Molecular profiles of blood from numerous species that differ in sensitivity to acute inflammation

Authors: David J. Gregory, Feifei Han, Peng Li, Marina A. Gritsenko, Jennifer Kyle, Frank E. Riley, Deborah Chavez, Vania Yotova, Renata H. M. Sindeaux, Mohamed B. F. Hawash, Fengyun Xu, Li-Yuan Hung, Douglas L. Hayden, Ronald G. Tompkins, Robert E. Lanford, Lester Kobzik, Judith Hellman, Jon M. Jacobs, Luis B. Barreiro, Wenzhong Xiao, H. Shaw Warren

Source: Molecular Medicine, Vol 30, Iss 1, Pp 1-14 (2024)

Subject Terms: Inflammation, Animal models, Genomic response, Therapeutics. Pharmacology, RM1-950, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://doaj.org/toc/1528-3658

Access URL: https://doaj.org/article/614dfb029e6d45748ab85ba693c86421

A network medicine approach to investigating ME/CFS pathogenesis in severely ill patients: a pilot study

Authors: Li-Yuan Hung, Chan-Shuo Wu, Chia-Jung Chang, Peng Li, Kimberly Hicks, Joshua J. Dibble, Braxton Morrison, Chimere L. Smith, Ronald W. Davis, Wenzhong Xiao

Source: Frontiers in Human Neuroscience, Vol 19 (2025)

Subject Terms: network medicine, ME/CFS, chronic fatigue syndrome, neuroimmunology, neurodegenerative diseases, cognitive disorders, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnhum.2025.1509346/full; https://doaj.org/toc/1662-5161

Access URL: https://doaj.org/article/c6991c93d23a4e8abe06c2d3965e14d5

Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing

Authors: Binsheng Gong, Dan Li, Paweł P. Łabaj, Bohu Pan, Natalia Novoradovskaya, Danielle Thierry-Mieg, Jean Thierry-Mieg, Guangchun Chen, Anne Bergstrom Lucas, Jennifer S. LoCoco, Todd A. Richmond, Elizabeth Tseng, Rebecca Kusko, Scott Happe, Timothy R. Mercer, Carlos Pabón-Peña, Michael Salmans, Hagen U. Tilgner, Wenzhong Xiao, Donald J. Johann, Wendell Jones, Weida Tong, Christopher E. Mason, David P. Kreil, Joshua Xu

Source: Scientific Data, Vol 11, Iss 1, Pp 1-13 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2052-4463

Access URL: https://doaj.org/article/73cc5c3ee70441e7acfa9bce7c026093

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Authors: Yifan Zhang, Thomas M. Blomquist, Rebecca Kusko, Daniel Stetson, Zhihong Zhang, Lihui Yin, Robert Sebra, Binsheng Gong, Jennifer S. Lococo, Vinay K. Mittal, Natalia Novoradovskaya, Ji-Youn Yeo, Nicole Dominiak, Jennifer Hipp, Amelia Raymond, Fujun Qiu, Hanane Arib, Melissa L. Smith, Jay E. Brock, Daniel H. Farkas, Daniel J. Craig, Erin L. Crawford, Dan Li, Tom Morrison, Nikola Tom, Wenzhong Xiao, Mary Yang, Christopher E. Mason, Todd A. Richmond, Wendell Jones, Donald J. Johann, Leming Shi, Weida Tong, James C. Willey, Joshua Xu

Source: Genome Biology, Vol 23, Iss 1, Pp 1-21 (2022)

Subject Terms: Cancer genomics, Next-generation sequencing, FFPE, Preanalytics, Precision medicine, Oncopanel sequencing, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/e207f3a869da4a6c9e54ed39c85b42dd

Editorial: Critical assessment of massive data analysis (CAMDA) annual conference 2021

