Publications

Stephany Flores Ramos, Nicole Siguenza, Wuling Zhong, Ipsita Mohanty, Amulya Lingaraju, R. Alexander Richter, Smruthi Karthikeyan, April L. Lukowski, Qiyun Zhu, Wilhan D.G. Nunes, et al. (2025). Metatranscriptomics uncovers diurnal functional shifts in bacterial transgenes with profound metabolic effects. Cell Host & Microbe.

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Hongli Ma, Letian Gao, Yunfan Jin, Jianwei Ma, Yilan Bai, Xiaofan Liu, Pengfei Bao, Ke Liu, Zhenjiang Zech Xu, Zhi John Lu (2025). RNA–ligand interaction scoring via data perturbation and augmentation modeling. Nature Computational Science.

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Zewen Han, Yichen Hu, Xin Lin, Hongyu Cheng, Biao Dong, Xuan Liu, Buling Wu, Zhenjiang Zech Xu (2025). Systematic Analyses Uncover Robust Salivary Microbial Signatures and Host-Microbiome Perturbations in Oral Squamous Cell Carcinoma. mSystems.

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Ping Li, Ru Qu, Ming Li, Ping Sheng, Liang Jin, Xiaochang Huang, Zhenjiang Zech Xu (2024). Impacts of Food Additives on Gut Microbiota and Host Health. Food Research International.

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Ming Li, Ru Qu, Ping Li, Xuan Mo, Juan Liu, Zhenjiang Zech Xu (2024). Green Tea Polyphenols Reduced Porphyromonas Gingivalis Virulence and Ameliorated Aggravated Gut Inflammation by Improving Immunity and Gut Microbiota Dysbiosis. Food Bioscience.

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Huiyu Zhang, Qiwen Zhang, Yan Li, Zhenjiang Zech Xu, Xiaochang Huang (2024). Screening of Lactic Acid Bacteria from Freshwater Fish Intestines and Their Effects on Growth, Immunity, and Disease Resistance in Zebrafish. Aquaculture International.

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Wenjing Li, Bin Wang, Jin Dai, Yan Kou, Xiaojun Chen, Yi Pan, Shuangwei Hu, Zhenjiang Zech Xu (2024). Partial Order Relation--Based Gene Ontology Embedding Improves Protein Function Prediction. Briefings in Bioinformatics.

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Zachary M. Burcham, Aeriel D. Belk, Bridget B. McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R. Zhang, Pixu Shi, Alexandra Emmons, et al. (2024). A Conserved Interdomain Microbial Network Underpins Cadaver Decomposition despite Environmental Variables. Nature Microbiology.

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Bin Wang, Yulong Shen, Jingyan Fang, Xiaoquan Su, Zhenjiang Zech Xu (2024). DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis. Advanced Science.

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Yan Li, Yichen Hu, Xiang Zhan, Ying Song, Meng Xu, Shijie Wang, Xiaochang Huang, Zhenjiang Zech Xu (2023). Meta-Analysis Reveals Helicobacter Pylori Mutual Exclusivity and Reproducible Gastric Microbiome Alterations during Gastric Carcinoma Progression. Gut Microbes.

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Ting Fu, Tao Huan, Gibraan Rahman, Hui Zhi, Zhenjiang Zech Xu, Tae Gyu Oh, Jian Guo, Sally Coulter, Anupriya Tripathi, Cameron Martino, et al. (2023). Paired Microbiome and Metabolome Analyses Associate Bile Acid Changes with Colorectal Cancer Progression. Cell Reports.

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Lepeng Zhou, Wen Qiu, Jie Wang, Aihua Zhao, Chuhui Zhou, Tao Sun, Ziyu Xiong, Peihua Cao, Wei Shen, Jingfen Chen, et al. (2023). Effects of Vaginal Microbiota Transfer on the Neurodevelopment and Microbiome of Cesarean-Born Infants: A Blinded Randomized Controlled Trial. Cell Host & Microbe.

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Feng Liu, Hui Lu, Biao Dong, Xiaochang Huang, Hongyu Cheng, Ru Qu, Yichen Hu, Luyun Zhong, Zhenni Guo, Yuehua You, et al. (2023). Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/-- Bacteria. mSystems.

