Article
Multidisciplinary Sciences
Ruiqi Li, Shuchong Mei, Qiang Ding, Qingming Wang, Li Yu, Fuming Zi
Summary: HK2 is highly expressed in most tumors and related to the progression of some tumors. HK2 expression is associated with the infiltration of specific cell types in certain tumors.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Isabella Wu, Xin Wang
Summary: This article investigates the early diagnosis and treatment of non-small cell lung cancer (NSCLC) and proposes a novel composite selection index (C-Index) to identify effective biomarkers. Through topological data analysis and validation with machine learning models, they discovered a 4-gene biomarker signature that holds promise for the treatment and personalized medicine of NSCLC.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Feng Bo, Li Shengdong, Wang Zongshuai, Cao Fang, Wang Zheng, Gao Chunhua, Li Geng, Kong Ling'An
Summary: This study conducted the analysis of lysine 2-hydroxyisobutyrylation (Khib) modifications in wheat root tissues for the first time, revealing that Khib modification affects various cellular functions and metabolism pathways by influencing a wide range of proteins.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Yunjin Xie, Weiwei Zhou, Jingyi Shi, Mengjia Xu, Zijing Lin, Donghao Li, Jianing Li, Shujun Cheng, Tingting Shao, Juan Xu
Summary: The communication between tumor cells and immune cells plays a vital role in shaping tumor immunity. A comprehensive database, TICCom, was developed to model and characterize the interactions between tumor cells and immune cells. The database collects experimentally-validated and predicted interactions from thousands of studies, providing valuable resources for studying TIC communications.
Review
Plant Sciences
Haoqiang Yu, Qingqing Yang, Fengling Fu, Wanchen Li
Summary: Heterologous expression of exogenous genes and suppression of undesirable genes by RNA interference and CRISPR/Cas technology are more effective than overexpression of endogenous genes for transgenic improvement of crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Kailin Tang, Xuejie Ji, Mengdi Zhou, Zeliang Deng, Yuwei Huang, Genhui Zheng, Zhiwei Cao
Summary: Although transcriptomics technologies have advanced rapidly in the past decades, integrating mixed data from microarray and RNA-seq remains challenging due to inherent variability differences. Rank-In is a novel method proposed to correct nonbiological effects and enable consolidated analysis of blended data. Validated on public cell and tissue samples, Rank-In demonstrated superior classification and prediction accuracy, showing potential for integrative study of cancer profiles.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Kailin Tang, Xuejie Ji, Mengdi Zhou, Zeliang Deng, Yuwei Huang, Genhui Zheng, Zhiwei Cao
Summary: Rank-In is a method that corrects nonbiological effects in mixed microarray and RNA-seq data for integrated analysis. It has been validated to accurately classify samples and achieve high accuracy in predicting differentially expressed genes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Kyung Won Hwang, Jae Won Yun, Hong Sook Kim
Summary: This study aims to unravel the intricate molecular characteristics of FOXA1 mutant prostate cancer through comprehensive in silico analysis. The study identified 1525 differentially expressed genes and discovered KDM1A, MAOA, PDGFB, and HSP90AB1 as potential drug targets. The approved drugs targeting MAOA and KDM1A have the potential to cure FOXA1 mutant primary prostate cancer without lethal side effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jianhan Zhang, Xu Han, Liang Ma, Shuhui Xu, Yihan Lin
Summary: This study reveals the presence of non-genetic heterogeneity within cancer cells, which is characterized by global modulation of gene transcriptional activity. This heterogeneity contributes to variability in the transcriptome size and shows both dynamic and static characteristics. ATP metabolism is suggested to play a role in this heterogeneity, with implications for cancer drug tolerance.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Yunhe Wang, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li
Summary: Detection and diagnosis of cancer are crucial for early prevention and treatment. This article introduces a multiobjective PSO-based hybrid algorithm (MOPSOHA) for optimizing feature selection and diagnosis of cancer data, which outperforms other algorithms in various cancer datasets. The effectiveness of MOPSOHA is demonstrated through its novel encoding strategy, mutation operator, and local search method.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Gongyu Tang, Minsu Cho, Xiaowei Wang
Summary: OncoDB is an online database resource that integrates multi-omics data from TCGA and GTEx studies to study gene expression dysregulation and viral infection in cancer, providing valuable insights into clinical features and outcomes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yuhei Uda, Jordan M. Spatz, Amira Hussein, Joseph H. Garcia, Forest Lai, Chris Dedic, Keertik Fulzele, Sean Dougherty, Margaret Eberle, Chris Adamson, Lowell Misener, Louis Gerstenfeld, Paola Divieti Pajevic
Summary: Bone loss is a significant health concern for astronauts and patients in extended periods of bed rest or paralysis. Osteocytes play a key role in sensing and responding to mechanical forces applied to the skeleton, and under microgravity conditions, there is impairment in osteocyte differentiation and downregulation of key osteocytic genes. Additionally, a genome-wide response to microgravity including changes in glycolysis pathways and mechanical sensitive genes has been observed.
