Michigan State University
Patrick P Edger*, Melanie J.A. Body, Sonia De Donno, Adrian E Platts, Jianrong Wang, and Jiming Jiang
Genome Evolution through Polyploidy: Enhancing Plant Stress Resilience in Agriculture
PNAS (Accepted), 2026
Emma L. Bush, Brigette Berke-Reynolds, Kaitlyn M. Hutchins, Xinrui Yu, Jorge Colon-Rosado, FuJung Chang, John Curran, Jiaxin Yang, Liangliang Sun, Jianrong Wang* and Yu Zhang*
CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire
Nature Communications, 2025
Sikta Das Adhikari, Nina G Steele, Brian Theisen, Jianrong Wang*, Yuehua Cui*
SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection
Nucleic Acids Research, 2025
Hao Wang, Jiaxin Yang, Xinrui Yu, Yu Zhang*, Jianliang Qian*, Jianrong Wang*
Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution
Nature Communications, 2025 (Featured Article in Nature Communications Editors’ Highlights)
Sikta Das Adhikari, Jiaxin Yang, Jianrong Wang, Yuehua Cui
Recent advances in spatially variable gene detection in spatial transcriptomics
Computational and Structural Biotechnology Journal, 2024
Jiaxin Yang, Sikta Das Adhikari, Hao Wang, Binbin Huang, Wenjie Qi, Yuehua Cui, Jianrong Wang
De novo prediction of functional effects of genetic variants from DNA sequences based on context-specific molecular information
Frontiers in Systems Biology, 2024
Sikta Das Adhikari, Yuehua Cui*, Jianrong Wang*
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases
Briefings in Bioinformatics, 2024
Yi-Yin Tai, Qiujun Yu, Ying Tang, Wei Sun, Neil J Kelly, Satoshi Okawa, Jingsi Zhao, Tae-Hwi Schwantes-An, Caroline Lacoux, Stephanie Torrino, Yassmin Al Aaraj, Wadih El Khoury, Vinny Negi, Mingjun Liu, Catherine G Corey, Frances Belmonte, Sara O Vargas, Brian Schwartz, Bal Bhat, B Nelson Chau, Jason H Karnes, Taijyu Satoh, Robert J Barndt, Haodi Wu, Victoria N Parikh, Jianrong Wang, Yingze Zhang, Dennis McNamara, Gang Li, Gil Speyer, Bing Wang, Sruti Shiva, Brett Kaufman, Seungchan Kim, Delphine Gomez, Bernard Mari, Michael H Cho, Adel Boueiz, Michael W Pauciulo, Laura Southgate, Richard C Trembath, Olivier Sitbon, Marc Humbert, Stefan Graf, Nicholas W Morrell, Christopher J Rhodes, Martin R Wilkins, Mehdi Nouraie, William C Nichols, Ankit A Desai, Thomas Bertero, Stephen Y Chan
Allele-specific control of rodent and human lncRNA KMT2E-AS1 promotes hypoxic endothelial pathology in pulmonary hypertension
Science translational medicine, 2024
Anissia Ait Saada, Wenying Guo, Alex B Costa, Jiaxin Yang, Jianrong Wang, Kirill S Lobachev
Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions
Nucleic Acids Research, 2023
Sambit Roy, Aierken Abudu, Irving Salinas, Niharika Sinha, Holly Cline-Fedewa, Alexandra M Yaw, Wenjie Qi, Todd A Lydic, Diana L Takahashi, Jon D Hennebold, Hanne M Hoffmann, Jianrong Wang, Aritro Sen
Androgen-mediated Perturbation of the Hepatic Circadian System Through Epigenetic Modulation Promotes NAFLD in PCOS Mice
Endocrinology, 2022
Niharika Sinha, Chad S Driscoll, Wenjie Qi, Binbin Huang, Sambit Roy, Jason G Knott, Jianrong Wang, Aritro Sen
Anti-Müllerian hormone treatment enhances oocyte quality, embryonic development and live birth rate
Biology of Reproduction, 2022
Hao Wang, Jiaxin Yang, Yu Zhang, Jianliang Qian*, Jianrong Wang*
Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO
Nature Communications, 2022
Yan Liu, Yuzhao Gao, Ruiling Fang, Hongyan Cao, Jian Sa, Jianrong Wang, Hongqi Liu, Tong Wang, Yuehua Cui
Identifying complex gene–gene interactions: a mixed kernel omnibus testing approach
Briefings in Bioinformatics, 2021
Hao Wang, Binbin Huang, Jianrong Wang
Predict long-range enhancer regulation based on protein–protein interactions between transcription factors
Nucleic Acids Research, 2021
Bryce D Warren, Soo H Ahn, Kathryn S Brittain, Manjunatha K Nanjappa, Hao Wang, Jianrong Wang, Gustavo Blanco, Gladis Sanchez, Yong Fan, Brian K Petroff, Paul S Cooke, Margaret G Petroff
Multiple lesions contribute to infertility in males lacking autoimmune regulator
The American Journal of Pathology, 2021
Hao Wang, Jiaxin Yang, Yu Zhang, Jianrong Wang
Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions
Methods, 2021
Sambit Roy^, Binbin Huang^, Niharika Sinha, Jianrong Wang, Aritro Sen
