Jennifer L Clarke

  • 2711 Citations
  • 25 h-Index
19982019
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Research Output 1998 2019

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Article
2019
1 Citation (Scopus)

A General Hybrid Clustering Technique

Amiri, S., Clarke, B. S., Clarke, J. L. & Koepke, H., Jul 3 2019, In : Journal of Computational and Graphical Statistics. 28, 3, p. 540-551 12 p.

Research output: Contribution to journalArticle

Open Access
Clustering
Dendrogram
Number of Clusters
Hamming Distance
K-means Clustering

Assessment of the Dose–Response Relationship Between Folate Exposure and Cognitive Impairment: Synthesizing Data from Documented Studies

Wang, B., Sahyoun, N. R., Shao, K., Dutta, E. & Clarke, J., Jan 1 2019, (Accepted/In press) In : Risk Analysis.

Research output: Contribution to journalArticle

Folic Acid
Vitamins
Association reactions
Vitamin B 12 Deficiency
Risk assessment
1 Citation (Scopus)

Modeling association in microbial communities with clique loglinear models

Dobra, A., Valdes, C., Ajdic, D., Clarke, B. & Clarke, J., Jan 1 2019, In : Annals of Applied Statistics. 13, 2, p. 931-957 27 p.

Research output: Contribution to journalArticle

Open Access
Log-linear Models
Clique
Association reactions
Modeling
Wound Healing

Time series modeling of cell cycle exit identifies Brd4 dependent regulation of cerebellar neurogenesis

Penas, C., Maloof, M. E., Stathias, V., Long, J., Tan, S. K., Mier, J., Fang, Y., Valdes, C., Rodriguez-Blanco, J., Chiang, C. M., Robbins, D. J., Liebl, D. J., Lee, J. K., Hatten, M. E., Clarke, J. & Ayad, N. G., Dec 1 2019, In : Nature communications. 10, 1, 3028.

Research output: Contribution to journalArticle

Open Access
Neurogenesis
Time series
Cell Cycle
Stem Cells
Cells
2018
3 Citations (Scopus)

Analysis of genetic and nongenetic factors influencing triglycerides-lowering drug effects based on paired observations

Xu, Z., Duan, Q., Cui, J., Qiu, Y., Jia, Q., Wu, C. & Clarke, J. L., Sep 17 2018, In : BMC Proceedings. 12, 46.

Research output: Contribution to journalArticle

Triglycerides
Pharmaceutical Preparations
Obesity
Fenofibrate
Hydroxymethylglutaryl-CoA Reductase Inhibitors
3 Citations (Scopus)

Clustering Categorical Data via Ensembling Dissimilarity Matrices

Amiri, S., Clarke, B. S. & Clarke, J. L., Jan 2 2018, In : Journal of Computational and Graphical Statistics. 27, 1, p. 195-208 14 p.

Research output: Contribution to journalArticle

Nominal or categorical data
Dissimilarity
Clustering
High-dimensional Data
Phylogenetic Tree
12 Citations (Scopus)

Probiotic Bifidobacterium strains and galactooligosaccharides improve intestinal barrier function in obese adults but show no synergism when used together as synbiotics

Krumbeck, J. A., Rasmussen, H. E., Hutkins, R. W., Clarke, J., Shawron, K., Keshavarzian, A. & Walter, J., Jun 28 2018, In : Microbiome. 6, 1, 121.

Research output: Contribution to journalArticle

Synbiotics
Bifidobacterium
Probiotics
Prebiotics
trichlorosucrose
4 Citations (Scopus)
Vegetables
Fruit
Randomized Controlled Trials
Obesity
Inflammation
4 Citations (Scopus)

Safety and quality assessment of smallholder farmers' maize in the western highlands of Guatemala

Mendoza, J. R., Rodas, A., Oliva, A., Sabillón, L., Colmenares, A., Clarke, J., Hallen-Adams, H. E., Campabadal, C. & Bianchini, A., May 2018, In : Journal of food protection. 81, 5, p. 776-784 9 p.

