Publications

Peer-reviewed publications covering genomics, small RNA analysis, multi-omics integration, and computational biology methods.

Kathleen Hanlon, Alex Thompson, Lorena Pantano, John N Hutchinson, Arshed Al-Obeidi, Shu Wang, Meghan Bliss-Moreau, Jennifer Helble, Gabriela Alexe, Kimberly Stegmaier, Daniel E Bauer, Ben a Croker (2019). Single-cell cloning of human T-cell lines reveals clonal variation in cell death responses to chemotherapeutics.. Cancer genetics.

William C Engeland, Logan Massman, Lauren Miller, Sining Leng, Emanuele Pignatti, Lorena Pantano, Diana L Carlone, Paulo Kofuji, David T Breault (2019). Sex Differences in Adrenal Bmal1 Deletion-Induced Augmentation of Glucocorticoid Responses to Stress and ACTH in Mice.. Endocrinology.

Mira Pavkovic, Lorena Pantano, Cory v Gerlach, Sergine Brutus, Sarah a Boswell, Robert a Everley, Jagesh v Shah, Shannan H Sui, Vishal S Vaidya (2019). Multi omics analysis of fibrotic kidneys in two mouse models.. Scientific data.

Joan Pallarès-Albanell, M Teresa Zomeño-Abellán, Georgia Escaramís, Lorena Pantano, Aroa Soriano, Miguel F Segura, Eulàlia Martí (2019). A High-Throughput Screening Identifies MicroRNA Inhibitors That Influence Neuronal Maintenance and/or Response to Oxidative Stress.. Molecular therapy. Nucleic acids.

Maria Mavrikaki, Lorena Pantano, David N Potter, Maximilian Aaron Rogers-Grazado, Eleni Anastasiadou, Sami Amr, Frank John Slack, Kerry J Ressler, Nikolaos P Daskalakis, Elena Chartoff (2019). Sex-dependent changes in miRNA expression in the bed nucleus of the stria terminalis following stress. Frontiers in molecular neuroscience.

Carla Giner-Delgado, Sergi Villatoro, Jon Lerga-Jaso, Magdalena Gayà-Vidal, Meritxell Oliva, David Castellano, Lorena Pantano, Bárbara D Bitarello, David Izquierdo, Isaac Noguera, Others (2019). Evolutionary and functional impact of common polymorphic inversions in the human genome. Nature communications.

Matthew L. Steinhauser, Benjamin A. Olenchock, John O'Keefe, Mingyue Lun, Kerry A. Pierce, Hang Lee, Lorena Pantano, Anne Klibanski, Gerald I. Shulman, Clary B. Clish, Pouneh K. Fazeli (2018). The circulating metabolome of human starvation. JCI Insight.

Mercedes Rubio, Mariona Bustamante, Carles Hernandez-Ferrer, Dietmar Fernandez-Orth, Lorena Pantano, Yaris Sarria, Maria Piqué-Borras, Kilian Vellve, Silvia Agramunt, Ramon Carreras, Xavier Estivill, Juan R. Gonzalez, Alfredo Mayor (2018). Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk. PLoS ONE.

Michael J. Steinbaugh, Lorena Pantano, Rory D. Kirchner, Victor Barrera, Brad A. Chapman, Mary E. Piper, Meeta Mistry, Radhika S. Khetani, Kayleigh D. Rutherford, Oliver Hofmann, John N. Hutchinson, Shannan Ho Sui (2017). bcbioRNASeq: R package for bcbio RNA-seq analysis. F1000Research.

B. Busby, E.M. Weitz, L. Pantano, J. Zhu, B. Upton (2017). Viewing RNA-seq data on the entire human genome. F1000Research.

Juan J. Carmona, William P. Accomando, Alexandra M. Binder, John N. Hutchinson, Lorena Pantano, Benedetta Izzi, Allan C. Just, Xihong Lin, Joel Schwartz, Pantel S. Vokonas, Sami S. Amr, Andrea A. Baccarelli, Karin B. Michels (2017). Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans. npj Genomic Medicine.

E. Ransey, A. Björkbom, V.S. Lelyveld, P. Biecek, L. Pantano, J.W. Szostak, P. Sliz (2017). Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. RNA Biology.