Authors: Paweł P. Łabaj, Joaquin Dopazo, Wenzhong Xiao, David P. Kreil

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: data analysis, benchmarking, open-ended competition, disease mechanisms, COVID-19, drug induced liver injury (DILI), Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1154398/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/b040f96e650f409395625da20868474e

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Authors: Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan, Rebecca Kusko, Steve Bruinsma, Len Trigg, Andreas Scherer, Baitang Ning, Chaoyang Zhang, Christine Glidewell-Kenney, Chunlin Xiao, Eric Donaldson, Fritz J. Sedlazeck, Gary Schroth, Gokhan Yavas, Haiying Grunenwald, Haodong Chen, Heather Meinholz, Joe Meehan, Jing Wang, Jingcheng Yang, Jonathan Foox, Jun Shang, Kelci Miclaus, Lianhua Dong, Leming Shi, Marghoob Mohiyuddin, Mehdi Pirooznia, Ping Gong, Rooz Golshani, Russ Wolfinger, Samir Lababidi, Sayed Mohammad Ebrahim Sahraeian, Steve Sherry, Tao Han, Tao Chen, Tieliu Shi, Wanwan Hou, Weigong Ge, Wen Zou, Wenjing Guo, Wenjun Bao, Wenzhong Xiao, Xiaohui Fan, Yoichi Gondo, Ying Yu, Yongmei Zhao, Zhenqiang Su, Zhichao Liu, Weida Tong, Wenming Xiao, Justin M. Zook, Yuanting Zheng, Huixiao Hong

Source: Genome Biology, Vol 23, Iss 1, Pp 1-26 (2022)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/a888ae17e58a4cf188efc452ccec0462

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Authors: Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann, James C. Willey, Pierre R. Bushel, Ying Yu, Chang Xu, Guangchun Chen, Daniel Burgess, Simon Cawley, Kristina Giorda, Nathan Haseley, Fujun Qiu, Katherine Wilkins, Hanane Arib, Claire Attwooll, Kevin Babson, Longlong Bao, Wenjun Bao, Anne Bergstrom Lucas, Hunter Best, Ambica Bhandari, Halil Bisgin, James Blackburn, Thomas M. Blomquist, Lisa Boardman, Blake Burgher, Daniel J. Butler, Chia-Jung Chang, Alka Chaubey, Tao Chen, Marco Chierici, Christopher R. Chin, Devin Close, Jeffrey Conroy, Jessica Cooley Coleman, Daniel J. Craig, Erin Crawford, Angela del Pozo, Ira W. Deveson, Daniel Duncan, Agda Karina Eterovic, Xiaohui Fan, Jonathan Foox, Cesare Furlanello, Abhisek Ghosal, Sean Glenn, Meijian Guan, Christine Haag, Xinyi Hang, Scott Happe, Brittany Hennigan, Jennifer Hipp, Huixiao Hong, Kyle Horvath, Jianhong Hu, Li-Yuan Hung, Mirna Jarosz, Jennifer Kerkhof, Benjamin Kipp, David Philip Kreil, Paweł Łabaj, Pablo Lapunzina, Peng Li, Quan-Zhen Li, Weihua Li, Zhiguang Li, Yu Liang, Shaoqing Liu, Zhichao Liu, Charles Ma, Narasimha Marella, Rubén Martín-Arenas, Dalila B. Megherbi, Qingchang Meng, Piotr A. Mieczkowski, Tom Morrison, Donna Muzny, Baitang Ning, Barbara L. Parsons, Cloud P. Paweletz, Mehdi Pirooznia, Wubin Qu, Amelia Raymond, Paul Rindler, Rebecca Ringler, Bekim Sadikovic, Andreas Scherer, Egbert Schulze, Robert Sebra, Rita Shaknovich, Qiang Shi, Tieliu Shi, Juan Carlos Silla-Castro, Melissa Smith, Mario Solís López, Ping Song, Daniel Stetson, Maya Strahl, Alan Stuart, Julianna Supplee, Philippe Szankasi, Haowen Tan, Lin-ya Tang, Yonghui Tao, Shraddha Thakkar, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkat J. Thodima, David Thomas, Boris Tichý, Nikola Tom, Elena Vallespin Garcia, Suman Verma, Kimbley Walker, Charles Wang, Junwen Wang, Yexun Wang, Zhining Wen, Valtteri Wirta, Leihong Wu, Chunlin Xiao, Wenzhong Xiao, Shibei Xu, Mary Yang, Jianming Ying, Shun H. Yip, Guangliang Zhang, Sa Zhang, Meiru Zhao, Yuanting Zheng, Xiaoyan Zhou, Christopher E. Mason, Timothy Mercer, Weida Tong, Leming Shi, Wendell Jones, Joshua Xu

