• 2048 Citations
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20032020

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Article
2020

Dynamic incorporation of prior knowledge from multiple domains in biomarker discovery

Guan, X., Runger, G. & Liu, L., Mar 11 2020, In : BMC bioinformatics. 21, 77.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2019

Biological relevance of computationally predicted pathogenicity of noncoding variants

Liu, L., Sanderford, M. D., Patel, R., Chandrashekar, P., Gibson, G. & Kumar, S., Dec 1 2019, In : Nature communications. 10, 1, 330.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Breast cancer detection using targeted plasma metabolomics

Jasbi, P., Wang, D., Cheng, S. L., Fei, Q., Cui, J. Y., Liu, L., Wei, Y., Raftery, D. & Gu, H., Jan 15 2019, In : Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences. 1105, p. 26-37 12 p.

Research output: Contribution to journalArticle

19 Scopus citations

Coccidioidomycosis Detection Using Targeted Plasma and Urine Metabolic Profiling

Jasbi, P., Mitchell, N. M., Shi, X., Grys, T. E., Wei, Y., Liu, L., Lake, D. & Gu, H., Jan 1 2019, In : Journal of Proteome Research.

Research output: Contribution to journalArticle

3 Scopus citations

Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans

Xu, K., Kosoy, R., Shameer, K., Kumar, S., Liu, L., Readhead, B., Belbin, G. M., Lee, H. C., Chen, R. & Dudley, J. T., Jul 2 2019, In : BMC Genetics. 20, 1, 52.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
2018
6 Scopus citations
2017

FlyExpress 7: An integrated discovery platform to study coexpressed genes using in situ hybridization images in Drosophila

Kumar, S., Konikoff, C., Sanderford, M., Liu, L., Newfeld, S., Ye, J. & Kulathinal, R. J., 2017, In : G3: Genes, Genomes, Genetics. 7, 8, p. 2791-2797 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

Genome Sequence of Porphyromonas gingivalis Strain 381

Chastain-Gross, R. P., Xie, G., Bélanger, M., Kumar, D., Whitlock, J. A., Liu, L., Raines, S. M., Farmerie, W. G., Daligault, H. E., Han, C. S., Brettin, T. S. & Progulske-Fox, A., Jan 1 2017, In : Genome Announcements. 5, 2, e01467-16.

Research output: Contribution to journalArticle

7 Scopus citations

Genome sequence of Porphyromonas gingivalis strain A7A1-28

Xie, G., Chastain-Gross, R. P., Bélanger, M., Kumar, D., Whitlock, J. A., Liu, L., Farmerie, W. G., Zeng, C. L., Daligault, H. E., Han, C. S., Brettin, T. S. & Progulske-Fox, A., Jan 1 2017, In : Genome Announcements. 5, 10, e00021-17.

Research output: Contribution to journalArticle

2 Scopus citations

Prescreening of Nicotine Hapten Linkers in Vitro To Select Hapten-Conjugate Vaccine Candidates for Pharmacokinetic Evaluation in Vivo

Arutla, V., Leal, J., Liu, X., Sokalingam, S., Raleigh, M., Adaralegbe, A., Liu, L., Pentel, P. R., Hecht, S. & Chang, Y., May 8 2017, In : ACS Combinatorial Science. 19, 5, p. 286-298 13 p.

Research output: Contribution to journalArticle

2 Scopus citations
2016

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis

DREAM 9 AML-OPC Consortium, Jun 2016, In : PLoS computational biology. 12, 6, e1004890.

Research output: Contribution to journalArticle

14 Scopus citations

A molecular evolutionary reference for the human variome

Liu, L., Tamura, K., Sanderford, M., Gray, V. E. & Kumar, S., Jan 1 2016, In : Molecular biology and evolution. 33, 1, p. 245-254 10 p.

Research output: Contribution to journalArticle

8 Scopus citations

Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks

Szedlak, A., Smith, N., Liu, L., Paternostro, G. & Piermarocchi, C., Jun 1 2016, In : PLoS Computational Biology. 12, 6, e1005009.