Article
Biochemical Research Methods
Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L. Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, Fabian J. Theis
Summary: Squidpy is a Python framework that combines tools from omics and image analysis to efficiently store, manipulate, and visualize spatial omics data. It is extensible and can be interfaced with other libraries for scalable analysis of spatial omics data.
Review
Oncology
Richard F. Riedel, Mark Agulnik
Summary: Desmoid tumors (DTs) are rare soft tissue mesenchymal neoplasms that can cause impairments, disfigurement, morbidity, and rarely mortality. Most DTs are sporadic with somatic mutations in the gene encoding beta-catenin, while DTs in patients with familial adenomatous polyposis are associated with germline mutations in the APC gene. Pathology review and magnetic resonance imaging are crucial for diagnosis. Surgery, once the standard of care, is now associated with high risk of recurrence and avoidable morbidity, so active surveillance and pain management are recommended. Medical treatment options include tyrosine kinase inhibitors and conventional chemotherapy, while gamma-secretase inhibitors show promise. Multidisciplinary evaluation and personalized management are essential.
Article
Multidisciplinary Sciences
Sen Chen, Jun Ran, Zhouqian Fan, Mingyou Liu, Liang Wu, Qiude Li, Jian Peng, Zuquan Hu
Summary: This study revealed that RNH1 has clinical value in bladder cancer therapy, as low expression of RNH1 is associated with invasion and metastasis of bladder cancer, as well as immune activation and tumor immune response. Moreover, high expression of RNH1 is significantly linked with therapeutic signaling pathways and drug targets in bladder cancer. Therefore, RNH1 could provide new insights into invasion of bladder cancer and predict immunotherapy response.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Sandra Jansen, Alexander Hoischen, Bradley P. Coe, Gemma L. Carvill, Hilde Van Esch, Danielle G. M. Bosch, Ulla A. Andersen, Carl Baker, Marijke Bauters, Raphael A. Bernier, Bregje W. van Bon, Hedi L. Claahsen-van der Grinten, Jozef Gecz, Christian Gilissen, Lucia Grillo, Anna Hackett, Tjitske Kleefstra, David Koolen, Malin Kvarnung, Martin J. Larsen, Carlo Marcelis, Fiona McKenzie, Marie-Lorraine Monin, Caroline Nava, Janneke H. Schuurs-Hoeijmakers, Rolph Pfundt, Marloes Steehouwer, Servi J. C. Stevens, Connie T. Stumpel, Fleur Vansenne, Mirella Vinci, Maartje van de Vorst, Petra de Vries, Kali Witherspoon, Joris A. Veltman, Han G. Brunner, Heather C. Mefford, Corrado Romano, Lisenka E. L. M. Vissers, Evan E. Eichler, Bert B. A. de Vries
EUROPEAN JOURNAL OF HUMAN GENETICS
(2018)
Article
Genetics & Heredity