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Zhiyuan Pan, Yichen Hu, Zongyu Huang, Ni Han, Yan Li, Xiaomei Zhuang, Jiye Yin, Hui Peng, Quansheng Gao, Wenpeng Zhang, et al. (2022). Alterations in Gut Microbiota and Metabolites Associated with Altitude-Induced Cardiac Hypertrophy in Rats during Hypobaric Hypoxia Challenge. Science China Life Sciences.

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Ping Li, Ming Li, Tao Wu, Ying Song, Yan Li, Xiaochang Huang, Hui Lu, Zhenjiang Zech Xu (2022). Systematic Evaluation of Antimicrobial Food Preservatives on Glucose Metabolism and Gut Microbiota in Healthy Mice. npj Science of Food.

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Shanwen Chen, Yunfan Jin, Siqi Wang, Shaozhen Xing, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, et al. (2022). Cancer Type Classification Using Plasma Cell-Free RNAs Derived from Human and Microbes. eLife.

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Yichen Hu, Amnon Amir, Xiaochang Huang, Yan Li, Shi Huang, Elaine Wolfe, Sophie Weiss, Rob Knight, Zhenjiang Zech Xu (2022). Diurnal and Eating-Associated Microbial Patterns Revealed via High-Frequency Saliva Sampling. Genome Research.

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Ya-Shuai Kong, Hong-Yu Ren, Rui Liu, Ricardo R. da Silva, Alexander A. Aksenov, Alexey V. Melnik, Ming Zhao, Miao-Miao Le, Zhi-Wei Ren, Feng-Qing Xu, et al. (2022). Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation. Journal of Agricultural and Food Chemistry.

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Yichen Hu, Zhiyuan Pan, Zongyu Huang, Yan Li, Ni Han, Xiaomei Zhuang, Hui Peng, Quansheng Gao, Qing Wang, B. J. Yang Lee, et al. (2022). Gut Microbiome-Targeted Modulations Regulate Metabolic Profiles and Alleviate Altitude-Related Cardiac Hypertrophy in Rats. Microbiology Spectrum.

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Han Hu, Yuxiang Tan, Chenhao Li, Junyu Chen, Yan Kou, Zhenjiang Zech Xu, Yang-Yu Liu, Yan Tan, Lei Dai (2022). StrainPanDA: Linked Reconstruction of Strain Composition and Gene Content Profiles via Pangenome-Based Decomposition of Metagenomic Data. iMeta.

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Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Zech Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, et al. (2021). Gut Microbiota from Green Tea Polyphenol-Dosed Mice Improves Intestinal Epithelial Homeostasis and Ameliorates Experimental Colitis. Microbiome.

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Hui Lu, Ping Li, Xiaochang Huang, Charles Hantsing Wang, Ming Li, Zhenjiang Zech Xu (2021). Zebrafish Model for Human Gut Microbiome-Related Studies: Advantages and Limitations. Medicine in Microecology.

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Ping Li, Shengliang Deng, Zhenjiang Zech Xu (2021). Toxicant Substitutes in Immunological Assays for Mycotoxins Detection: A Mini Review. Food Chemistry.

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Zhi Liu, Kai Mi, Zhenjiang Zech Xu, Qiangkun Zhang, Xingyin Liu (2021). PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community. Genomics, Proteomics & Bioinformatics.

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Heather Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David O. Carter, Aaron Lynne, Rob Knight, Zhenjiang Zech Xu, Sibyl Bucheli, Jessica L. Metcalf (2021). A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere.

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Robert L. Thomas, Lingjing Jiang, John S. Adams, Zhenjiang Zech Xu, Jian Shen, Stefan Janssen, Gail Ackermann, Dirk Vanderschueren, Steven Pauwels, Rob Knight, et al. (2020). Vitamin D Metabolites and the Gut Microbiome in Older Men. Nature Communications.

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Mengchen Guo, Huixia Wang, Sixie Xu, Yaoyao Zhuang, Jingang An, Chuan Su, Yankai Xia, Jingyun Chen, Zhenjiang Zech Xu, Qisha Liu, et al. (2020). Alteration in Gut Microbiota Is Associated with Dysregulation of Cytokines and Glucocorticoid Therapy in Systemic Lupus Erythematosus. Gut Microbes.

