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1. Full Text Abstract 2293: Outstanding chromosomal expression patterning in human cancers
by Barnes, Spencer and Song, Mingzhou
Cancer Research, ISSN 0008-5472, 07/2018, Volume 78, Issue 13 Supplement, pp. 2293 - 2293
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2. Full Text Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations
by Said, Joseph I and Knapka, Joseph A and Song, Mingzhou and Zhang, Jinfa
Molecular Genetics and Genomics, ISSN 1617-4615, 8/2015, Volume 290, Issue 4, pp. 1615 - 1625
A specialized database currently containing more than 2200 QTL is established, which allows graphic presentation, visualization and submission of QTL. In... 
Life Sciences | Biochemistry, general | Gossypium barbadense | Microbial Genetics and Genomics | QTL | Database | Gossypium hirsutum | Fiber quality | Cell Biology | Plant Genetics & Genomics | Animal Genetics and Genomics | CottonQTLdb | Gossypiumhirsutum | Computational Biology - methods | Phenotype | Genes, Plant - genetics | Gossypium - genetics | Databases, Genetic | Chromosome Mapping | Internet | Chromosomes, Plant - genetics | Lod Score | Crosses, Genetic | Quantitative Trait Loci - genetics
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3. Full Text A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations
by Said, Joseph I and Song, Mingzhou and Wang, Hantao and Lin, Zhongxu and Zhang, Xianlong and Fang, David D and Zhang, Jinfa
Molecular Genetics and Genomics, ISSN 1617-4615, 6/2015, Volume 290, Issue 3, pp. 1003 - 1025
Based on 1075 and 1059 QTL from intraspecific Upland and interspecific Upland × Pima populations, respectively, the identification of QTL clusters and hotspots... 
Life Sciences | Biochemistry, general | Quantitative trait loci | Gossypium barbadense | Meta analysis | Microbial Genetics and Genomics | Gossypium hirsutum | Cotton | Cell Biology | Plant Genetics & Genomics | Animal Genetics and Genomics | Tetraploidy | Phenotype | Genome, Plant - genetics | Species Specificity | Breeding | Gossypium - genetics | Chromosome Mapping | Chromosomes, Plant - genetics | Cluster Analysis | Quantitative Trait Loci - genetics
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4. Full Text Wisdom of crowds for robust gene network inference
by Marbach, Daniel and Costello, James C and Küffner, Robert and Vega, Nicole M and Prill, Robert J and Camacho, Diogo M and Allison, Kyle R and Kellis, Manolis and Collins, James J and Aderhold, Andrej and Stolovitzky, Gustavo and Bonneau, Richard and Chen, Yukun and Cordero, Francesca and Crane, Martin and Dondelinger, Frank and Drton, Mathias and Esposito, Roberto and Foygel, Rina and De La Fuente, Alberto and Gertheiss, Jan and Geurts, Pierre and Greenfield, Alex and Grzegorczyk, Marco and Haury, Anne-Claire and Holmes, Benjamin and Hothorn, Torsten and Husmeier, Dirk and Huynh-Thu, Vân Anh and Irrthum, Alexandre and Karlebach, Guy and Lèbre, Sophie and De Leo, Vincenzo and Madar, Aviv and Mani, Subramani and Mordelet, Fantine and Ostrer, Harry and Ouyang, Zhengyu and Pandya, Ravi and Petri, Tobias and Pinna, Andrea and Poultney, Christopher S and Rezny, Serena and Ruskin, Heather J and Saeys, Yvan and Shamir, Ron and Sîrbu, Alina and Song, Mingzhou and Soranzo, Nicola and Statnikov, Alexander and Vega, Nicci and Vera-Licona, Paola and Vert, Jean-Philippe and Visconti, Alessia and Wang, Haizhou and Wehenkel, Louis and Windhager, Lukas and Zhang, Yang and Zimmer, Ralf and DREAM5 Consortium and The DREAM5 Consortium
Nature Methods, ISSN 1548-7091, 08/2012, Volume 9, Issue 8, pp. 796 - 804
Reconstructing gene regulatory networks from high-throughput data is a long-standing challenge. Through the Dialogue on Reverse Engineering Assessment and... 
