journal articles

Y.-R. Shen, S. Zaballa, X. Bech, A. Sancho-Balsells, I. Rodríguez-Navarro, C. Cifuentes-Díaz, G. Seyit-Bremer, S. H. Chun, T. Straub, J. Abante, I. Merino-Valverde, L. Richart, V. Gupta, H.-Y. Li, I. Ballasch, N. Alcázar, J. Alberch, J. M. Canals, M. Abad, and D. del Toro. Expansion of the neocortex and protection from neurodegeneration by in vivo transient reprogramming. Cell Stem Cell (2024). URL

J. Abante, P. L. Wang, J. Salzman. DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery. Genome Biol 24, 240 (2023). URL

Y. Fang, Z. Jin (†), W. Zhou (†), J. Abante (†), M.A. Koldobskiy, H. Ji, and A.P. Feinberg. DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence. Nucleic Acids Research (2023), gkad050. † Equal contribution. URL

J. Abante, S. Kambhampati, A.P. Feinberg, J. Goutsias. Estimating DNA methylation potential energy landscapes from nanopore sequencing data. Science Direct (2021):11-21619, URL.

M.A. Koldobskiy, G. Jenkinson, J. Abante, V.A. Rodriguez DiBlasi, W. Zhou, E. Pujadas, A. Idrizi, R. Tryggvadottir, C. Callahan, C. Bonifant, K. Rabin, P.A. Brown, H. Ji, J. Goutsias, and A.P. Feinberg. Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukaemia identified by an information-theoretic analysis. Nature Biomedical Engineering 5.4 (2021):360-376, URL.

J. Abante, Y. Fang, A.P. Feinberg, J. Goutsias. Detection of haplotype-dependent allele-speciﬁc DNA methylation in WGBS data. Nature Communications 11, 5238 (2020), URL. Article featured in Nature Communications Editors’ Highlights.

C. Qiu, H. Jin, I. Vvedenskaya, J. Abante, T. Zhao, I. Malik, S. Schwartz, P. Cui, P. Cabart, K. Hoo, R.P. Metz, C.D. Johnson, S. Sze, B.F. Pugh, B.E. Nickels, C.D. Kaplan. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biology (2020), 21:132, URL.

M. Koldobskiy, J. Abante, G. Jenkinson, E. Pujadas, A. Tetens, F. Zhao, R. Tryggvadottir, A. Idrizi, A. Reinisch, R. Majeti, J. Goutsias, and A. P. Feinberg. A Dysregulated DNA Methylation Landscape Linked to Gene Expression in MLL-Rearranged AML. Epigenetics (2020), 1-18, URL.

M. P. Menden, D. Wang, M. J. Mason, B. Szalai, K. C. Bulusu, Y. Guan, J. Kang, M. Jeon, R. Wolfinger, T. Nguyen, M. Zaslavskiy, J. Abante, et al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications 10.1 (2019): 2674, URL.

G. Jenkinson, J. Abante, A.P. Feinberg, and J. Goutsias. Ranking genomic features using an information-theoretic measure of epigenetic discordance. BMC Bioinformatics (2019), 20:175, URL.

G. Jenkinson, J. Abante, A.P. Feinberg, and J. Goutsias. An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data. BMC Bioinformatics (2018), 19:87, URL.

J. Abante, N. Ghaffari, C.D. Johnson, A. Datta. HiMMe: using genetic patterns as a proxy for genome assembly reliability assessment. BMC Genomics (2017), 18:694, URL.

peer-reviewed conference proceedings

R. Smeriglio, J. Rosell-Mirmi, P. Radeva, and J. Abante. Leveraging protein-protein interactions in phenotype prediction through graph neural networks. 2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 1–8 (2024). URL

A. Meléndez, C. López, D. Bonet, G. Sant, D. M. Montserrat, J. Abante, M. Rivas, F. Marqués, and A. G. Ioannidis. Assessing Tree-Based Phenotype Prediction on the UK Biobank. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 3804–3810 (2023).

P. Blood, N. Ghaﬀari, A. S. Seetharam, L. Pipes, R. Singh, J. Abante, A. Severin, C. D. Johnson, C. Mason. Fast, ﬂexible, and free: enabling large-scale genome assembly and analysis with the Bridges supercomputer. In Plant and Animal Genome XXVI Conference, San Diego, CA, U.S., 2018, URL.

N. Ghaffari, J. Abante, R. Singh, P.D. Blood, C.D. Johnson. Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data. Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16 (2016). ACM Press, New York, New York, USA, pp. 1–4, URL.

preprint

J. Abante, P.L. Wang, J. Salzman. DIVE: a reference-free statistical approach to diversity-generating & mobile genetic element discovery. bioRxiv (2022), 495703, URL.

J. Abante, S. Kambhampati, A.P. Feinberg, J. Goutsias. Estimating DNA methylation potential energy landscapes from nanopore sequencing data. bioRxiv (2021), 431480, URL.

J. Abante, J. Goutsias. CpelTdm.jl: a Julia package for targeted differential DNA methylation analysis. bioRxiv (2020), 343020, URL.

C. Qiu, H. Jin, I. Vvedenskaya, J. Abante, T. Zhao, I. Malik, A.M. Visbisky, S.L. Schwartz, P. Cui, P. Cabart, K.H. Han, W.K.M. Lai, R.P. Metz, C.D. Johnson, S.H. Sze, B.F. Pugh, B.E. Nickels, C.D. Kaplan. Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”. bioRxiv (2019), 810127, URL.

N. Ghaﬀari, J. Abante, R. Singh, P. D. Blood, L. Pipes, C. Mason, C. D. Johnson. What are the most inﬂuencing factors in reconstructing a reliable transcriptome assembly?. bioRxiv (2017), 220269, URL.