eprint = {https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpmb.56},
abstract = {Abstract The latent HIV reservoir is the main barrier to curing AIDS, because infected cells escape the immune system and antiretroviral therapies. Developing new treatment strategies requires technologies to trace latent proviruses. Here, we describe a genome‐wide technique called Barcoded HIV Ensembles (B‐HIVE) to measure HIV expression at the single provirus level. The principle of B‐HIVE is to tag the genome of HIV with DNA barcodes to trace viral transcripts produced by single proviruses in an infected cell population. This in turn reveals which proviruses are active and which are latent or expressed at low level. B‐HIVE is a high‐throughput method to identify and quantify thousands of individual viral transcripts per round of infection. It can be applied in different conditions, characterizing the response of single proviruses to different treatments. Overall, B‐HIVE gives unprecedented insight into the expression of single proviruses in populations of HIV‐infected cells. © 2018 by John Wiley \& Sons, Inc.}
}

@Article{Chen2017,
author={Chen, Heng-Chang
and Martinez, Javier P.
and Zorita, Eduard
and Meyerhans, Andreas
and Filion, Guillaume J.},
title={Position effects influence HIV latency reversal},
journal={Nature Structural \& Molecular Biology},
year={2017},
month={1},
publisher={Nature Publishing Group},
volume={24},
number={1},
pages={47-54},
note={Article},
issn={1545-9993},
url={http://dx.doi.org/10.1038/nsmb.3328}
}

@article{doi:10.1093/bioinformatics/btv053,
author = {Zorita, Eduard and Cuscó, Pol and Filion, Guillaume J.},
title = {Starcode: sequence clustering based on all-pairs search},
journal = {Bioinformatics},
volume = {31},
number = {12},
pages = {1913-1919},
year = {2015},
doi = {10.1093/bioinformatics/btv053},
URL = { + http://dx.doi.org/10.1093/bioinformatics/btv053},
eprint = {/oup/backfile/Content_public/Journal/bioinformatics/31/12/10.1093/bioinformatics/btv053/2/btv053.pdf}
}

@ARTICLE{6812215,
author={E. Zorita and M. Stojanovic},
journal={IEEE Journal of Oceanic Engineering},
title={Space-Frequency Block Coding for Underwater Acoustic Communications},
year={2015},
volume={40},
number={2},
pages={303-314},
keywords={OFDM modulation;block codes;channel estimation;error statistics;quadrature phase shift keying;underwater acoustic communication;Alamouti coherence requirement;Alamouti space-frequency block coding;Doppler prediction;OFDM system;QPSK;adaptive channel estimation method;bit error rate;decision-directed operation;orthogonal frequency-division multiplexing system;quadrature phase-shift keying;shallow-water channel;time smoothing;underwater acoustic channel;underwater acoustic communications;Acoustics;Block codes;Channel estimation;Delays;Doppler effect;OFDM;Transmitters;Adaptive channel estimation;Alamouti;multiple-input–multiple-output (MIMO);orthogonal frequency-division multiplexing (OFDM);space–frequency block coding;underwater acoustic communication},
doi={10.1109/JOE.2014.2316558},
ISSN={0364-9059},
month={4},}

@INPROCEEDINGS{5947098,
author={J. Vidal and A. Agustín and S. Lagén and E. Zorita and O. Muñoz and A. Garcia Armada and M. S. Fernández},
booktitle={2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)},
title={Network-MIMO backhauling for QOS-constrained relay transmission},
year={2011},
pages={3332-3335},
keywords={Equations;Interference;MIMO;Relays;Resource management;Strontium;Wireless communication;Network-MIMO;QoS;Relay transmissions},
doi={10.1109/ICASSP.2011.5947098},
ISSN={1520-6149},
month={5},}

@INPROCEEDINGS{6404916,
author={E. Zorita and M. Stojanovic},
booktitle={2012 Oceans},
title={Space-frequency coded OFDM for underwater acoustic communications},
year={2012},
pages={1-5},
keywords={OFDM modulation;acoustic receivers;adaptive codes;adaptive estimation;block codes;channel coding;channel estimation;quadrature phase shift keying;time-varying channels;transfer functions;underwater acoustic communication;Alamouti coding;Doppler prediction;OFDM system;QPSK;adaptive channel estimation method;adaptive receiver;channel transfer function;data transmission;diversity transmission;frequency 10 kHz to 15 kHz;pilot overhead reduction;shallow water channel;single-transmitter case;space-frequency block coding scheme;time-smoothing;time-varying channel;underwater acoustic communication channel;velocity 0.5 m/s to 2 m/s;Acoustics;Bit error rate;Channel estimation;Coherence;Matching pursuit algorithms;OFDM;Receivers},
doi={10.1109/OCEANS.2012.6404916},
ISSN={0197-7385},
month={11},}

@INPROCEEDINGS{7074081,
author={A. Agustin and J. Vidal and S. Lagen and E. Zorita},
booktitle={2011 19th European Signal Processing Conference},
title={Network MIMO for downlink in-band relay transmissions with relaying phases of fixed duration},
year={2011},
pages={1819-1823},
keywords={MIMO communication;cellular radio;energy conservation;network coding;optimisation;precoding;radiofrequency interference;relay networks (telecommunication);telecommunication power management;BS-RS based cellular system deployment;N-MIMO;RS-MS access;base stations;coverage homogeneity enhancement;downlink in-band relay transmission;half-duplex relay station;network-MIMO;power allocation;power efficiency enhancement;precoder optimization;relay-transmit phases;spectral efficiency enhancement;wireless backhaul;Bit rate;Downlink;Interference;MIMO;Optimization;Relays;Resource management;Network-MIMO;QoS;Relay transmissions},
ISSN={2076-1465},
month={8},}