Androgens regulate ovarian gene expression by balancing Ezh2-Jmjd3 mediated H3K27me3 dynamics
PLoS genetics, 2021
Hao Wang, Jiaxin Yang, Jianrong Wang
Leverage large-scale biological networks to decipher the genetic basis of human diseases using machine learning
Artificial Neural Networks, 2020
Jiao Chen, Jiayu Shang, Jianrong Wang, Yanni Sun
A binning tool to reconstruct viral haplotypes from assembled contigs
BMC bioinformatics, 2019
Sean L Nguyen, Jacob W Greenberg, Hao Wang, Benjamin W Collaer, Jianrong Wang, Margaret G Petroff
Quantifying murine placental extracellular vesicles across gestation and in preterm birth data with tidyNano: A computational framework for analyzing and visualizing nanoparticle data in R
PLoS One, 2019
Lavanya Rishishwar, Lu Wang, Jianrong Wang, Soojin V Yi, Joseph Lachance, I King Jordan
Evidence for positive selection on recent human transposable element insertions
Gene, 2018
Feng Shao, Jianrong Wang, Hongen Xu, Zuogang Peng
FishTEDB: a collective database of transposable elements identified in the complete genomes of fish
Database, 2018
Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis, Guo-Cheng Yuan
Multi-scale chromatin state annotation using a hierarchical hidden Markov model
Nature communications, 2017
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Patterns of transposable element expression and insertion in cancer
Frontiers in Molecular Biosciences, 2016
Jianrong Wang, Cristina Vicente-García, Davide Seruggia, Eduardo Moltó, Ana Fernandez-Miñán, Ana Neto, Elbert Lee, José Luis Gómez-Skarmeta, Lluís Montoliu, Victoria V Lunyak, I King Jordan
MIR retrotransposon sequences provide insulators to the human genome
Proceedings of the National Academy of Sciences, 2015
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Pouya Kheradpour, Zhizhuo Zhang, Alireza Heravi-Moussavi, Yaping Liu, Viren Amin, Michael J Ziller, John W Whitaker, Matthew D Schultz, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Jianrong Wang, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Andreas Pfenning, Xinchen Wang, Melina Claussnitzer, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven Jones, Wei Li, Marco Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis, Roadmap Epigenomics Consortium
Integrative analysis of 111 reference human epigenomes
Nature, 2015
Daudi Jjingo, Andrew B Conley, Jianrong Wang, Leonardo Mariño-Ramírez, Victoria V Lunyak, I King Jordan
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression
Mobile DNA, 2014
Daudi Jjingo, Jianrong Wang, Andrew B Conley, Victoria V Lunyak, I King Jordan
Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome
Bioinformatics, 2013
Ke Xu, Jianrong Wang, Navin Elango, Soojin V Yi
The evolution of lineage-specific clusters of single nucleotide substitutions in the human genome
Molecular Phylogenetics and Evolution, 2013
Aswathy Sebastian, Lavanya Rishishwar, Jianrong Wang, Karen F Bernard, Andrew B Conley, Nael A McCarty, I King Jordan
Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain
Gene, 2013
Jianrong Wang, Victoria V Lunyak, I King Jordan
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets
Bioinformatics, 2013
Jianrong Wang, Victoria V Lunyak, I King Jordan
Chromatin signature discovery via histone modification profile alignments
Nucleic acids research, 2012
Benjamin J Blackwell, Mary F Lopez, Jianrong Wang, Bryan Krastins, David Sarracino, James R Tollervey, Marek Dobke, I King Jordan, Victoria V Lunyak
Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly
Mobile Genetic Elements, 2012
Jianrong Wang, Victoria V Lunyak, I King Jordan
Genome-wide prediction and analysis of human chromatin boundary elements
Nucleic acids research, 2012
Jianrong Wang, Glenn J Geesman, Sirkka Liisa Hostikka, Michelle Atallah, Benjamin Blackwell, Elbert Lee, Peter J Cook, Bogdan Pasaniuc, Goli Shariat, Eran Halperin, Marek Dobke, Michael G Rosenfeld, I King Jordan, Victoria V Lunyak
Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal
Cell cycle, 2011
Jianrong Wang, Ahsan Huda, Victoria V Lunyak, I King Jordan
A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags
Bioinformatics, 2010
Jianrong Wang, Nathan J Bowen, Leonardo Mariño-Ramírez, I King Jordan
A c-Myc regulatory subnetwork from human transposable element sequences
Molecular BioSystems, 2009