Research output: Contribution to journalArticle

Guatemala
Zea mays
highlands
fumonisins
Fumonisins
1 Citation (Scopus)

Short term dynamics of the sputum microbiome among COPD patients

Sinha, R., Weissenburger-Moser, L. A., Clarke, J. L., Smith, L. M., Heires, A. J., Romberger, D. & LeVan, T. D., Mar 2018, In : PloS one. 13, 3, e0191499.

Research output: Contribution to journalArticle

Pulmonary diseases
Microbiota
Sputum
respiratory tract diseases
Chronic Obstructive Pulmonary Disease
2 Citations (Scopus)

The human brainome: Network analysis identifies HSPA2 as a novel Alzheimer's disease target

Petyuk, V. A., Chang, R., Ramirez-Restrepo, M., Beckmann, N. D., Henrion, M. Y. R., Piehowski, P. D., Zhu, K., Wang, S., Clarke, J., Huentelman, M. J., Xie, F., Andreev, V., Engel, A., Guettoche, T., Navarro, L., De Jager, P., Schneider, J. A., Morris, C. M., McKeith, I. G., Perry, R. H. & 17 others, Lovestone, S., Woltjer, R. L., Beach, T. G., Sue, L. I., Serrano, G. E., Lieberman, A. P., Albin, R. L., Ferrer, I., Mash, D. C., Hulette, C. M., Ervin, J. F., Reiman, E. M., Hardy, J. A., Bennett, D. A., Schadt, E., Smith, R. D. & Myers, A. J., Sep 1 2018, In : Brain. 141, 9, p. 2721-2739 19 p.

Research output: Contribution to journalArticle

Heat-Shock Proteins
Alzheimer Disease
Amyloid
Cell Line
Gene Expression
2017
6 Citations (Scopus)

A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself

Gomes-Neto, J. C., Kittana, H., Mantz, S., Segura Munoz, R. R., Schmaltz, R. J., Bindels, L. B., Clarke, J., Hostetter, J. M., Benson, A. K., Walter, J. & Ramer-Tait, A. E., Dec 1 2017, In : Scientific reports. 7, 1, 17707.

Research output: Contribution to journalArticle

Microbiota
Inflammatory Bowel Diseases
Inflammation
Helicobacter
Dextran Sulfate
4 Citations (Scopus)

Body composition, pre-diabetes and cardiovascular disease risk in early schizophrenia

Strassnig, M., Clarke, J., Mann, S., Remington, G. & Ganguli, R., Jun 2017, In : Early Intervention in Psychiatry. 11, 3, p. 229-236 8 p.

Research output: Contribution to journalArticle

Body Composition
Antipsychotic Agents
Schizophrenia
Body Mass Index
Cardiovascular Diseases
14 Citations (Scopus)

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans

Brahma, S., Martínez, I., Walter, J., Clarke, J., Gonzalez, T., Menon, R. & Rose, D. J., Feb 1 2017, In : Journal of Functional Foods. 29, p. 281-289 9 p.

Research output: Contribution to journalArticle

whole grain foods
Microbiota
bran
eating habits
Fermentation
2016
20 Citations (Scopus)

Effects of processing moisture on the physical properties and in vitro digestibility of starch and protein in extruded brown rice and pinto bean composite flours

Sumargo, F., Gulati, P., Weier, S. A., Clarke, J. & Rose, D. J., Nov 15 2016, In : Food Chemistry. 211, p. 726-733 8 p.

Research output: Contribution to journalArticle

Vigna umbellata
pinto beans
brown rice
in vitro digestibility
Flour

EnsCat: Clustering of categorical data via ensembling

Clarke, B. S., Amiri, S. & Clarke, J. L., Sep 15 2016, In : BMC bioinformatics. 17, 1, 380.