REGRESSION | MODELS | INTEGRATION | REGULATORY NETWORKS | RECONSTRUCTION | ALGORITHM | BIOCHEMICAL RESEARCH METHODS | SELECTION | TRANSCRIPTIONAL REGULATION | EXPRESSION DATA | DISCOVERY | Staphylococcus aureus - genetics | Gene Expression Regulation, Bacterial - genetics | Algorithms | Oligonucleotide Array Sequence Analysis | Escherichia coli - genetics | Saccharomyces cerevisiae - genetics | Computational Biology | Software | Transcription, Genetic - genetics | Gene Regulatory Networks | Physiological aspects | Genetic aspects | Research | Escherichia coli | Genes | Staphylococcus aureus | Genetics | Bacteria | Statistical inference | Genetic algorithms
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5. Full Text A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton
by Said, Joseph I and Lin, Zhongxu and Zhang, Xianlong and Song, Mingzhou and Zhang, Jinfa
BMC Genomics, ISSN 1471-2164, 11/2013, Volume 14, Issue 1, pp. 776 - 776
Background: The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have... 
1ST FRUITING BRANCH | GOSSYPIUM-HIRSUTUM L | UPLAND COTTON | SSR MARKERS | POLYPLOID FORMATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | MOLECULAR DISSECTION | VERTICILLIUM WILT RESISTANCE | BACKCROSS-SELF APPROACH | INTERSPECIFIC VARIATION | BARBADENSE COTTON | Cotton Fiber | Genetic Variation | Tetraploidy | Droughts | Gossypium - genetics | Chromosome Mapping | Disease Resistance - genetics | Gossypium - growth & development | Crosses, Genetic | Quantitative Trait Loci - genetics | Textiles | Quantitative genetics | Quantitative trait loci | Analysis | Genomics | Studies | Genotype & phenotype | Cotton | Chromosomes | Meta-analysis
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6. Full Text A genome-wide analysis of pentatricopeptide repeat (PPR) protein-encoding genes in four Gossypium species with an emphasis on their expression in floral buds, ovules, and fibers in upland cotton
by Han, Zongfu and Qin, Yuxiang and Li, Xihua and Yu, Jiwen and Li, Ruzhong and Xing, Chaozhu and Song, Mingzhou and Wu, Jianyong and Zhang, Jinfa
Molecular genetics and genomics : MGG, ISSN 1617-4615, 08/2019, pp. 1 - 12
Cotton is the most important natural fiber used in textiles. Breeding for "three-lines", i.e., cytoplasmic male sterility (CMS)-based sterile (A), maintainer... 
Synteny | Ovules | Hybrid vigor | Genomes | Ribonucleic acid--RNA | Gene expression | Cotton | Sterility | Fibers | Textiles | Polymerase chain reaction | Male sterility | Flowering | Inbreeding | Vigor | Species | Buds | Chromosomes | Cytoplasmic male sterility
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7. Full Text Genetic analysis of Verticillium wilt resistance in a backcross inbred line population and a meta-analysis of quantitative trait loci for disease resistance in cotton
by Zhang, Jinfa and Yu, Jiwen and Pei, Wenfeng and Li, Xingli and Said, Joseph and Song, Mingzhou and Sanogo, Soum
BMC Genomics, ISSN 1471-2164, 08/2015, Volume 16, Issue 1, p. 577
Background: Verticillium wilt (VW) and Fusarium wilt (FW), caused by the soil-borne fungi Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum,... 
