Jennifer L Clarke

  • 2836 Citations
  • 25 h-Index
19982021

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

2020

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., Feb 1 2020, In : Risk Analysis. 40, 2, p. 276-293 18 p.

Research output: Contribution to journalArticle

Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs

Min, K. R., Galvis, A., Nole, K. L. B., Sinha, R., Clarke, J., Kirsner, R. S. & Ajdic, D., Jan 1 2020, In : PloS one. 15, 1, e0227006.

Research output: Contribution to journalArticle

Open Access

Quantitative assessment of microbial quality and safety risk: A preliminary case study of strengthening raspberry supply system in Chile

Ortúzar, J. E., Dogan, O. B., Sotomayor, G., Jiménez, C., Clarke, J., Flores, R. A., Gray, G. M., Rupnow, J. H. & Wang, B., Jul 2020, In : Food Control. 113, 107166.

Research output: Contribution to journalArticle

2019

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
2 Scopus citations

A quantitative microbial risk assessment model of Campylobacter in broiler chickens: Evaluating processing interventions

Dogan, O. B., Clarke, J., Mattos, F. & Wang, B., Jun 2019, In : Food Control. 100, p. 97-110 14 p.

Research output: Contribution to journalArticle

2 Scopus citations

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
1 Scopus citations

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
1 Scopus citations

Validation of MaSTR™ software: Extensive study of fully-continuous probabilistic mixture analysis using PowerPlex®Fusion 2 – 5 contributor mixtures

Adamowicz, M., Clarke, J., Rambo, T., Makam, H., Copeland, S., Erb, D., Hendricks, K., McGuigan, J., Prosser, C., Todd, J. & Snyder-Leiby, T., Dec 2019, In : Forensic Science International: Genetics Supplement Series. 7, 1, p. 641-643 3 p.

Research output: Contribution to journalArticle

2018

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., Sep 17 2018, In : BMC Proceedings. 12, 46.

Research output: Contribution to journalArticle

3 Scopus citations

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

4 Scopus citations

Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots

Xu, Z., Valdes, C. & Clarke, J., Jan 1 2018, In : Agronomy. 8, 5, 71.

Research output: Contribution to journalReview article

2 Scopus citations

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

25 Scopus citations
8 Scopus citations

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

6 Scopus citations

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. J. & LeVan, T. D., Mar 2018, In : PloS one. 13, 3, e0191499.

Research output: Contribution to journalArticle

3 Scopus citations

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

3 Scopus citations
2017

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

10 Scopus citations

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

5 Scopus citations

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

16 Scopus citations

When technology meets technology: Retrained 'Inception V3' classifier for NGS based pathogen detection

Sinha, R. & Clarke, J., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1-5 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations
2016

Cranberries and cancer: An update of preclinical studies evaluating the cancer inhibitory potential of cranberry and cranberry derived constituents

Weh, K. M., Clarke, J. & Kresty, L. A., Sep 2016, In : Antioxidants. 5, 3, 27.

Research output: Contribution to journalReview article

16 Scopus citations

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

22 Scopus citations

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

2015

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

3 Scopus citations

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

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

28 Scopus citations

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

1 Scopus citations

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

4 Scopus citations

Editor's Choice: 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. iii

Research output: Contribution to journalEditorial

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

7 Scopus citations
2014

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

1 Scopus citations

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

6 Scopus citations

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

26 Scopus citations

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

12 Scopus citations

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

3 Scopus citations
2013

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

5 Scopus citations

Epigenetic pathways and glioblastoma treatment

Clarke, J., Penas, C., Pastori, C., Komotar, R. J., Bregy, A., Shah, A. H., Wahlestedt, C. & Ayad, N. G., 2013, In : Epigenetics. 8, 8, p. 785-795 11 p.

Research output: Contribution to journalReview article

35 Scopus citations

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

4 Scopus citations
2012

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

74 Scopus citations

An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer (Journal of Clinical Oncology (2007) 25 (517-525))

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 20 2012, In : Journal of Clinical Oncology. 30, 6, 1 p.

Research output: Contribution to journalComment/debate

4 Scopus citations

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

73 Scopus citations

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

2 Scopus citations

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

4 Scopus citations

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

10 Scopus citations

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

139 Scopus citations
2011
12 Scopus citations

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

57 Scopus citations

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

13 Scopus citations
2010

Response

Iorns, E., Hnatyszyn, H. J., Seo, P., Clarke, J., Ward, T. & Lippman, M. E., Dec 15 2010, In : Journal of the National Cancer Institute. 102, 24, p. 1880-1881 2 p.

Research output: Contribution to journalLetter

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

46 Scopus citations