Research output: Contribution to journalArticle

Nominal or categorical data
Cluster Analysis
Clustering
Hamming distance
Unsupervised learning
2015
3 Citations (Scopus)

A Bayes testing approach to metagenomic profiling in bacteria

Clarke, B., Valdes, C., Dobra, A. & Clarke, J., Jan 1 2015, In : Statistics and its Interface. 8, 2, p. 173-185 13 p.

Research output: Contribution to journalArticle

Bayes
Profiling
Bacteria
Testing
Sequencing

Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data

Sinha, R., Clarke, J. & Benson, A. K., Dec 21 2015, In : BMC genomics. 16, 1, 1080.

Research output: Contribution to journalArticle

Metagenomics
Peptides
Proteins
Peptide Fragments
27 Citations (Scopus)

A novel MAPK-microRNA signature is predictive of hormone-therapy resistance and poor outcome in ER-positive breast cancer

Miller, P. C., Clarke, J., Koru-Sengul, T., Brinkman, J. & El-Ashry, D., Jan 15 2015, In : Clinical Cancer Research. 21, 2, p. 373-385 13 p.

Research output: Contribution to journalArticle

MicroRNAs
Estrogen Receptors
Hormones
Breast Neoplasms
Recurrence
1 Citation (Scopus)

Detecting bacterial genomes in a metagenomic sample using NGS reads

Valdes, C., Brennan, M., Clarke, B. & Clarke, J., Jan 1 2015, In : Statistics and its Interface. 8, 4, p. 477-494 18 p.

Research output: Contribution to journalArticle

Sequencing
Genome
Genes
Nucleotides
Adjusted P-value
4 Citations (Scopus)

Development of advanced imaging criteria for the endoscopic identification of inflammatory polyps

Sussman, D. A., Barkin, J. A., Martin, A. M., Varma, T., Clarke, J., Quintero, M. A., Barkin, H. B., Deshpande, A. R., Barkin, J. S. & Abreu, M. T., Nov 19 2015, In : Clinical and Translational Gastroenterology. 6, 11, e128.

Research output: Contribution to journalArticle

Polyps
Light
Colonoscopy
Inflammatory Bowel Diseases
Colon
5 Citations (Scopus)

Epigenetic Pathways and Glioblastoma Treatment: Insights from Signaling Cascades

Allen, B. K., Stathias, V., Maloof, M. E., Vidovic, D., Winterbottom, E. F., Capobianco, A. J., Clarke, J., Schurer, S., Robbins, D. J. & Ayad, N. G., Mar 1 2015, In : Journal of Cellular Biochemistry. 116, 3, p. 351-363 13 p.

Research output: Contribution to journalArticle

DNA sequences
Cell proliferation
Drug Combinations
Glioblastoma
Epigenomics
2014
1 Citation (Scopus)

Estimating the proportions in a mixed sample using transcriptomics

Clarke, B. & Clarke, J., Jan 1 2014, In : Stat. 3, 1, p. 313-325 13 p.

Research output: Contribution to journalArticle

Proportion
Tumor
Cell
Neoplasms
Stromal Cells
6 Citations (Scopus)

Identifying glioblastoma gene networks based on hypergeometric test analysis

Stathias, V., Pastori, C., Griffin, T. Z., Komotar, R., Clarke, J., Zhang, M. & Ayad, N. G. A., Dec 31 2014, In : PloS one. 9, 12, e115842.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Glioblastoma
Genes
neoplasms
Tumors
25 Citations (Scopus)

Infiltrating S100A8+ myeloid cells promote metastatic spread of human breast cancer and predict poor clinical outcome

Drews-Elger, K., Iorns, E., Dias, A., Miller, P., Ward, T. M., Dean, S., Clarke, J., Campion-Flora, A., Rodrigues, D. N., Reis-Filho, J. S., Rae, J. M., Thomas, D., Berry, D., El-Ashry, D. & Lippman, M. E., Oct 14 2014, In : Breast Cancer Research and Treatment. 148, 1, p. 41-59 19 p.