Holly A. F. Stessman, Bo Xiong, Bradley P. Coe, Tianyun Wang, Kendra Hoekzema, Michaela Fenckova, Malin Kvarnung, Jennifer Gerdts, Sandy Trinh, Nele Cosemans, Laura Vives, Janice Lin, Tychele N. Turner, Gijs Santen, Claudia Ruivenkamp, Marjolein Kriek, Arie van Haeringen, Emmelien Aten, Kathryn Friend, Jan Liebelt, Christopher Barnett, Eric Haan, Marie Shaw, Jozef Gecz, Britt-Marie Anderlid, Ann Nordgren, Anna Lindstrand, Charles Schwartz, R. Frank Kooy, Geert Vandeweyer, Celine Helsmoortel, Corrado Romano, Antonino Alberti, Mirella Vinci, Emanuela Avola, Stefania Giusto, Eric Courchesne, Tiziano Pramparo, Karen Pierce, Srinivasa Nalabolu, David G. Amaral, Ingrid E. Scheffer, Martin B. Delatycki, Paul J. Lockhart, Fereydoun Hormozdiari, Benjamin Harich, Anna Castells-Nobau, Kun Xia, Hilde Peeters, Magnus Nordenskjold, Annette Schenck, Raphael A. Bernier, Evan E. Eichler
Article
Genetics & Heredity
Hui Guo, Michael H. Duyzend, Bradley P. Coe, Carl Baker, Kendra Hoekzema, Jennifer Gerdts, Tychele N. Turner, Michael C. Zody, Jennifer S. Beighley, Shwetha C. Murali, Bradley J. Nelson, Michael J. Bamshad, Deborah A. Nickerson, Raphael A. Bernier, Evan E. Eichler
GENETICS IN MEDICINE
(2019)
Article
Genetics & Heredity
Bradley P. Coe, Holly A. F. Stessman, Arvis Sulovari, Madeleine R. Geisheker, Trygve E. Bakken, Allison M. Lake, Joseph D. Dougherty, Ed S. Lein, Fereydoun Hormozdiari, Raphael A. Bernier, Evan E. Eichler
Article
Biology
Cheen Euong Ang, Qing Ma, Orly L. Wapinski, ShengHua Fan, Ryan A. Flynn, Qian Yi Lee, Bradley Coe, Masahiro Onoguchi, Victor Hipolito Olmos, Brian T. Do, Lynn Dukes-Rimsky, Jin Xu, Koji Tanabe, LiangJiang Wang, Ulrich Elling, Josef M. Penninger, Yang Zhao, Kun Qu, Evan E. Eichler, Anand Srivastava, Marius Wernig, Howard Y. Chang
Article
Genetics & Heredity
Hui Guo, Tianyun Wang, Huidan Wu, Min Long, Bradley P. Coe, Honghui Li, Guanglei Xun, Jianjun Ou, Biyuan Chen, Guiqin Duan, Ting Bai, Ningxia Zhao, Yidong Shen, Yun Li, Yazhe Wang, Yu Zhang, Carl Baker, Yanling Liu, Nan Pang, Lian Huang, Lin Han, Xiangbin Jia, Cenying Liu, Hailun Ni, Xinyi Yang, Lu Xia, Jingjing Chen, Lu Shen, Ying Li, Rongjuan Zhao, Wenjing Zhao, Jing Peng, Qian Pan, Zhigao Long, Wei Su, Jieqiong Tan, Xiaogang Du, Xiaoyan Ke, Meiling Yao, Zhengmao Hu, Xiaobing Zou, Jingping Zhao, Raphael A. Bernier, Evan E. Eichler, Kun Xia
Article
Genetics & Heredity
Flavia A. M. Maggiolini, Stuart Cantsilieris, Pietro D'Addabbo, Michele Manganelli, Bradley P. Coe, Beth L. Dumont, Ashley D. Sanders, Andy Wing Chun Pang, Mitchell R. Vollger, Orazio Palumbo, Pietro Palumbo, Maria Accadia, Massimo Carella, Evan E. Eichler, Francesca Antonacci
Article
Oncology
Hannah O'Farrell, Bryant Harbourne, Zimple Kurlawala, Yusuke Inoue, Amy L. Nagelberg, Victor D. Martinez, Daniel Lu, Min Hee Oh, Bradley P. Coe, Kelsie L. Thu, Romel Somwar, Stephen Lam, Wan L. Lam, Arun M. Unni, Levi Beverly, William W. Lockwood
JOURNAL OF THORACIC ONCOLOGY
(2019)
Article
Medicine, General & Internal
Joseph M. Tilghman, Albee Y. Ling, Tychele N. Turner, Maria X. Sosa, Niklas Krumm, Sumantra Chatterjee, Ashish Kapoor, Bradley P. Coe, Khanh-Dung H. Nguyen, Namrata Gupta, Stacey Gabriel, Evan E. Eichler, Courtney Berrios, Aravinda Chakravarti
NEW ENGLAND JOURNAL OF MEDICINE
(2019)
Article
Multidisciplinary Sciences