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Xiaoquan Su, Gongchao Jing, Zheng Sun, Lu Liu, Zhenjiang Xu, Daniel McDonald, Zengbin Wang, Honglei Wang, Antonio Gonzalez, Yufeng Zhang, et al. (2020). Multiple-Disease Detection and Classification across Cohorts via Microbiome Search. mSystems.

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Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vázquez-Baeza, et al. (2020). Human Skin, Oral, and Gut Microbiomes Predict Chronological Age. mSystems.

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Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G. Sanders, Pedro Belda-Ferre, Gabriel A. Al-Ghalith, Evguenia Kopylova, Daniel McDonald, et al. (2019). Phylogenomics of 10,575 Genomes Reveals Evolutionary Proximity between Domains Bacteria and Archaea. Nature Communications.

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Yanwen Xue, Fang Huang, Rongxue Tang, Qingsheng Fan, Bing Zhang, Zhenjiang Xu, Xiaoming Sun, Zheng Ruan (2019). Chlorogenic Acid Attenuates Cadmium-Induced Intestinal Injury in Sprague–Dawley Rats. Food and Chemical Toxicology.

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Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, et al. (2019). Optimizing Sequencing Protocols for Leaderboard Metagenomics by Combining Long and Short Reads. Genome Biology.

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Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, et al. (2019). Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2. Nature Biotechnology.

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Whitney A. Kodama, Zhenjiang Z. Xu, Jessica L. Metcalf, Se Jin Song, Nicholas Harrison, Rob Knight, David O. Carter, Christopher B. Happy (2019). Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. Journal of Forensic Sciences.

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Anupriya Tripathi, Zhenjiang Zech Xu, Jin Xue, Orit Poulsen, Antonio Gonzalez, Gregory Humphrey, Michael J. Meehan, Alexey V. Melnik, Gail Ackermann, Dan Zhou, et al. (2019). Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems. mSystems.

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Cyrielle Caussy, Anupriya Tripathi, Greg Humphrey, Shirin Bassirian, Seema Singh, Claire Faulkner, Ricki Bettencourt, Emily Rizo, Lisa Richards, Zhenjiang Z. Xu, et al. (2019). A Gut Microbiome Signature for Cirrhosis Due to Nonalcoholic Fatty Liver Disease. Nature Communications.

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Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, et al. (2019). Calour: An Interactive, Microbe-Centric Analysis Tool. mSystems.

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Yuqing Feng, Yunfeng Duan, Zhenjiang Xu, Na Lyu, Fei Liu, Shihao Liang, Baoli Zhu (2019). An Examination of Data from the American Gut Project Reveals That the Dominance of the Genus Bifidobacterium Is Associated with the Diversity and Robustness of the Gut Microbiota. MicrobiologyOpen.

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Johannes Braun, Sandra Fischer, Zhenjiang Z. Xu, Hongying Sun, Dalia H. Ghoneim, Anna T. Gimbel, Uwe Plessmann, Henning Urlaub, David H. Mathews, Julia E. Weigand (2018). Identification of New High Affinity Targets for Roquin Based on Structural Conservation. Nucleic Acids Research.

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Daniel McDonald, Yoshiki Vázquez-Baeza, David Koslicki, Jason McClelland, Nicolai Reeve, Zhenjiang Xu, Antonio Gonzalez, Rob Knight (2018). Striped UniFrac: Enabling Microbiome Analysis at Unprecedented Scale. Nature Methods.

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Rob Knight, Alison Vrbanac, Bryn C. Taylor, Alexander Aksenov, Chris Callewaert, Justine Debelius, Antonio Gonzalez, Tomasz Kosciolek, Laura-Isobel McCall, Daniel McDonald, et al. (2018). Best Practices for Analysing Microbiomes. Nature Reviews Microbiology.

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Amir Zarrinpar, Amandine Chaix, Zhenjiang Z. Xu, Max W. Chang, Clarisse A. Marotz, Alan Saghatelian, Rob Knight, Satchidananda Panda (2018). Antibiotic-Induced Microbiome Depletion Alters Metabolic Homeostasis by Affecting Gut Signaling and Colonic Metabolism. Nature Communications.

