Combined IL6 and CCR2 blockade potentiates antitumor activity of NK cells in HPV-negative head and neck cancer

Authors: Fan Yang, Chenyang Yuan, Fanghui Chen, Zhaohui S. Qin, Nicole C. Schmitt, Gregory B. Lesinski, Nabil F. Saba, Yong Teng

Source: Journal of Experimental & Clinical Cancer Research, Vol 43, Iss 1, Pp 1-17 (2024)

Subject Terms: Head and neck cancer, NK cells, IL6 and CCR2, scRNA-seq, HPV, The tumor microenvironment, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

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Relation: https://doaj.org/toc/1756-9966

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NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity

Authors: Kenong Su, Ataur Katebi, Vivek Kohar, Benjamin Clauss, Danya Gordin, Zhaohui S. Qin, R. Krishna M. Karuturi, Sheng Li, Mingyang Lu

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

Subject Terms: Systems biology, Gene regulatory networks, Gene regulatory circuits, Cellular state transitions, Mathematical modeling, Transcriptional activity, Biology (General), QH301-705.5, Genetics, QH426-470

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

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Role of TET1-mediated epigenetic modulation in Alzheimer's disease

Authors: Matthew J. Armstrong, Yulin Jin, Selina M. Vattathil, Yanting Huang, Jason P. Schroeder, David A. Bennet, Zhaohui S. Qin, Thomas S. Wingo, Peng Jin

Source: Neurobiology of Disease, Vol 185, Iss , Pp 106257- (2023)

Subject Terms: 5-hydroxymethylcytosine, Alzheimer's disease, Tet1 protein, Gene expression, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

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Relation: http://www.sciencedirect.com/science/article/pii/S0969996123002723; https://doaj.org/toc/1095-953X

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Integrative Bayesian tensor regression for imaging genetics applications

Authors: Yajie Liu, Nilanjana Chakraborty, Zhaohui S. Qin, Suprateek Kundu, The Alzheimer’s Disease Neuroimaging Initiative

Source: Frontiers in Neuroscience, Vol 17 (2023)

Subject Terms: Alzheimer's disease, Bayesian tensor regression models, collinearity, imaging genetics analysis, transcriptomics, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

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Relation: https://www.frontiersin.org/articles/10.3389/fnins.2023.1212218/full; https://doaj.org/toc/1662-453X

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UALCAN: An update to the integrated cancer data analysis platform

Authors: Darshan Shimoga Chandrashekar, Santhosh Kumar Karthikeyan, Praveen Kumar Korla, Henalben Patel, Ahmedur Rahman Shovon, Mohammad Athar, George J. Netto, Zhaohui S. Qin, Sidharth Kumar, Upender Manne, Chad J. Crieghton, Sooryanarayana Varambally

Source: Neoplasia: An International Journal for Oncology Research, Vol 25, Iss , Pp 18-27 (2022)

Subject Terms: UALCAN, Cancer gene expression, Bioinformatics, Transcriptomics, Patient survival, lncRNA, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

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Relation: http://www.sciencedirect.com/science/article/pii/S147655862200001X; https://doaj.org/toc/1476-5586

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Comprehensive 100-bp resolution genome-wide epigenomic profiling data for the hg38 human reference genome

Authors: Ronnie Y. Li, Yanting Huang, Zhiyue Zhao, Zhaohui S. Qin

Source: Data in Brief, Vol 46, Iss , Pp 108827- (2023)

Subject Terms: ENCODE, Genomics, Epigenomics, High-throughput sequencing, Bioinformatics, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390

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Relation: http://www.sciencedirect.com/science/article/pii/S2352340922010307; https://doaj.org/toc/2352-3409

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Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference

Authors: Ramin Homayouni, Prashanti Manda, Aik Choon Tan, Zhaohui S. Qin

Source: Frontiers in Big Data, Vol 6 (2023)

Subject Terms: deep learning, NLP, genomics (G), regulatory science research, metagenomics, Information technology, T58.5-58.64

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fdata.2023.1156811/full; https://doaj.org/toc/2624-909X

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A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer’s disease

Authors: Yanting Huang, Xiaobo Sun, Huige Jiang, Shaojun Yu, Chloe Robins, Matthew J. Armstrong, Ronghua Li, Zhen Mei, Xiaochuan Shi, Ekaterina Sergeevna Gerasimov, Philip L. De Jager, David A. Bennett, Aliza P. Wingo, Peng Jin, Thomas S. Wingo, Zhaohui S. Qin

Source: Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/65c87e8eceb04148ada622868111db36

Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Authors: Jonathan D. Wren, Yongsheng Bai, Zhaohui S. Qin, Da Yan, Ramin Homayouni

Source: BMC Bioinformatics, Vol 21, Iss S4, Pp 1-7 (2020)

Subject Terms: Bioinformatics, Conferences, MCBIOS, ISCB, 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/s12859-020-03580-9; https://doaj.org/toc/1471-2105

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Multiomics Analysis of Structural Magnetic Resonance Imaging of the Brain and Cerebrospinal Fluid Metabolomics in Cognitively Normal and Impaired Adults

Authors: Ronald C. Eldridge, Karan Uppal, Mahsa Shokouhi, M. Ryan Smith, Xin Hu, Zhaohui S. Qin, Dean P. Jones, Ihab Hajjar

Source: Frontiers in Aging Neuroscience, Vol 13 (2022)

Subject Terms: MRI imaging, metabolomics (OMICS), multiomics analysis, mild cognition impairment, amino acids (AA), Alzheimer’s disease, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

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Relation: https://www.frontiersin.org/articles/10.3389/fnagi.2021.796067/full; https://doaj.org/toc/1663-4365

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Systematic Exploration in Tissue-Pathway Associations of Complex Traits Using Comprehensive eQTLs Catalog

Authors: Boqi Wang, James Yang, Steven Qiu, Yongsheng Bai, Zhaohui S. Qin

Source: Frontiers in Big Data, Vol 4 (2021)

Subject Terms: eQTLs, gene pathway sets, gene set enrichment analyses, tissue-pathway association, complex traits, Information technology, T58.5-58.64

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Relation: https://www.frontiersin.org/articles/10.3389/fdata.2021.719737/full; https://doaj.org/toc/2624-909X

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Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure

Authors: Yue Hou, Fuyu Li, Rongxin Zhang, Sheng Li, Hongde Liu, Zhaohui S. Qin, Xiao Sun

Source: Epigenetics, Vol 14, Iss 9, Pp 894-911 (2019)

Subject Terms: chromatin structure, enhancer-promoter interaction, g-quadruplex, hi-c, loop extrusion, transcription factor, Genetics, QH426-470

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Relation: https://doaj.org/toc/1559-2294; https://doaj.org/toc/1559-2308

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Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

Authors: Vishnu Dileep, Korey A. Wilson, Claire Marchal, Xiaowen Lyu, Peiyao A. Zhao, Ben Li, Axel Poulet, Daniel A. Bartlett, Juan Carlos Rivera-Mulia, Zhaohui S. Qin, Allan J. Robins, Thomas C. Schulz, Michael J. Kulik, Rachel Patton McCord, Job Dekker, Stephen Dalton, Victor G. Corces, David M. Gilbert

Source: Stem Cell Reports, Vol 13, Iss 1, Pp 193-206 (2019)

Subject Terms: Medicine (General), R5-920, Biology (General), QH301-705.5

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Relation: http://www.sciencedirect.com/science/article/pii/S2213671119301882; https://doaj.org/toc/2213-6711

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Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity

Authors: Yutong Jin, Jiahui Jiang, Ruixuan Wang, Zhaohui S. Qin

Source: Frontiers in Genetics, Vol 12 (2021)

Subject Terms: non-coding variant annotation, transcription regulation, transcription factor binding motif, gapped k-mer SVM classifier, genome-wide association study, position weight matrix, Genetics, QH426-470

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Relation: https://www.frontiersin.org/articles/10.3389/fgene.2021.667866/full; https://doaj.org/toc/1664-8021

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Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis

Authors: Kenong Su, Qi Yu, Ronglai Shen, Shi-Yong Sun, Carlos S. Moreno, Xiaoxian Li, Zhaohui S. Qin

Source: Cell Reports: Methods, Vol 1, Iss 4, Pp 100050- (2021)

Subject Terms: pathway, biomarker, gene set, pan-cancer, The Cancer Genome Atlas, RNA-seq, Biotechnology, TP248.13-248.65, Biochemistry, QD415-436, Science

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Relation: http://www.sciencedirect.com/science/article/pii/S2667237521000989; https://doaj.org/toc/2667-2375

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DeconPeaker, a Deconvolution Model to Identify Cell Types Based on Chromatin Accessibility in ATAC-Seq Data of Mixture Samples

Authors: Huamei Li, Amit Sharma, Kun Luo, Zhaohui S. Qin, Xiao Sun, Hongde Liu

Source: Frontiers in Genetics, Vol 11 (2020)