Research output: Contribution to journalArticle

Myeloid Cells
Breast Neoplasms
Neoplasms
Heterografts
Survival
10 Citations (Scopus)

In silico and Ex vivo approaches identify a role for toll-like receptor 4 in colorectal cancer

Sussman, D. A., Santaolalla, R., Bejarano, P. A., Garcia-Buitrago, M. T., Perez, M. T., Abreu, M. T. & Clarke, J., May 22 2014, In : Journal of Experimental and Clinical Cancer Research. 33, 1, 45.

Research output: Contribution to journalArticle

Toll-Like Receptor 4
Computer Simulation
Colorectal Neoplasms
Staining and Labeling
Colonic Neoplasms
3 Citations (Scopus)

Statistical Problem Classes and Their Links to Information Theory

Clarke, B., Clarke, J. & Yu, C. W., Feb 1 2014, In : Econometric Reviews. 33, 1-4, p. 337-371 35 p.

Research output: Contribution to journalArticle

Information theory
Prediction
Model selection
Model averaging
Information criterion
2013
5 Citations (Scopus)

Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays

Valdes, C., Seo, P., Tsinoremas, N. & Clarke, J., Apr 18 2013, In : Journal of Clinical Bioinformatics. 3, 1, 8.

Research output: Contribution to journalArticle

Heterografts
RNA
Genes
Consensus Sequence
Neoplasms
3 Citations (Scopus)

Prediction in M-complete problems with limited sample size

Clarke, J. L., Clarke, B. & Yu, C. W., Oct 2 2013, In : Bayesian Analysis. 8, 3, p. 647-690 44 p.

Research output: Contribution to journalArticle

Predictors
Sample Size
Prediction
Model
Squared Error Loss
2012
65 Citations (Scopus)

A New Mouse Model for the Study of Human Breast Cancer Metastasis

Iorns, E., Drews-Elger, K., Ward, T. M., Dean, S., Clarke, J., Berry, D., Ashry, D. E. & Lippman, M., Oct 31 2012, In : PloS one. 7, 10, e47995.

Research output: Contribution to journalArticle

metastasis
breast neoplasms
animal models
Breast Neoplasms
Neoplasm Metastasis
65 Citations (Scopus)

Label-free quantitative LC-MS proteomics of alzheimer's disease and normally aged human brains

Andreev, V. P., Petyuk, V. A., Brewer, H. M., Karpievitch, Y. V., Xie, F., Clarke, J., Camp, D., Smith, R. D., Lieberman, A. P., Albin, R. L., Nawaz, Z., El Hokayem, J. & Myers, A. J., Jun 1 2012, In : Journal of proteome research. 11, 6, p. 3053-3067 15 p.

Research output: Contribution to journalArticle

Proteomics
Labels
Brain
Alzheimer Disease
Proteins
2 Citations (Scopus)

Prediction in several conventional contexts

Clarke, B. & Clarke, J., Dec 1 2012, In : Statistics Surveys. 6, 1, p. 1-73 73 p.

Research output: Contribution to journalArticle

Longitudinal Data Analysis
Empirical Distribution Function
Survival Analysis
Prediction
Mechanics
4 Citations (Scopus)

Retinoblastoma treatment: Impact of the glycolytic inhibitor 2-deoxy-d-glucose on molecular genomics expression in LH BETAT AG retinal tumors

Piña, Y., Houston, S. K., Murray, T. G., Koru-Sengul, T., Decatur, C., Scott, W. K., Nathanson, L., Clarke, J. & Lampidis, T. J., May 27 2012, In : Clinical Ophthalmology. 6, 1, p. 817-830 14 p.

Research output: Contribution to journalArticle

Retinal Neoplasms
Retinoblastoma
Genomics
Deoxyglucose
Glucose
10 Citations (Scopus)

Simultaneous analysis of tumor and stromal gene expression profiles from xenograft models

Iorns, E., Clarke, J., Ward, T., Dean, S. & Lippman, M., Jan 1 2012, In : Breast Cancer Research and Treatment. 131, 1, p. 321-324 4 p.

