RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. by Sabah Kadri, Veronica F Hinman, Panayiotis V Benos

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DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. by Shaun Mahony, Philip E Auron, Panayiotis V Benos

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An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs by Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello, Claudia Coronnello

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Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. by David L Corcoran, Kusum V Pandit, Ben Gordon, Arindam Bhattacharjee, Naftali Kaminski, Panayiotis V Benos

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miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19 via Targeting SARS-CoV-2 RNA by Giorgio Bertolazzi, Giorgio Bertolazzi, Chiara Cipollina, Chiara Cipollina, Panayiotis V. Benos, Michele Tumminello, Michele Tumminello, Claudia Coronnello

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Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets by Xin Bing, Tyler Lovelace, Florentina Bunea, Marten Wegkamp, Sudhir Pai Kasturi, Harinder Singh, Panayiotis V. Benos, Jishnu Das

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Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers by Jordan Mandel, Huabo Wang, Daniel P. Normolle, Wei Chen, Qi Yan, Peter C. Lucas, Panayiotis V. Benos, Edward V. Prochownik

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Expression of regulatory platelet microRNAs in patients with sickle cell disease. by Shilpa Jain, Maria G Kapetanaki, Nalini Raghavachari, Kimberly Woodhouse, Guoying Yu, Suchitra Barge, Claudia Coronnello, Panayiotis V Benos, Gregory J Kato, Naftali Kaminski, Mark T Gladwin

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Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis by Minxue Jia, Lorena Rosas, Maria G. Kapetanaki, Tracy Tabib, John Sebrat, Tamara Cruz, Anna Bondonese, Ana L. Mora, Robert Lafyatis, Mauricio Rojas, Panayiotis V. Benos

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Human ex vivo lung perfusion: a novel model to study human lung diseases by Nayra Cárdenes, John Sembrat, Kentaro Noda, Tyler Lovelace, Diana Álvarez, Humberto E. Trejo Bittar, Brian J. Philips, Mehdi Nouraie, Panayiotis V. Benos, Pablo G. Sánchez, Mauricio Rojas

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The plasma degradome reflects later development of NASH fibrosis after liver transplant by Jiang Li, Toshifumi Sato, María Hernández-Tejero, Juliane I. Beier, Khaled Sayed, Panayiotis V. Benos, Daniel W. Wilkey, Abhinav Humar, Michael L. Merchant, Andres Duarte-Rojo, Gavin E. Arteel

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Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes by Oren Barak, Tyler Lovelace, Samantha Piekos, Tianjiao Chu, Zhishen Cao, Elena Sadovsky, Jean-Francois Mouillet, Yingshi Ouyang, W. Tony Parks, Leroy Hood, Nathan D. Price, Panayiotis V. Benos, Yoel Sadovsky

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Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells by Uma R. Chandran, Soumya Luthra, Lucas Santana-Santos, Ping Mao, Sung-Hak Kim, Mutsuko Minata, Jianfeng Li, Panayiotis V. Benos, Mao DeWang, Bo Hu, Shi-Yuan Cheng, Ichiro Nakano, Robert W. Sobol

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Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. by Guy Zinman, Rachel Brower-Sinning, Chineye H Emeche, Jason Ernst, Grace Tzu-Wei Huang, Shaun Mahony, Amy J Myers, Dawn M O'Dee, JoAnne L Flynn, Gerard J Nau, Ted M Ross, Russell D Salter, Panayiotis V Benos, Ziv Bar Joseph, Penelope A Morel

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Plasma 1,3-β-d-glucan levels predict adverse clinical outcomes in critical illness by Georgios D. Kitsios, Daniel Kotok, Haopu Yang, Malcolm A. Finkelman, Yonglong Zhang, Noel Britton, Xiaoyun Li, Marina S. Levochkina, Amy K. Wagner, Caitlin Schaefer, John J. Villandre, Rui Guo, John W. Evankovich, William Bain, Faraaz Shah, Yingze Zhang, Barbara A. Methé, Panayiotis V. Benos, Bryan J. McVerry, Alison Morris

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Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients by Georgios D. Kitsios, Georgios D. Kitsios, Adam Fitch, Dimitris V. Manatakis, Sarah F. Rapport, Kelvin Li, Shulin Qin, Shulin Qin, Joseph Huwe, Yingze Zhang, Yohei Doi, John Evankovich, William Bain, Janet S. Lee, Barbara Methé, Barbara Methé, Panayiotis V. Benos, Alison Morris, Alison Morris, Alison Morris, Bryan J. McVerry, Bryan J. McVerry

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Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis by Kristina L. Buschur, Craig Riley, Aabida Saferali, Peter Castaldi, Grace Zhang, Francois Aguet, Kristin G. Ardlie, Peter Durda, W. Craig Johnson, Silva Kasela, Yongmei Liu, Ani Manichaikul, Stephen S. Rich, Jerome I. Rotter, Josh Smith, Kent D. Taylor, Russell P. Tracy, Tuuli Lappalainen, R. Graham Barr, Frank Sciurba, Craig P. Hersh, Panayiotis V. Benos

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Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. by Katherine Belov, Janine E Deakin, Anthony T Papenfuss, Michelle L Baker, Sandra D Melman, Hannah V Siddle, Nicolas Gouin, David L Goode, Tobias J Sargeant, Mark D Robinson, Matthew J Wakefield, Shaun Mahony, Joseph G R Cross, Panayiotis V Benos, Paul B Samollow, Terence P Speed, Jennifer A Marshall Graves, Robert D Miller

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The upper and lower respiratory tract microbiome in severe aspiration pneumonia by Georgios D. Kitsios, Vi D. Nguyen, Khaled Sayed, Nameer Al-Yousif, Caitlin Schaefer, Faraaz A. Shah, William Bain, Haopu Yang, Adam Fitch, Kelvin Li, Xiaohong Wang, Shulin Qin, Heather Gentry, Yingze Zhang, Jack Varon, Antonio Arciniegas Rubio, Joshua A. Englert, Rebecca M. Baron, Janet S. Lee, Barbara Methé, Panayiotis V. Benos, Alison Morris, Bryan J. McVerry

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Lipidomic signatures align with inflammatory patterns and outcomes in critical illness by Junru Wu, Anthony Cyr, Danielle S. Gruen, Tyler C. Lovelace, Panayiotis V. Benos, Jishnu Das, Upendra K. Kar, Tianmeng Chen, Francis X. Guyette, Mark H. Yazer, Brian J. Daley, Richard S. Miller, Brian G. Harbrecht, Jeffrey A. Claridge, Herb A. Phelan, Brian S. Zuckerbraun, Matthew D. Neal, Pär I. Johansson, Jakob Stensballe, Rami A. Namas, Yoram Vodovotz, Jason L. Sperry, Timothy R. Billiar, PAMPer study group

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