Quantitative trait loci | Resistance | Root-knot nematodes | Fusarium wilt | Reniform nematodes | Cotton | Verticillium wilt | Meta-analysis | FIBER QUALITY | QTL | MARKERS | CHROMOSOMES | IDENTIFICATION | INTROGRESSION | GOSSYPIUM-HIRSUTUM | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | ROOT-KNOT NEMATODE | BARBADENSE | RENIFORM NEMATODE | Genes, Plant | Plant Diseases - microbiology | Chromosome Mapping | Genetic Markers | Gossypium - genetics | Verticillium | Gossypium - microbiology | Inbreeding | Plant Diseases - genetics | Quantitative Trait Loci | Disease Resistance - genetics | Cluster Analysis | Crosses, Genetic | Physiological aspects | Genetic aspects | Drug resistance | Analysis | Cotton verticillium wilt | Genes | Research
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8. Full Text Inferring causal molecular networks: Empirical assessment through a community-based effort
by Hill, Steven M and Heiser, Laura M and Cokelaer, Thomas and Linger, Michael and Nesser, Nicole K and Carlin, Daniel E and Zhang, Yang and Sokolov, Artem and Paull, Evan O and Wong, Chris K and Graim, Kiley and Bivol, Adrian and Wang, Haizhou and Zhu, Fan and Afsari, Bahman and Danilova, Ludmila V and Favorov, Alexander V and Lee, Wai Shing and Taylor, Dane and Hu, Chenyue W and Long, Byron L and Noren, David P and Bisberg, Alexander J and Mills, Gordon B and Gray, Joe W and Kellen, Michael and Norman, Thea and Friend, Stephen and Qutub, Amina A and Fertig, Elana J and Guan, Yuanfang and Song, Mingzhou and Stuart, Joshua M and Spellman, Paul T and Koeppl, Heinz and Stolovitzky, Gustavo and Saez-Rodriguez, Julio and Mukherjee, Sach and Al-Ouran, Rami and Anton, Bernat and Arodz, Tomasz and Sichani, Omid Askari and Bagheri, Neda and Berlow, Noah and Bohler, Anwesha and Bonet, Jaume and Bonneau, Richard and Budak, Gungor and Bunescu, Razvan and Caglar, Mehmet and Cai, Binghuang and Cai, Chunhui and Carlon, Azzurra and Chen, Lujia and Ciaccio, Mark F and Cooper, Gregory and Coort, Susan and Creighton, Chad J and Daneshmand, Seyed-Mohammad-Hadi and De La Fuente, Alberto and Di Camillo, Barbara and Dutta-Moscato, Joyeeta and Emmett, Kevin and Evelo, Chris and Fassia, Mohammad-Kasim H and Finotello, Francesca and Finkle, Justin D and Gao, Xi and Garcia-Garcia, Javier and Ghosh, Samik and Giaretta, Alberto and Großeholz, Ruth and Guinney, Justin and Hafemeister, Christoph and Hahn, Oliver and Haider, Saad and Hase, Takeshi and Hodgson, Jay and Hoff, Bruce and Hsu, Chih Hao and Hu, Ying and Huang, Xun and Jalili, Mahdi and Jiang, Xia and Kacprowski, Tim and Kaderali, Lars and Kang, Mingon and Kannan, Venkateshan and Kikuchi, Kaito and Kim, Dong-Chul and Kitano, Hiroaki and Knapp, Bettina and Komatsoulis, George and Krämer, Andreas and Kursa, Miron Bartosz and Kutmon, Martina and Li, Yichao and Liang, Xiaoyu and Liu, Zhaoqi and Liu, Yu and ... and HPN-DREAM Consortium and The HPN-DREAM Consortium
Nature Methods, ISSN 1548-7091, 03/2016, Volume 13, Issue 4, pp. 310 - 322
It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here... 
GENE NETWORKS | BAYESIAN NETWORKS | MODELS | BIOCHEMICAL RESEARCH METHODS | SENSITIVITY | VALIDATION | ALGORITHMS | INFERENCE | EXPRESSION DATA | CHALLENGES | SIGNALING NETWORKS | Signal Transduction | Humans | Computational Biology | Gene Expression Profiling | Gene Regulatory Networks | Systems Biology | Protein Interaction Mapping - methods | Algorithms | Neoplasms - genetics | Models, Biological | Computer Simulation | Software | Tumor Cells, Cultured | Causality | Biological research | Physiological aspects | Cellular signal transduction | Research | Molecular biology | Phosphotransferases | Biology, Experimental | Proteins | Cancer
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9. Full Text Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G-hirsutum x G-barbadense populations
by Said, JI and Knapka, JA and Song, MZ and Zhang, JF
MOLECULAR GENETICS AND GENOMICS, ISSN 1617-4615, 08/2015, Volume 290, Issue 4, pp. 1615 - 1625
A specialized database currently containing more than 2200 QTL is established, which allows graphic presentation, visualization and submission of QTL. In... 