Subject Terms: chromatin accessibility, cell type, deconvolution, mixture samples, gene expression, Genetics, QH426-470

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Relation: https://www.frontiersin.org/article/10.3389/fgene.2020.00392/full; https://doaj.org/toc/1664-8021

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Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Authors: Michelle Daya, Nicholas Rafaels, Tonya M. Brunetti, Sameer Chavan, Albert M. Levin, Aniket Shetty, Christopher R. Gignoux, Meher Preethi Boorgula, Genevieve Wojcik, Monica Campbell, Candelaria Vergara, Dara G. Torgerson, Victor E. Ortega, Ayo Doumatey, Henry Richard Johnston, Nathalie Acevedo, Maria Ilma Araujo, Pedro C. Avila, Gillian Belbin, Eugene Bleecker, Carlos Bustamante, Luis Caraballo, Alvaro Cruz, Georgia M. Dunston, Celeste Eng, Mezbah U. Faruque, Trevor S. Ferguson, Camila Figueiredo, Jean G. Ford, Weiniu Gan, Pierre-Antoine Gourraud, Nadia N. Hansel, Ryan D. Hernandez, Edwin Francisco Herrera-Paz, Silvia Jiménez, Eimear E. Kenny, Jennifer Knight-Madden, Rajesh Kumar, Leslie A. Lange, Ethan M. Lange, Antoine Lizee, Pissamai Maul, Trevor Maul, Alvaro Mayorga, Deborah Meyers, Dan L. Nicolae, Timothy D. O’Connor, Ricardo Riccio Oliveira, Christopher O. Olopade, Olufunmilayo Olopade, Zhaohui S. Qin, Charles Rotimi, Nicolas Vince, Harold Watson, Rainford J. Wilks, James G. Wilson, Steven Salzberg, Carole Ober, Esteban G. Burchard, L. Keoki Williams, Terri H. Beaty, Margaret A. Taub, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes, CAAPA

Source: Nature Communications, Vol 10, Iss 1, Pp 1-13 (2019)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/52d5362512b747ddbffccc263d738739

Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale

Authors: Li Chen, Zhaohui S. Qin

Source: BMC Research Notes, Vol 10, Iss 1, Pp 1-7 (2017)

Subject Terms: Non-coding variants, D-score, DIVAN, Software, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390

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Relation: http://link.springer.com/article/10.1186/s13104-017-2851-y; https://doaj.org/toc/1756-0500

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An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure

Authors: Guodong Yang, Aiqun Ma, Zhaohui S. Qin

Source: Frontiers in Genetics, Vol 10 (2019)

Subject Terms: heart failure, drug repositioning, gene signature, systems biology, connectivity map, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fgene.2019.00916/full; https://doaj.org/toc/1664-8021

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A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

Authors: Rasika Ann Mathias, Margaret A. Taub, Christopher R. Gignoux, Wenqing Fu, Shaila Musharoff, Timothy D. O'Connor, Candelaria Vergara, Dara G. Torgerson, Maria Pino-Yanes, Suyash S. Shringarpure, Lili Huang, Nicholas Rafaels, Meher Preethi Boorgula, Henry Richard Johnston, Victor E. Ortega, Albert M. Levin, Wei Song, Raul Torres, Badri Padhukasahasram, Celeste Eng, Delmy-Aracely Mejia-Mejia, Trevor Ferguson, Zhaohui S. Qin, Alan F. Scott, Maria Yazdanbakhsh, James G. Wilson, Javier Marrugo, Leslie A. Lange, Rajesh Kumar, Pedro C. Avila, L. Keoki Williams, Harold Watson, Lorraine B. Ware, Christopher Olopade, Olufunmilayo Olopade, Ricardo Oliveira, Carole Ober, Dan L. Nicolae, Deborah Meyers, Alvaro Mayorga, Jennifer Knight-Madden, Tina Hartert, Nadia N. Hansel, Marilyn G. Foreman, Jean G. Ford, Mezbah U. Faruque, Georgia M. Dunston, Luis Caraballo, Esteban G. Burchard, Eugene Bleecker, Maria Ilma Araujo, Edwin Francisco Herrera-Paz, Kimberly Gietzen, Wendy E. Grus, Michael Bamshad, Carlos D. Bustamante, Eimear E. Kenny, Ryan D. Hernandez, Terri H. Beaty, Ingo Ruczinski, Joshua Akey, CAAPA, Kathleen C. Barnes

Source: Nature Communications, Vol 7, Iss 1, Pp 1-10 (2016)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/5900ff2f826d4d3b88e21eee23d8e158