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Other IDs

Scopus Author ID: 7401474114
Loop profile: 223276

Keywords

Biomedical data science, Bioinformatics, Network inference, Statistical inference, FunChisq, Causal inference, Image processing, Pattern recognition, Computer vision, Ckmeans.1d.dp

Countries

United States

Activities

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Employment (2)

New Mexico State University: Las Cruces, NM, US

2005-08-16 to present | Professor (Department of Computer Science; Graduate Program in Molecular Biology and Interdisciplinary Life Sciences)
Employment
Source: Self-asserted source
Mingzhou Song

Queens College Department of Computer Science: Flushing, NY, US

2002-02-01 to 2005-06-30 | Assistant Professor (Department of Computer Science)
Employment
Source: Self-asserted source
Mingzhou Song

Education and qualifications (1)

University of Washington: Seattle, WA, US

1997-09-01 to 2002-03-22 | Ph. D. (Department of Electrical Engineering)
Education
Source: Self-asserted source
Mingzhou Song

Funding (4)

ABI INNOVATION: Molecular Network Inference via Nonparametric Functional Dependencies

Source: Self-asserted source
Mingzhou Song via DimensionsWizard

COORDINATED DEVELOPMENT OF GENETIC TOOLS FOR PECAN

2016-09-01 to 2021-08-31 | Grant
National Institute of Food and Agriculture (n/a, US)
URL: https://grants.uberresearch.com/100005825/2016-51181-25408/COORDINATED-DEVELOPMENT-OF-GENETIC-TOOLS-FOR-PECAN
GRANT_NUMBER: grant.2016-51181-25408
Source: Self-asserted source
Mingzhou Song via DimensionsWizard

MRI: Acquisition of an Instrument for Research in Irregularly Parallel Big Data Computation

2013-10-01 to 2016-09-30 | Grant
Directorate for Computer & Information Science & Engineering (n/a, US)
URL: https://grants.uberresearch.com/100000083/1337884/MRI-Acquisition-of-an-Instrument-for-Research-in-Irregularly-Parallel-Big-Data-Computation
GRANT_NUMBER: grant.1337884
Source: Self-asserted source
Mingzhou Song via DimensionsWizard

IGERT: Computational Molecular Biology Training Group

2005-07-01 to 2012-06-30 | Grant
Directorate for Education & Human Resources (n/a, US)
URL: https://grants.uberresearch.com/100000081/0504304/IGERT-Computational-Molecular-Biology-Training-Group
GRANT_NUMBER: grant.0504304
Source: Self-asserted source
Mingzhou Song via DimensionsWizard

Works (50 of 70)

Items per page:
Page 1 of 2

Exact model-free function inference using uniform marginal counts for null population

2025-03-18 | Other
DOI: 10.1093/bioinformatics/btaf121
Contributors: Yiyi Li; Mingzhou Song
Source: check_circle
Crossref

Circular Silhouette and a Fast Algorithm

IEEE Transactions on Pattern Analysis and Machine Intelligence
2023 | Journal article
DOI: 10.1109/TPAMI.2023.3310495
Contributors: Yinong Chen; Tathagata Debnath; Andrew Cai; Mingzhou Song
Source: check_circle
Crossref

Statistical evidence for the presence of trajectory in single-cell data

BMC Bioinformatics
2022-08-16 | Journal article
DOI: 10.1186/s12859-022-04875-9
Contributors: Lovemore Tenha; Mingzhou Song
Source: check_circle
Crossref

Norcantharidin overcomes vemurafenib resistance in melanoma by inhibiting pentose phosphate pathway and lipogenesis via downregulating the mTOR pathway

Frontiers in Pharmacology
2022-08-12 | Journal article
DOI: 10.3389/fphar.2022.906043
Part of ISSN: 1663-9812
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song

Detecting genetic epistasis by differential departure from independence

Molecular Genetics and Genomics
2022-07 | Journal article
DOI: 10.1007/s00438-022-01893-3
Contributors: Ruby Sharma; Zeinab Sadeghian Tehrani; Sajal Kumar; Mingzhou Song
Source: check_circle
Crossref