P Bailey, D K Chang, K Nones, A L Johns, A M Patch, M C Gingras, D K Miller, A N Christ, T J Bruxner, M C Quinn, C Nourse, L C Murtaugh, I Harliwong, S Idrisoglu, S Manning, E Nourbakhsh, S Wani, L Fink, O Holmes, V Chin, M J Anderson, S Kazakoff, C Leonard, F Newell, S Wood, Q Xu, P J Wilson, N Cloonan, K S Kassahn, D Taylor, K Quek, A Robertson, L Pantano, L Mincarelli, L N Sanchez, L Evers, J Wu, M Pinese, M J Cowley, M D Jones, E K Colvin, A M Nagrial, E S Humphrey, L a Chantrill, A Mawson, J Humphris, A Chou, M Pajic, C J Scarlett, A v Pinho, M Giry-Laterriere, I Rooman, J S Samra, J G Kench, J a Lovell, N D Merrett, C W Toon, K Epari, N Q Nguyen, A Barbour, N Zeps, K Moran-Jones, N B Jamieson, J S Graham, F Duthie, K Oien, J Hair, R Grutzmann, A Maitra, C a Iacobuzio-Donahue, C L Wolfgang, R a Morgan, R T Lawlor, V Corbo, C Bassi, B Rusev, P Capelli, R Salvia, G Tortora, D Mukhopadhyay, G M Petersen, Initiative Australian Pancreatic Cancer Genome, D M Munzy, W E Fisher, S a Karim, J R Eshleman, R H Hruban, C Pilarsky, J P Morton, O J Sansom, A Scarpa, E a Musgrove, U M Bailey, O Hofmann, R L Sutherland, D a Wheeler, A J Gill, R a Gibbs, J v Pearson, N Waddell, A v Biankin, S M Grimmond (2016). Genomic analyses identify molecular subtypes of pancreatic cancer. Nature.

Lorena Pantano, Marc R Friedlander, Georgia Escaramis, Esther Lizano, Joan Pallares-Albanell, Isidre Ferrer, Xavier Estivill, Eulalia Marti (2015). Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis.. Bioinformatics (Oxford, England).

Lorena Pantano, Meritxell Jodar, Mads Bak, Josep Lluís Ballescà, Niels Tommerup, Rafael Oliva, Tanya Vavouri (2015). The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes.. RNA (New York, N.Y.).

Marta Puig, David Castellano, Lorena Pantano, Carla Giner-Delgado, David Izquierdo, Magdalena Gayà-Vidal, José Ignacio Lucas-Lledó, Tõnu Esko, Chikashi Terao, Fumihiko Matsuda, Mario Cáceres (2015). Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript. PLoS Genetics.

Hedda a Meijer, Ewan M Smith, Martin Bushell, A. Kozomara, V.N. Kim, J. Han, M.C. Siomi, Y. Wang, S. Juranek, G. Sheng, G.S. Wardle, T. Tuschl, D.J. Patel, S.W. Chi, J.B. Zang, A. Mele, R.B. Darnell, M. Hafner, M. Landthaler, L. Burger, M. Khorshid, J. Hausser, P. Berninger, A. Rothballer, M. Ascano, A.-C. Jungkamp, M. Munschauer, S. Djuranovic, A. Nahvi, R. Green, E. Huntzinger, D. Kuzuoğlu-Öztürk, J.E. Braun, A. Eulalio, L. Wohbold, E. Izaurralde, P.J. Halvey, Y. Shyr, R.J.C. Slebos, D.C. Liebler, B. Zhang, H.A. Meijer, Y.W. Kong, W.T. Lu, A. Wilczynska, R.V. Spriggs, S.W. Robinson, J.D. Godfrey, A.E. Willis, M. Bushell, I. Loedige, G. Sales, M. Lionetti, L. Agnelli, K. Todoerti, A. Coppe, C. Romualdi, A. Neri, Y. Liu, X. Wang, M.Q. Zhang, G. Hannon, Z.J. Huang, A. Mathelier, A. Carbone, F.V. Rivas, N.H. Tolia, J.-J. Song, J.P. Aragon, F.A. Kolb, H. Zhang, K. Jaronczyk, W. Filipowicz, J.M. Pare, N. Tahbaz, J. López-Orozco, P. LaPointe, P. Lasko, T.C. Hobman, S. Gu, L. Jin, F. Zhang, Y. Huang, D. Grimm, J.J. Rossi, M.A. Kay, M. Kobayashi, Y. Sakaguchi, S. Katsuma, T. Suzuki, E. Elkayam, C.-D. Kuhn, A. Tocilj, A.D. Haase, E.M. Greene, G.J. Hannon, L. Joshua-Tor, M. Yoda, T. Kawamata, Z. Paroo, X. Ye, S. Iwasaki, Q. Liu, P.B. Kwak, C. Matranga, Y. Tomari, C. Shin, D.P. Bartel, D.S. Schwarz, G. Hutvágner, T. Du, Z. Xu, N. Aronin, P.D. Zamore, K. Sobczak, U. Wilczynska, M. Drath, A. Jasinska, D. Kaczynska, W.J. Krzyzosiak, A.S. O'Toole, N. Haines, M.C. Zink, S. Miller, L.E. Jones, K. Giovannitti, D. Piper, M.J. Serra, H.Y. Hu, Y. Zheng, Y. Xu, H. Hu, C. Menzel, Y.H. Zhou, W. Chen, P. Khaitovich, M. Ohanian, E. Anderson, E. Marti, L. Pantano, M. Bañez-Coronel, F. Llorens, E. Miñones-Moyano, S. Porta, L. Sumoy, I. Ferrer, X. Estivill, C.T. Neilsen, G.J. Goodall, C.P. Bracken, D.T. Humphreys, C.J. Hynes, H.R. Patel, G.H. Wei, L. Cannon, D. Fatkin, C.M. Suter, J.L. Clancy, T. Preiss, M.L. Arcila, Z. Li, E.J. Lee, C. Henzler, J. Liu, T.M. Rana, K.S. Kosik, M. Xie, A. Vilborg, N. Lee, M.-D. Shu, V. Yartseva, N. Sestan, J.A. Steitz, H.Y. Lee, K. Zhou, A.M. Smith, C.L. Noland, J.A. Doudna, J. Winter, S. Diederichs, J.-S. Yang, M.D. Philips, D. Betel, P. Mu, A. Ventura, A.C. Siepel, K.C. Chen, E.C. Lai, L. Guo, Z. Lu, S. Ro, C. Park, D. Young, K.M. Sanders, W. Yan, H.R. Chiang, L.W. Schoenfeld, J.G. Ruby, V.C. Auyeung, N. Spies, D. Baek, W.K. Johnston, C. Russ, S. Luo, J.E. Babiarz, S. Bortoluzzi, A. Bisognin, M. Biasiolo, P. Guglielmelli, F. Biamonte, R. Norfo, R. Manfredini, A.M. Vannucchi, S. Griffiths-Jones, J.H.L. Hui, A. Marco, M. Ronshaugen, A.N. Packer, Y. Xing, S.Q. Harper, L. Jones, B.L. Davidson, L. Jiang, C. Lin, L. Song, J. Wu, B. Chen, Z. Ying, X. Yan, M. He, J. Li, M. Li, M. Rubio, R. Montañez, L. Perez, M. Milan, X. Belles, S.W. Shan, L. Fang, T. Shatseva, W.-Y. Lu, J.W. Xuan, Z. Deng, X. Yang, W.W. Du, H. Li, F. Liu, A. Khorshidi, Z.J. Rutnam, B.B. Yang, H. Zhou, X. Huang, H. Cui, X. Luo, Y. Tang, S. Chen, L. Wu, N. Shen, L. Tarassishin, O. Loudig, A. Bauman, B. Shafit-Zagardo, H.-S. Suh, S.C. Lee, C.B. Giles, R. Girija-Devi, M.G. Dozmorov, J.D. Wren, S. Chatterjee, M. Fasier, I. Büssing, H. Gro$eta$hans, M.P. Gantier, C.E. McCoy, I. Rusinova, D. Saulep, D. Wang, D. Xu, A.T. Irving, M.A. Behlke, P.J. Hertzog, F. Mackay, B.R.J. Williams, J. Krol, V. Busskamp, I. Markiewicz, M.B. Stadler, S. Ribi, J. Richter, J. Duebel, S. Bicker, H.J. Fehling, D. Schrubeler, T.S. Miki, H. Grosshans, S. Balaraman, E.R. Lunde, O. Sawant, T.A. Cudd, S.E. Washburn, R.C. Miranda (2014). Regulation of miRNA strand selection: follow the leader?. Biochemical Society transactions.