Source: Genome Biology, Vol 22, Iss 1, Pp 1-23 (2021)

Subject Terms: Oncopanel sequencing, Target enrichment, Molecular diagnostics, Reproducibility, Analytical performance, Precision medicine, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/c5365bb671514dddbb3d5b324f62ed28

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Authors: Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott Basehore, Anne Bergstrom Lucas, Daniel Burgess, Daniel J. Butler, Simon Cawley, Chia-Jung Chang, Guangchun Chen, Tao Chen, Yun-Ching Chen, Daniel J. Craig, Angela del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, Yingyi Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff Jasper, Giuseppe Jurman, David Philip Kreil, Paweł Łabaj, Kevin Lai, Jianying Li, Quan-Zhen Li, Yulong Li, Zhiguang Li, Zhichao Liu, Mario Solís López, Kelci Miclaus, Raymond Miller, Vinay K. Mittal, Marghoob Mohiyuddin, Carlos Pabón-Peña, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Weida Tong, Leming Shi, Joshua Xu

Source: Genome Biology, Vol 22, Iss 1, Pp 1-38 (2021)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/7cb57d840cc4477294d87b6e0d997c1a

FastMM: an efficient toolbox for personalized constraint-based metabolic modeling

Authors: Gong-Hua Li, Shaoxing Dai, Feifei Han, Wenxin Li, Jingfei Huang, Wenzhong Xiao

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-7 (2020)

Subject Terms: FastMM, Constraint-based model, Metabolic modeling, Metabolism, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-3410-4; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/4f5c4bd877d94e75932160cf465a614c

Correction to: FastMM: an efficient toolbox for personalized constraint-based metabolic modeling

Authors: Gong-Hua Li, Shaoxing Dai, Feifei Han, Wenxing Li, Jingfei Huang, Wenzhong Xiao

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-1 (2020)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-03723-y; https://doaj.org/toc/1471-2105

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Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies

Authors: Weihong Xu, Hong Gao, Junhee Seok, Julie Wilhelmy, Michael N. Mindrinos, Ronald W. Davis, Wenzhong Xiao

Source: BioTechniques, Vol 52, Iss 6, Pp 386-388 (2012)

Subject Terms: microarray, transcriptome profiling, coding SNP, outlier detection, sample tracking, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/0736-6205; https://doaj.org/toc/1940-9818

Access URL: https://doaj.org/article/15e95a5158ed46cc9f62367ca96f8cfd

A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data.

Authors: Junhee Seok, Ronald W Davis, Wenzhong Xiao

Source: PLoS ONE, Vol 10, Iss 5, p e0122103 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4416884?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/20fe7185f4244a32b8affdb270e14bfb

Yeast tRNA as Carrier in the Isolation of Microscale RNA for Global Amplification and Expression Profiling

Authors: Q. Tian Wang, Wenzhong Xiao, Michael Mindrinos, Ronald W. Davis

Source: BioTechniques, Vol 33, Iss 4, Pp 788-796 (2002)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/0736-6205; https://doaj.org/toc/1940-9818

Access URL: https://doaj.org/article/c65941ac593a4698b38b3c10813f3d88

Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.

