2018: Isthmin 1 (ism1) is required for normal hematopoiesis in developing zebrafish.
A. Berrun, E. Harris, D. L. Stachura Lonardi
PLoS ONE, doi: 10.1371/journal.pone.0196872.

2016: BRAT-nova: Fast and accurate mapping of bisulfite-treated reads.
Elena Y. Harris, Rachid Ounit, and Stefano Lonardi
Bioinformatics, doi: 10.1093/bioinformatics/btw226.

2015: Zebrafish embryonic stromal trunk (ZEST) cells support hematopoietic stem and progenitor cell (HSPC) proliferation, survival, and differentiation.
C. Campbell, T. Su, R. P. Lau, A. Shah, P. C. Laurie, B. Avalos, J. Aggio, E. Harris, D. Traver, D. L. Stachura
Cell Host & Microbe, doi: 10.1016/j.exphem.2015.09.001.

2013: Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum.
N. Ponts, L. Fu, E. Y. Harris, J. Zhang, D. Chung, M. Cervantes, J. Prudhomme, V. Atanasova-Penichon, E. Zehraoui, E. Bunnik, E. Rodrigues, S. Lonardi, G. Hicks, Y. Wang and K. Le Roch
Cell Host & Microbe, doi: 10.1016/j.chom.2013.11.007.

2013: Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells.
C.O. dos Santos, C. Rebbeck, E. Rozhkova, A. Valentine, A. Samuels, L.R. Kadiri, P. Osten, E.Y. Harris, P. J. Uren, A. D. Smith, G. J. Hannon
PNAS, doi: 10.1073/pnas.1303919110.

2012: BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads.
E.Y. Harris, N. Ponts, K. Le Roch, S. Lonardi
Bioinformatics, 28(13), 1795-1796, doi: 10.1093/bioinformatics/bts264.

2011: Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite.
E.Y.Harris, N. Ponts, K. G. Le Roch, S. Lonardi
BMC Genomics, doi:10.1186/1471-2164-12-601.

2011: Nucleosome occupancy at transcription start sites in the human malaria parasite: A hard-wired evolution of virulence?
N. Ponts, E. Y. Harris, S. Lonardi, K. G. Le Roch
Infection, Genetics and Evolution, doi:10.1016/j.meegid.2010.08.002.

2010: Nucleosome landscape and control of transcription in the human malaria parasite.
Nadia Ponts*, Elena Y. Harris*, Jacques Prudhomme, Ivan Wick, Colleen Eckhardt-Ludka, Glenn R. Hicks, Gary Hardiman, Stefano Lonardi, Karine G. Le Roch
Genome Research, 20, 228-238, doi: 10.1101/gr.101063.109.

2009: BRAT: Bisulfite-treated Reads Analysis Tool.
E.Y.Harris, N. Ponts, A. Levchuk, K. Le Roch, S. Lonardi
Bioinformatics, 26(4), 572-573, doi:10.1093/bioinformatics/btp706.

*Joint first authors.


2019: Identifying DNA Sequence Motifs of Pdx-1 and NeuroD1 Transcription Factors.
Hassan Aldarwish, David Keller, and E. Y. Harris
BICOB 2019, 11th International Conference on Bioinformatics and Computational Biology, Honolulu, HI. PDF.

2018: Practical Space-efficient Linear Time Construction of FM-index for Large Genomes.
E. Y. Harris
BICOB 2018, 10th International Conference on Bioinformatics and Computational Biology, Vol. 60, pp. 27-35, Las Vegas, CA. PDF.

2010: Novel Gene Discovery in the Human Malaria Parasite using Nucleosome Positioning Data.
N. Pokhriyal, N. Ponts, E. Y. Harris, K. G. Le Roch, S. Lonardi
CSB 2010 - Computational Systems Bioinformatics Conference, pp. 124-135, Stanford, CA, Proceedings. PDF.

2010: Exploration of short reads mapping in hardware.
E. B. Fernandez, E. Harris, W. Najjar, S. Lonardi
FPL 2010 - International Conference on Field Programmable Logic and Applications, 360-363, Milano, Italy, Proceedings, doi:10.1109/FPL.2010.78.

2009: CPM’s 20th Anniversary: A Statistical Retrospective.
E. Y. Harris, T. Lecroq, G. Kucherov, S. Lonardi
CPM 2009 - Annual Symposium on Combinatorial Pattern Matching, pp.1-11, Lille, France, 2009, Proceedings, LNCS 5577, doi:10.1007/978-3-642-02441-2_1.