Alexander Martínez-Fundichely, Sònia Casillas, Raquel Egea, Miquel Ràmia, Antonio Barbadilla, Lorena Pantano, Marta Puig, Mario Cáceres (2014). InvFEST, a database integrating information of polymorphic inversions in the human genome. Nucleic Acids Research.

Franc Llorens, Mónica Bañez-Coronel, Lorena Pantano, Jose Antonio Del Río, Isidre Ferrer, Xavier Estivill, ́ Eulàlia Marti (2013). A highly expressed miR-101 isomiR is a functional silencing small RNA.. BMC genomics.

Mónica Bañez-Coronel, Silvia Porta, Birgit Kagerbauer, Elisabet Mateu-Huertas, Lorena Pantano, Isidre Ferrer, Manuel Guzmán, Xavier Estivill, Eulàlia Martí (2012). A Pathogenic Mechanism in Huntington's Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity.. PLoS genetics.

Lorena Pantano, Xavier Estivill, Eulalia Martí (2011). A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.. Bioinformatics (Oxford, England).

Lorena Pantano, Xavier Estivill, Eulàlia Martí (2010). SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Research.

Eulàlia Martí, Lorena Pantano, Mónica Bañez-Coronel, Franc Llorens, Elena Miñones-Moyano, Sĺvia Porta, Lauro Sumoy, Isidre Ferrer, Xavier Estivill (2010). A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing. Nucleic Acids Research.

Florencio Varas, Matthias Stadtfeld, Luisa De Andres-Aguayo, Nimet Maherali, Alessandro Di Tullio, Lorena Pantano, Cedric Notredame, Konrad Hochedlinger, Thomas Graf (2009). Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.. Stem cells (Dayton, Ohio).

Lluis Armengol, Sergi Villatoro, Juan R. Gonzalez, Lorena Pantano, Manel Garcá-Aragonés, Raquel Rabionet, Mario Cáceres, Xavier Estivill (2009). Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups. PLoS ONE.

Lorena Pantano, Lluís Armengol, Sergi Villatoro, Xavier Estivill (2008). ProSeeK: A web server for MLPA probe design. BMC Genomics.

Priscila Grynberg, Thomas Abeel, Pedro Lopes, Geoff Macintyre, Lorena Pantano (2007). Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology. BMC Bioinformatics.