Authors: Junhee Seok, Weihong Xu, Hui Jiang, Ronald W Davis, Wenzhong Xiao

Source: PLoS ONE, Vol 7, Iss 2, p e31440 (2012)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3270033?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/1a5b0a99b1e7439c9914b5fb64cb6671

Distinctive responsiveness to stromal signaling accompanies histologic grade programming of cancer cells.

Authors: Maria Gloria Luciani, Junhee Seok, Aejaz Sayeed, Stacey Champion, William H Goodson, Stefanie S Jeffrey, Wenzhong Xiao, Michael Mindrinos, Ronald W Davis, Shanaz H Dairkee

Source: PLoS ONE, Vol 6, Iss 5, p e20016 (2011)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3098270?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/ea64fe19d3094af0bcce89a1ef5923f8

Involvement of skeletal muscle gene regulatory network in susceptibility to wound infection following trauma.

Authors: Yiorgos Apidianakis, Michael N Mindrinos, Wenzhong Xiao, George P Tegos, Michail I Papisov, Michael R Hamblin, Ronald W Davis, Ronald G Tompkins, Laurence G Rahme

Source: PLoS ONE, Vol 2, Iss 12, p e1356 (2007)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC2131783?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/5410d6b7992c484083fdc4b07a1bb33f

A transcriptional profile of aging in the human kidney.

Authors: Graham E J Rodwell, Rebecca Sonu, Jacob M Zahn, James Lund, Julie Wilhelmy, Lingli Wang, Wenzhong Xiao, Michael Mindrinos, Emily Crane, Eran Segal, Bryan D Myers, James D Brooks, Ronald W Davis, John Higgins, Art B Owen, Stuart K Kim

Source: PLoS Biology, Vol 2, Iss 12, p e427 (2004)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0020427&type=printable; https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/220b24b3bca64240ad25a83ca74106dc

Integrative analysis of the mitochondrial proteome in yeast.

Authors: Holger Prokisch, Curt Scharfe, David G Camp, Wenzhong Xiao, Lior David, Christophe Andreoli, Matthew E Monroe, Ronald J Moore, Marina A Gritsenko, Christian Kozany, Kim K Hixson, Heather M Mottaz, Hans Zischka, Marius Ueffing, Zelek S Herman, Ronald W Davis, Thomas Meitinger, Peter J Oefner, Richard D Smith, Lars M Steinmetz

Source: PLoS Biology, Vol 2, Iss 6, p e160 (2004)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC423137?pdf=render; https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/25c00d4e3c8142d496a874910156ef45

A comprehensive rat transcriptome built from large scale RNA-seq-based annotation.

Authors: Xiangjun Ji, Peng Li, Fuscoe, James C., Geng Chen, Wenzhong Xiao, Leming Shi, Baitang Ning, Zhichao Liu, Huixiao Hong, Jun Wu, Jinghua Liu, Lei Guo, Kreil, David P., Łabaj, Paweł P., Liping Zhong, Wenjun Bao, Yong Huang, Jian He, Yongxiang Zhao, Weida Tong

Source: Nucleic Acids Research; 9/4/2020, Vol. 48 Issue 15, p8320-8331, 12p, 1 Chart, 5 Graphs

Prospective Validation of a Transcriptomic Metric in Severe Trauma.

Authors: Raymond, Steven L., Hawkins, Russell B., Zhongkai Wang, Mira, Juan C., Stortz, Julie A., Feifei Han, Lanz, Jennifer D., Hennessy, Laura V., Brumback, Babette A., Baker, Henry V., Efron, Philip A., Brakenridge, Scott C., Wenzhong Xiao, Tompkins, Ronald G., Cuschieri, Joseph, Moore, Frederick A., Maier, Ronald V., Moldawer, Lyle L.

Source: Annals of Surgery; May2020, Vol. 271 Issue 5, p802-810, 9p