Research output: Contribution to journalArticle

Transcriptome
Heterografts
Neoplasms
Gene Expression
Microarray Analysis
117 Citations (Scopus)

The effects of child abuse and neglect on cognitive functioning in adulthood

Gould, F., Clarke, J., Heim, C., Harvey, P. D., Majer, M. & Nemeroff, C. B., Apr 2012, In : Journal of Psychiatric Research. 46, 4, p. 500-506 7 p.

Research output: Contribution to journalArticle

Neuropsychological Tests
Child Abuse
Sex Offenses
Wounds and Injuries
Post-Traumatic Stress Disorders
2011
9 Citations (Scopus)
Vaccinium macrocarpon
Barrett Esophagus
Chemoprevention
MicroRNAs
Adenocarcinoma
56 Citations (Scopus)

Osteosarcoma: Improvement in survival limited to high-grade patients only

Jawad, M. U., Cheung, M. C., Clarke, J., Koniaris, L. G. & Scully, S. P., Apr 1 2011, In : Journal of Cancer Research and Clinical Oncology. 137, 4, p. 597-607 11 p.

Research output: Contribution to journalArticle

Osteosarcoma
Survival
Skeleton
Registries
Cause of Death
13 Citations (Scopus)

Regional and temporal differences in gene expression of LH BETAT AG retinoblastoma tumors

Houston, S. K., Pina, Y., Clarke, J., Koru-Sengul, T., Scott, W. K., Nathanson, L., Schefler, A. C. & Murray, T. G., Jul 1 2011, In : Investigative Ophthalmology and Visual Science. 52, 8, p. 5359-5368 10 p.

Research output: Contribution to journalArticle

Retinoblastoma
Gene Expression
Genes
Neoplasms
Retinal Neoplasms
2010
45 Citations (Scopus)

Statistical expression deconvolution from mixed tissue samples

Clarke, J., Seol, P. & Clarke, B., Mar 4 2010, In : Bioinformatics. 26, 8, p. 1043-1049 7 p., btq097.

Research output: Contribution to journalArticle

Deconvolution
Gene expression
Tissue
Gene Expression
Proportion
57 Citations (Scopus)

The role of SATB1 in breast cancer pathogenesis

Iorns, E., Hnatyszyn, H. J., Seo, P., Clarke, J., Ward, T. & Lippman, M., Aug 18 2010, In : Journal of the National Cancer Institute. 102, 16, p. 1284-1296 13 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Heterografts
Cultured Cells
Cell Proliferation
Neoplasm Metastasis
2009
187 Citations (Scopus)

Genetic Control of Human Brain Transcript Expression in Alzheimer Disease

Webster, J. A., Gibbs, J. R., Clarke, J., Ray, M., Zhang, W., Holmans, P., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., McCorquodale, D. S., Cuello, C., Leung, D., Bryden, L., Nath, P., Zismann, V. L., Joshipura, K., Huentelman, M. J., Hu-Lince, D., Coon, K. D. & 7 others, Craig, D. W., Pearson, J. V., Heward, C. B., Reiman, E. M., Stephan, D., Hardy, J. & Myers, A. J., Apr 10 2009, In : American Journal of Human Genetics. 84, 4, p. 445-458 14 p.

Research output: Contribution to journalArticle

Medical Genetics
Single Nucleotide Polymorphism
Alzheimer Disease
Transcriptome
Brain
50 Citations (Scopus)

Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome

Berchuck, A., Iversen, E. S., Luo, J., Clarke, J. P., Horne, H., Levine, D. A., Boyd, J., Alonso, M. A., Secord, A. A., Bernardini, M. Q., Barnett, J. C., Boren, T., Murphy, S. K., Dressman, H. K., Marks, J. R. & Lancaster, J. M., Apr 1 2009, In : Clinical Cancer Research. 15, 7, p. 2448-2455 8 p.