Michael D. Kessler, Douglas P. Loesch, James A. Perry, Nancy L. Heard-Costa, Daniel Taliun, Brian E. Cade, Heming Wang, Michelle Daya, John Ziniti, Soma Datta, Juan C. Celedon, Manuel E. Soto-Quiros, Lydiana Avila, Scott T. Weiss, Kathleen Barnes, Susan S. Redline, Ramachandran S. Vasan, Andrew D. Johnson, Rasika A. Mathias, Ryan Hernandez, James G. Wilson, Deborah A. Nickerson, Goncalo Abecasis, Sharon R. Browning, Sebastian Zollner, Jeffrey R. O'Connell, Braxton D. Mitchell, Timothy D. O'Connora
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Yun Rose Li, Joseph T. Glessner, Bradley P. Coe, Jian-jun Li, Maede Mohebnasab, Xiao Chang, John Connolly, Charlly Kao, Zhi Wei, Jonathan Bradfield, Cecilia Kim, Cuiping Hou, Munir Khan, Frank Mentch, Haijun Qiu, Marina Bakay, Christopher Cardinale, Maria Lemma, Debra Abrams, Andrew Bridglall-Jhingoor, Meckenzie Behr, Shanell Harrison, George Otieno, Alexandria Thomas, Fengxiang Wang, Rosetta Chiavacci, Lawrence Wu, Dexter Hadley, Elizabeth Goldmuntz, Josephine Elia, John Maris, Robert Grundmeier, Marcella Devoto, Brendan Keating, Michael March, Renata Pellagrino, Struan F. A. Grant, Patrick M. A. Sleiman, Mingyao Li, Evan E. Eichler, Hakon Hakonarson
NATURE COMMUNICATIONS
(2020)
Article
Genetics & Heredity
Brooke Sadler, Gabe Haller, Lilian Antunes, Momchil Nikolov, Ina Amarillo, Bradley Coe, Matthew B. Dobbs, Christina A. Gurnett
JOURNAL OF MEDICAL GENETICS
(2020)
Article
Multidisciplinary Sciences
Tianyun Wang, Kendra Hoekzema, Davide Vecchio, Huidan Wu, Arvis Sulovari, Bradley P. Coe, Madelyn A. Gillentine, Amy B. Wilfert, Luis A. Perez-Jurado, Malin Kvarnung, Yoeri Sleyp, Rachel K. Earl, Jill A. Rosenfeld, Madeleine R. Geisheker, Lin Han, Bing Du, Chris Barnett, Elizabeth Thompson, Marie Shaw, Renee Carroll, Kathryn Friend, Rachael Catford, Elizabeth E. Palmer, Xiaobing Zou, Jianjun Ou, Honghui Li, Hui Guo, Jennifer Gerdts, Emanuela Avola, Giuseppe Calabrese, Maurizio Elia, Donatella Greco, Anna Lindstrand, Ann Nordgren, Britt-Marie Anderlid, Geert Vandeweyer, Anke Van Dijck, Nathalie Van der Aa, Brooke McKenna, Miroslava Hancarova, Sarka Bendova, Marketa Havlovicova, Giovanni Malerba, Bernardo Dalla Bernardina, Pierandrea Muglia, Arie van Haeringen, Mariette J. V. Hoffer, Barbara Franke, Gerarda Cappuccio, Martin Delatycki, Paul J. Lockhart, Melanie A. Manning, Pengfei Liu, Ingrid E. Scheffer, Nicola Brunetti-Pierri, Nanda Rommelse, David G. Amaral, Gijs W. E. Santen, Elisabetta Trabetti, Zdenek Sedlacek, Jacob J. Michaelson, Karen Pierce, Eric Courchesne, R. Frank Kooy, Magnus Nordenskjold, Corrado Romano, Hilde Peeters, Raphael A. Bernier, Jozef Gecz, Kun Xia, Evan E. Eichler
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Tychele N. Turner, Bradley P. Coe, Diane E. Dickel, Kendra Hoekzema, Bradley J. Nelson, Michael C. Zody, Zev N. Kronenberg, Fereydoun Hormozdiari, Archana Raja, Len A. Pennacchio, Robert B. Darnell, Evan E. Eichler
Article
Genetics & Heredity
Daniel Seung Kim, Amber A. Burt, Jane E. Ranchalis, Beth Wilmot, Joshua D. Smith, Karynne E. Patterson, Bradley P. Coe, Yatong K. Li, Michael J. Bamshad, Molly Nikolas, Evan E. Eichler, James M. Swanson, Joel T. Nigg, Deborah A. Nickerson, Gail P. Jarvik
AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS
(2017)