Overcoming biases in causal inference of molecular interactions

Bioinformatics
2022-05-13 | Journal article
DOI: 10.1093/bioinformatics/btac206
Contributors: Sajal Kumar; Mingzhou Song; Peter Robinson
Source: check_circle
Crossref

Inference of trajectory presence by tree dimension and subset specificity by subtree cover

PLOS Computational Biology
2022-02-08 | Journal article
DOI: 10.1371/journal.pcbi.1009829
Contributors: Lovemore Tenha; Lilia M. Iakoucheva; Mingzhou Song
Source: check_circle
Crossref

Fast Optimal Circular Clustering and Applications on Round Genomes

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2021-11-01 | Journal article
DOI: 10.1109/TCBB.2021.3077573
Contributors: Tathagata Debnath; Mingzhou Song
Source: check_circle
Crossref

Fundamental gene network rewiring at the second order within and across mammalian systems

Bioinformatics
2021-10-11 | Journal article
DOI: 10.1093/bioinformatics/btab240
Contributors: Ruby Sharma; Sajal Kumar; Mingzhou Song; Janet Kelso
Source: check_circle
Crossref

Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers

Bioinformatics
2020-07-03 | Journal article
DOI: 10.1093/bioinformatics/btaa613
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 2)‎

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

Molecular Genetics and Genomics
2020-01 | Journal article
DOI: 10.1007/s00438-019-01604-5
Part of ISSN: 1617-4615
Part of ISSN: 1617-4623
Source: Self-asserted source
Mingzhou Song

Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs

BMC Medical Genomics
2019-12 | Journal article
DOI: 10.1186/s12920-019-0565-9
Part of ISSN: 1755-8794
Source: Self-asserted source
Mingzhou Song

Statistical inference of discrete combinatorial functional dependency in biological systems

Proceedings. The 14th Machine Learning in Computational Biology (MLCB) Meeting; Vancouver, Canada
2019-12 | Conference paper
Source: Self-asserted source
Mingzhou Song

Evaluating Model-free Directional Dependency Methods on Single-cell RNA Sequencing Data with Severe Dropout

Proceedings of the 2019 6th International Conference on Bioinformatics Research and Applications
2019-12-19 | Conference paper
DOI: 10.1145/3383783.3383793
ISBN: 9781450372183
Source: Self-asserted source
Mingzhou Song

'GenomicOZone': Delineate outstanding genomic zones of differential gene activity

2019-08 | Software
DOI: 10.18129/B9.BIOC.GENOMICOZONE
Source: Self-asserted source
Mingzhou Song

A fast exact functional test for directional association and cancer biology applications

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2018 | Journal article
DOI: 10.1109/TCBB.2018.2809743
EID:

2-s2.0-85042719741
Contributors: Zhong, H.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier
grade
Preferred source (of 2)‎

Scrutinizing functional interaction networks from RNA-binding proteins to their targets in cancer

2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2018-12 | Conference paper
DOI: 10.1109/bibm.2018.8621502
ISBN: 9781538654880
Source: Self-asserted source
Mingzhou Song

A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton

Molecular Genetics and Genomics
2017 | Journal article
DOI: 10.1007/s00438-017-1342-0
EID:

2-s2.0-85021225894
Contributors: Abdelraheem, A.; Liu, F.; Song, M.; Zhang, J.F.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Nonmonotonic Pathway Gene Expression Analysis Reveals Oncogenic Role of p27/Kip1 at Intermediate Dose

Cancer Informatics
2017 | Journal article
DOI: 10.1177/1176935117740132
EID:

2-s2.0-85038441280
Contributors: Nguyen, H.H.; Tilton, S.C.; Kemp, C.J.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Simulating noisy, nonparametric, and multivariate discrete patterns

R Journal
2017 | Journal article
EID:

2-s2.0-85041203355
Contributors: Sharma, R.; Kumar, S.; Zhong, H.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Inferring causal molecular networks: empirical assessment through a community-based effort

Nature Methods
2016-02 | Journal article
DOI: 10.1038/nmeth.3773
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 2)‎

Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing

Sci. Rep.
2016-01 | Journal article
DOI: 10.1038/srep19438
Contributors: Junjie Wang; Yan Zhao; Ian Ray; Mingzhou Song
Source: Self-asserted source
Mingzhou Song via Crossref Metadata Search

A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations

Molecular Genetics and Genomics
2015 | Journal article
DOI: 10.1007/s00438-014-0963-9
EID:

2-s2.0-84938847815
Contributors: Said, J.I.; Song, M.; Wang, H.; Lin, Z.; Zhang, X.; Fang, D.D.; Zhang, J.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

CbGRiTS: Cerebellar gene regulation in time and space

Developmental Biology
2015 | Journal article
DOI: 10.1016/j.ydbio.2014.09.032
EID:

2-s2.0-84915829364
Contributors: Ha, T.; Swanson, D.; Larouche, M.; Glenn, R.; Weeden, D.; Zhang, P.; Hamre, K.; Langston, M.; Phillips, C.; Song, M. et al.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion

Nucleic Acids Research
2015 | Journal article
DOI: 10.1093/nar/gkv358
EID:

2-s2.0-84936751150
Contributors: Zhang, Y.; Liu, Z.L.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Cotton QTLdb: a cotton QTL database for QTL analysis, visualization, and comparison between Gossypium hirsutum and G. hirsutum × G. barbadense populations

Molecular Genetics and Genomics
2015 | Journal article
DOI: 10.1007/s00438-015-1021-y
EID:

2-s2.0-84937974058
Contributors: Said, J.I.; Knapka, J.A.; Song, M.; Zhang, J.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics

Scientific Reports
2015 | Journal article
DOI: 10.1038/srep09634
EID:

2-s2.0-84929093927
Contributors: Cotton, T.B.; Nguyen, H.H.; Said, J.I.; Ouyang, Z.; Zhang, J.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

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

BMC Genomics
2015 | Journal article
DOI: 10.1186/s12864-015-1682-2
EID:

2-s2.0-84938686637
Contributors: Zhang, J.; Yu, J.; Pei, W.; Li, X.; Said, J.; Song, M.; Sanogo, S.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Constrained inference of protein interaction networks for invadopodium formation in cancer

IET Systems Biology
2015-10-06 | Journal article
DOI: 10.1049/iet-syb.2015.0009
Contributors: Haizhou Wang; Mingzhou Song; Laurie G. Hudson; Angela Wandinger-Ness; Ming Leung
Source: Self-asserted source
Mingzhou Song via Crossref Metadata Search

Hunting complex differential gene interaction patterns across molecular contexts

Nucleic Acids Research
2014 | Journal article
DOI: 10.1093/nar/gku086
EID:

2-s2.0-84899024021
Contributors: Song, M.; Zhang, Y.; Katzaroff, A.J.; Edgar, B.A.; Buttitta, L.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton

BMC Genomics
2013 | Journal article
DOI: 10.1186/1471-2164-14-776
EID:

2-s2.0-84887387829
Contributors: Said, J.I.; Lin, Z.; Zhang, X.; Song, M.; Zhang, J.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities

Applied and Environmental Microbiology
2012 | Journal article
DOI: 10.1128/AEM.00203-12
EID:

2-s2.0-84868611858
Contributors: Cruz-Martínez, K.; Rosling, A.; Zhang, Y.; Song, M.; Andersen, G.L.; Banfield, J.F.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Wisdom of crowds for robust gene network inference

Nature Methods
2012 | Journal article
DOI: 10.1038/nmeth.2016
EID:

2-s2.0-84870305264
Contributors: Marbach, D.; Costello, J.C.; Küffner, R.; Vega, N.M.; Prill, R.J.; Camacho, D.M.; Allison, K.R.; Kellis, M.; Collins, J.J.; Aderhold, A. et al.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Ckmeans.1d.dp: Optimal k-means clustering in one dimension by dynamic programming

R Journal
2011 | Journal article
EID:

2-s2.0-84873638356
Contributors: Wang, H.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Conserved and differential gene interactions in dynamical biological systems