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Stefan Janssen, Daniel McDonald, Antonio Gonzalez, Jose A. Navas-Molina, Lingjing Jiang, Zhenjiang Zech Xu, Kevin Winker, Deborah M. Kado, Eric Orwoll, Mark Manary, et al. (2018). Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems.

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Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, et al. (2018). American Gut: An Open Platform for Citizen Science Microbiome Research. mSystems.

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Jennifer M. Michaud, Luke R. Thompson, Drishti Kaul, Josh L. Espinoza, R. Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M. Pham, Charlotte M. Beall, Francesca Malfatti, et al. (2018). Taxon-Specific Aerosolization of Bacteria and Viruses in an Experimental Ocean-Atmosphere Mesocosm. Nature Communications.

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Joshua B. Richardson, Blair C. R. Dancy, Cassandra L. Horton, Young S. Lee, Michael S. Madejczyk, Zhenjiang Zech Xu, Gail Ackermann, Gregory Humphrey, Gustavo Palacios, Rob Knight, et al. (2018). Exposure to Toxic Metals Triggers Unique Responses from the Rat Gut Microbiota. Scientific Reports.

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Aeriel Belk, Zhenjiang Zech Xu, David O. Carter, Aaron Lynne, Sibyl Bucheli, Rob Knight, Jessica L. Metcalf (2018). Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. Genes.

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Youlian Zhou, Zhenjiang Zech Xu, Yan He, Yunsheng Yang, Le Liu, Qianyun Lin, Yuqiang Nie, Mingsong Li, Fachao Zhi, Side Liu, et al. (2018). Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. mSystems.

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Jeremiah J. Minich, Qiyun Zhu, Zhenjiang Zech Xu, Amnon Amir, Maxon Ngochera, Moses Simwaka, Eric E. Allen, Hastings Zidana, Rob Knight (2018). Microbial Effects of Livestock Manure Fertilization on Freshwater Aquaculture Ponds Rearing Tilapia (Oreochromis Shiranus) and North African Catfish (Clarias Gariepinus). MicrobiologyOpen.

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Yoshiki Vázquez-Baeza, Antonio Gonzalez, Zhenjiang Zech Xu, Alex Washburne, Hans H. Herfarth, R. Balfour Sartor, Rob Knight (2018). Guiding Longitudinal Sampling in IBD Cohorts. Gut.

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Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, et al. (2017). A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity. Nature.

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Jessica L. Metcalf, Zhenjiang Z. Xu, Amina Bouslimani, Pieter Dorrestein, David O. Carter, Rob Knight (2017). Microbiome Tools for Forensic Science. Trends in Biotechnology.

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Scott D. Wankel, Wiebke Ziebis, Carolyn Buchwald, Chawalit Charoenpong, Dirk de Beer, Jane Dentinger, Zhenjiang Xu, Karsten Zengler (2017). Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments. Nature Communications.

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Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez, et al. (2017). Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems.

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Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R. Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, et al. (2017). Normalization and Microbial Differential Abundance Strategies Depend upon Data Characteristics. Microbiome.

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Amina Bouslimani, Alexey V. Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R. da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein (2016). Lifestyle Chemistries from Phones for Individual Profiling. Proceedings of the National Academy of Sciences.

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Jack A. Gilbert, Robert A. Quinn, Justine Debelius, Zhenjiang Z. Xu, James Morton, Neha Garg, Janet K. Jansson, Pieter C. Dorrestein, Rob Knight (2016). Microbiome-Wide Association Studies Link Dynamic Microbial Consortia to Disease. Nature.

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Sophie Weiss, Will Van Treuren, Catherine Lozupone, Karoline Faust, Jonathan Friedman, Ye Deng, Li Charlie Xia, Zhenjiang Zech Xu, Luke Ursell, Eric J. Alm, et al. (2016). Correlation Detection Strategies in Microbial Data Sets Vary Widely in Sensitivity and Precision. The ISME Journal.

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Se Jin Song, Amnon Amir, Jessica L. Metcalf, Katherine R. Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight (2016). Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems.

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Evguenia Kopylova, Jose A. Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J. Gregory Caporaso, Rob Knight (2016). Open-Source Sequence Clustering Methods Improve the State Of the Art. mSystems.