Research output: Contribution to journalArticle

Microarray Analysis
Ovarian Neoplasms
Neoplasms
Survival
Survivors
6 Citations (Scopus)

Prequential analysis of complex data with adaptive model reselection

Clarke, J. & Clarke, B., Nov 1 2009, In : Statistical Analysis and Data Mining. 2, 4, p. 274-290 17 p.

Research output: Contribution to journalArticle

Predictors
Model
Averaging
Trade-offs
Weighted Likelihood
2008
9 Citations (Scopus)

Bayesian Weibull tree models for survival analysis of clinico-genomic data

Clarke, J. & West, M., May 1 2008, In : Statistical Methodology. 5, 3, p. 238-262 25 p.

Research output: Contribution to journalArticle

Survival Analysis
Weibull
Genomics
Prediction
Recursive Partitioning
2007
206 Citations (Scopus)

An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer

Dressman, H. K., Berchuck, A., Chan, G., Zhai, J., Bild, A., Sayer, R., Cragun, J., Clarke, J., Whitaker, R. S., Li, L. H., Gray, J., Marks, J., Ginsburg, G. S., Potti, A., West, M., Nevins, J. R. & Lancaster, J. M., Feb 10 2007, In : Journal of Clinical Oncology. 25, 5, p. 517-525 9 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Platinum
Drug Therapy
Therapeutics
Transcriptome
5 Citations (Scopus)

Information conversion, effective samples, and parameter size

Lin, X., Pittman, J. & Clarke, B., Dec 1 2007, In : IEEE Transactions on Information Theory. 53, 12, p. 4438-4456 19 p.

Research output: Contribution to journalArticle

entropy
Entropy
2006
67 Citations (Scopus)

Genomic prediction of locoregional recurrence after mastectomy in breast cancer

Cheng, S. H., Horng, C. F., West, M., Huang, E., Pittman, J., Tsou, M. H., Dressman, H., Chen, C. M., Tsai, S. Y., Jian, J. J., Liu, M. C., Nevins, J. R. & Huang, A. T., Oct 1 2006, In : Journal of Clinical Oncology. 24, 28, p. 4594-4602 9 p.

Research output: Contribution to journalArticle

Mastectomy
Breast Neoplasms
Recurrence
Transcriptome
Radiotherapy
44 Citations (Scopus)

Prognostic index score and clinical prediction model of local regional recurrence after mastectomy in breast cancer patients

Cheng, S. H., Horng, C. F., Clarke, J. L., Tsou, M. H., Tsai, S. Y., Chen, C. M., Jian, J. J., Liu, M. C., West, M., Huang, A. T. & Prosnitz, L. R., Apr 1 2006, In : International Journal of Radiation Oncology Biology Physics. 64, 5, p. 1401-1409 9 p.

Research output: Contribution to journalArticle

Mastectomy
breast
cancer
Breast Neoplasms
Recurrence
2005
69 Citations (Scopus)

High insulin-like growth factor-2 (IGF-2) gene expression is an independent predictor of poor survival for patients with advanced stage serous epithelial ovarian cancer

Sayer, R. A., Lancaster, J. M., Pittman, J., Gray, J., Whitaker, R., Marks, J. R. & Berchuck, A., Feb 1 2005, In : Gynecologic Oncology. 96, 2, p. 355-361 7 p.

Research output: Contribution to journalArticle

Somatomedins
Gene Expression
Survival
Ovarian Neoplasms
Genes
207 Citations (Scopus)

Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers

Berchuck, A., Iversen, E. S., Lancaster, J. M., Pittman, J., Luo, J., Lee, P., Murphy, S., Dressman, H. K., Febbo, P. G., West, M., Nevins, J. R. & Marks, J. R., May 15 2005, In : Clinical Cancer Research. 11, 10, p. 3686-3696 11 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Survivors
Gene Expression
Survival
Genes