Bioinformatics
2011 | Journal article
DOI: 10.1093/bioinformatics/btr472
EID:

2-s2.0-80054007194
Contributors: Ouyang, Z.; Song, M.; Güth, R.; Ha, T.J.; Larouche, M.; Goldowitz, D.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Integrated cellular and gene interaction modelling of pattern formation

International Journal of Computational Biology and Drug Design
2011 | Journal article
DOI: 10.1504/ijcbdd.2011.044444
Part of ISSN: 1756-0756
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Efficient and exact maximum likelihood quantisation of genomic features using dynamic programming

International Journal of Data Mining and Bioinformatics
2010 | Journal article
DOI: 10.1504/ijdmb.2010.032167
Part of ISSN: 1748-5673
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Integrated cellular and gene interaction model for cell migration in embryonic development

2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
2010 | Conference paper
DOI: 10.1109/bibmw.2010.5703804
Part of ISBN: 978-1-4244-8303-7
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Optimal In Silico Target Gene Deletion through Nonlinear Programming for Genetic Engineering

PLoS ONE
2010 | Journal article
DOI: 10.1371/journal.pone.0009331
Part of ISSN: 1932-6203
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Comparative generalized logic modeling reveals differential gene interactions during cell cycle exit in drosophila wing development

GCB 2009 - German Conference on Bioinformatics 2009
2009 | Conference paper
EID:

2-s2.0-84871207686
Contributors: Song, M.J.; Hong, C.-C.; Zhang, Y.; Buttitta, L.; Edgar, B.A.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Comparative identification of differential interactions from trajectories of dynamic biological networks

GCB 2009 - German Conference on Bioinformatics 2009
2009 | Conference paper
EID:

2-s2.0-84860916792
Contributors: Ouyang, Z.; Song, M.J.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast

IET Systems Biology
2009 | Journal article
DOI: 10.1049/iet-syb.2008.0089
EID:

2-s2.0-66249097762
Contributors: Song, M.; Ouyang, Z.; Liu, Z.L.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways

Molecular Genetics and Genomics
2009 | Journal article
DOI: 10.1007/s00438-009-0461-7
Part of ISSN: 1617-4615
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Genomic adaptation of saccharomyces cerevisiae to inhibitors for lignocellulosic biomass conversion to ethanol

Applied Mycology
2009 | Book
EID:

2-s2.0-84890255747
Contributors: Liu, Z.L.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling

IET Systems Biology
2009 | Journal article
DOI: 10.1049/iet-syb.2008.0164
EID:

2-s2.0-70349559072
Contributors: Angeles, J.G.C.; Ouyang, Z.; Aguirre, A.M.; Lammers, P.J.; Song, M.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier

Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data

EURASIP Journal on Bioinformatics and Systems Biology
2009 | Journal article
DOI: 10.1155/2009/545176
EID:

2-s2.0-63749101088
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 2)‎

Statistical Analysis of Discrete Dynamical System Models for Biological Networks

2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing
2009 | Conference paper
DOI: 10.1109/ijcbs.2009.10
Part of ISBN: 978-0-7695-3739-9
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Comparison of Cluster Representations from Partial Second- to Full Fourth-Order Cross Moments for Data Stream Clustering

2008 Eighth IEEE International Conference on Data Mining
2008 | Conference paper
DOI: 10.1109/icdm.2008.143
Part of ISBN: 978-0-7695-3502-9
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 3)‎

Genomic mechanisms of inhibitor-detoxification for low-cost lignocellulosic bioethanol conversion

Journal of Biotechnology
2008 | Journal article
DOI: 10.1016/j.jbiotec.2008.07.460
Part of ISSN: 0168-1656
Contributors: Mingzhou Song
Source: Self-asserted source
Mingzhou Song
grade
Preferred source (of 2)‎

A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2007 | Book
EID:

2-s2.0-38049129807
Contributors: Song, M.; Liu, Z.L.
Source: Self-asserted source
Mingzhou Song via Scopus - Elsevier
Items per page:
Page 1 of 2

Peer review (1 review for 1 publication/grant)

Review activity for BMC genomics (1)
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