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Justine Debelius, Se Jin Song, Yoshiki Vázquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight (2016). Tiny Microbes, Enormous Impacts: What Matters in Gut Microbiome Studies?. Genome Biology.

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Zhenjiang Zech Xu, David H. Mathews (2016). Secondary Structure Prediction of Single Sequences Using RNAstructure. RNA Structure Determination.

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Zhenjiang Zech Xu, David H. Mathews (2016). Prediction of Secondary Structures Conserved in Multiple RNA Sequences. RNA Structure Determination.

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Jessica L. Metcalf, Zhenjiang Zech Xu, Sophie Weiss, Simon Lax, Will Van Treuren, Embriette R. Hyde, Se Jin Song, Amnon Amir, Peter Larsen, Naseer Sangwan, et al. (2016). Microbial Community Assembly and Metabolic Function during Mammalian Corpse Decomposition. Science.

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Zhenjiang Zech Xu, David H. Mathews (2016). Experiment-Assisted Secondary Structure Prediction with RNAstructure. RNA Structure Determination.

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Justine W. Debelius, Yoshiki Vázquez-Baeza, Daniel McDonald, Zhenjiang Xu, Elaine Wolfe, Rob Knight (2015). Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project. Journal of Microbiology & Biology Education.

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Fei Teng, Fang Yang, Shi Huang, Cunpei Bo, Zhenjiang Xu, Amnon Amir, Rob Knight, Junqi Ling, Jian Xu (2015). Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota. Cell Host & Microbe.

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Yinghan Fu, Zhenjiang Xu, Zhi J. Lu, Shan Zhao, David H. Mathews (2015). Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS ONE.

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Daniel McDonald, Zhenjiang Xu, Embriette R. Hyde, Rob Knight (2015). Ribosomal RNA, the Lens into Life. RNA.

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Alexandra J. Obregon-Tito, Raul Y. Tito, Jessica Metcalf, Krithivasan Sankaranarayanan, Jose C. Clemente, Luke K. Ursell, Zhenjiang Xu, Will Van Treuren, Rob Knight, Patrick M. Gaffney, et al. (2015). Subsistence Strategies in Traditional Societies Distinguish Gut Microbiomes. Nature Communications.

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Gang Yang, Zhenjiang Xu, Xiangli Tian, Shuanglin Dong, Mo Peng (2015). Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation. Biochemical and Biophysical Research Communications.

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Zhenjiang Xu, Rob Knight (2015). Dietary Effects on Human Gut Microbiome Diversity. British Journal of Nutrition.

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Zhenjiang Xu, Daniel Malmer, Morgan G. I. Langille, Samuel F. Way, Rob Knight (2014). Which Is More Important for Classifying Microbial Communities: Who's There or What They Can Do?. The ISME Journal.

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William A. Walters, Zhenjiang Xu, Rob Knight (2014). Meta-Analyses of Human Gut Microbes Associated with Obesity and IBD. FEBS Letters.

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Jeremiah J. Trausch, Zhenjiang Xu, Andrea L. Edwards, Francis E. Reyes, Phillip E. Ross, Rob Knight, Robert T. Batey (2014). Structural Basis for Diversity in the SAM Clan of Riboswitches. Proceedings of the National Academy of Sciences.

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José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, et al. (2013). Advancing Our Understanding of the Human Microbiome Using QIIME. Methods in Enzymology.

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Karyn Schmidt, Zhenjiang Xu, David H. Mathews, J. Scott Butler (2012). Air Proteins Control Differential TRAMP Substrate Specificity for Nuclear RNA Surveillance. RNA.

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Zhenjiang Xu, Anthony Almudevar, David H. Mathews (2012). Statistical Evaluation of Improvement in RNA Secondary Structure Prediction. Nucleic Acids Research.

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Michael-Paul Vockenhuber, Cynthia M. Sharma, Michaela G. Statt, Denis Schmidt, Zhenjiang Xu, Sascha Dietrich, Heiko Liesegang, David H. Mathews, Beatrix Suess (2011). Deep Sequencing-Based Identification of Small Non-Coding RNAs in Streptomyces Coelicolor. RNA Biology.

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Zhenjiang Xu, David H. Mathews (2011). Multilign: An Algorithm to Predict Secondary Structures Conserved in Multiple RNA Sequences. Bioinformatics.

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