1ST FRUITING BRANCH | Gossypium barbadense | BIOCHEMISTRY & MOLECULAR BIOLOGY | QTL | Fiber quality | BACKCROSS-SELF APPROACH | QUANTITATIVE TRAIT LOCI | UPLAND COTTON | GENETIC DISSECTION | POLYPLOID FORMATION | GENETICS & HEREDITY | Database | Gossypium hirsutum | MOLECULAR DISSECTION | VERTICILLIUM WILT RESISTANCE | CottonQTLdb | INTERSPECIFIC VARIATION
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10. Full Text A Fast Exact Functional Test for Directional Association and Cancer Biology Applications
by Zhong, Hua and Song, Mingzhou
IEEE/ACM Transactions on Computational Biology and Bioinformatics, ISSN 1545-5963, 05/2019, Volume 16, Issue 3, pp. 818 - 826
Directional association measured by functional dependency can answer important questions on relationships between variables, for example, in discovery of... 
noncoding RNA | RNA | directional association | Lung | Liver | functional dependency | biomarker | lung cancer | Upper bound | Exact functional test | branch-and-bound | liver cancer | Random variables | Cancer | BIOCHEMICAL RESEARCH METHODS | STATISTICS & PROBABILITY | CONTINGENCY-TABLES | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | MATHEMATICS, INTERDISCIPLINARY APPLICATIONS | ROLES | GENES
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11. Full Text Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data
by Song, Mingzhou(Joe) and Lewis, Chris K and Lance, Eric R and Chesler, Elissa J and Yordanova, Roumyana Kirova and Langston, Michael A and Lodowski, Kerrie H and Bergeson, Susan E
EURASIP Journal on Bioinformatics and Systems Biology, ISSN 1687-4145, 12/2009, Volume 2009, Issue 1, pp. 1 - 13
Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem... 
Computational Biology/Bioinformatics | Biomedical Engineering | Engineering | Signal, Image and Speech Processing | Systems Biology | Physiological aspects | Brain | Mice | Research | Gene expression | Properties | Studies | Computer science | Hypothesis testing | Algorithms | Grants | Random variables
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12. Full Text A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton
by Abdelraheem, Abdelraheem and Liu, Feng and Song, Mingzhou and Zhang, Jinfa F
Molecular Genetics and Genomics, ISSN 1617-4615, 12/2017, Volume 292, Issue 6, pp. 1221 - 1235
The number and location of mapped quantitative trait loci (QTL) depend on genetic populations and testing environments. The identification of consistent QTL... 
Life Sciences | Biochemistry, general | Quantitative trait loci | Abiotic stress tolerance | Plant Genetics and Genomics | Biotic stress resistance | Meta analysis | Microbial Genetics and Genomics | Cotton | Cell Biology | Animal Genetics and Genomics | GOSSYPIUM-HIRSUTUM | BARBADENSE POPULATIONS | TOLERANCE | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENETICS & HEREDITY | QTL | Tetraploidy | Gossypium - physiology | Chromosomes, Plant | Quantitative Trait Loci | Stress, Physiological - genetics | Gossypium - genetics | Chlorophyll | Osmotic potential | Marker-assisted selection | Hot spots | Stomata | Genomes | Leaf area | Population genetics | Verticillium wilt | Meta-analysis | Genotype & phenotype | Transpiration | Plant breeding | Drought resistance | Nematodes | Conductance | Gene mapping
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13. Full Text Preparation of a biodegradable poly(vinyl alcohol)–starch composite film and its application in pesticide controlled release
by Wang, Song and Jia, Zhixin and Zhou, Xiangyang and Zhou, Dunbai and Chen, Mingzhou and Xie, Dong and Luo, Yuanfang and Jia, Demin
Journal of Applied Polymer Science, ISSN 0021-8995, 07/2017, Volume 134, Issue 28, pp. np - n/a
ABSTRACT With the herbicide 2,4‐dichlorophenoxyacetic acid (2,4‐D) as a model drug, a series of poly(vinyl alcohol)–starch (PVA–ST) composite films for... 
membranes | biodegradable | drug‐delivery systems | biopolymers and renewable polymers | applications | drug-delivery systems | HERBICIDE | POLYMER SCIENCE | ACID | MECHANISM | 2,4-D | STARCH | WATER | Drugs | Irrigation | Herbicides | Drug delivery systems | Biodegradability | Alginates | Leaching | Controlled release
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