Research output: Contribution to journalArticle

1 Scopus citations

Evolution-informed modeling improves outcome prediction for cancers

Liu, L., Chang, Y., Yang, T., Noren, D. P., Long, B., Kornblau, S., Qutub, A. & Ye, J., 2016, (Accepted/In press) In : Evolutionary Applications.

Research output: Contribution to journalArticle

10 Scopus citations
2015

Evolutionary Diagnosis of non-synonymous variants involved in differential drug response

Gerek, N. Z., Liu, L., Gerold, K., Biparva, P., Thomas, E. D. & Kumar, S., Jan 15 2015, (Accepted/In press) In : BMC Medical Genomics. p. 1-6 6 p.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Genome sequence of Porphyromonas gingivalis strain A7436

Chastain-Gross, R. P., Xie, G., Bélanger, M., Kumar, D., Whitlock, J. A., Liu, L., Farmerie, W. G., Daligault, H. E., Han, C. S., Brettin, T. S. & Progulske-Fox, A., 2015, In : Genome Announcements. 3, 5, e00927-15.

Research output: Contribution to journalArticle

8 Scopus citations

Genome sequence of Porphyromonas gingivalis strain AJW4

Xie, G., Chastain-Gross, R. P., Bélanger, M., Kumar, D., Whitlock, J. A., Liu, L., Farmerie, W. G., Daligault, H. E., Han, C. S., Brettin, T. S. & Progulske-Fox, A., 2015, In : Genome Announcements. 3, 6, e0130415.

Research output: Contribution to journalArticle

3 Scopus citations
2014

MEGA-MD: Molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation

Stecher, G., Liu, L., Sanderford, M., Peterson, D., Tamura, K. & Kumar, S., May 1 2014, In : Bioinformatics. 30, 9, p. 1305-1307 3 p.

Research output: Contribution to journalArticle

23 Scopus citations

Signatures of natural selection on mutations of residues with multiple posttranslational modifications

Gray, V. E., Liu, L., Nirankari, R., Hornbeck, P. V. & Kumar, S., Jul 2014, In : Molecular biology and evolution. 31, 7, p. 1641-1645 5 p.

Research output: Contribution to journalArticle

6 Scopus citations
2013

Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants

Liu, L. & Kumar, S., Jun 1 2013, In : Molecular biology and evolution. 30, 6, p. 1252-1257 6 p.

Research output: Contribution to journalArticle

12 Scopus citations

Genome-wide profiling of human cap-independent translation-enhancing elements

Wellensiek, B. P., Larsen, A. C., Stephens, B., Kukurba, K., Waern, K., Briones, N., Liu, L., Snyder, M., Jacobs, B. L., Kumar, S. & Chaput, J. C., Aug 1 2013, In : Nature Methods. 10, 8, p. 747-750 4 p.

Research output: Contribution to journalArticle

17 Scopus citations
2012

High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems

Yin, L., Liu, L., Sun, Y., Hou, W., Lowe, A. C., Gardner, B. P., Salemi, M., Williams, W. B., Farmerie, W. G., Sleasman, J. W. & Goodenow, M. M., Dec 17 2012, In : Retrovirology. 9, 108.

Research output: Contribution to journalArticle

21 Scopus citations
2010

Fathead minnow steroidogenesis: In silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk

Shoemaker, J. E., Gayen, K., Garcia-Reyero, N., Perkins, E. J., Villeneuve, D. L., Liu, L. & Doyle, F. J., Jun 28 2010, In : BMC systems biology. 4, 89.

Research output: Contribution to journalArticle

19 Scopus citations

Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the florida keys

Spade, D. J., Griffitt, R. J., Liu, L., Brown-Peterson, N. J., Kroll, K. J., Feswick, A., Glazer, O. A., Barber, D. S. & Denslow, N. D., Nov 1 2010, In : PloS one. 5, 9, p. 1-14 14 p., e12737.

Research output: Contribution to journalArticle

15 Scopus citations
2009

Bladder cancer-associated gene expression signatures identified by profiling of exfoliated urothelia

Rosser, C. J., Liu, L., Sun, Y., Villicana, P., McCullers, M., Porvasnik, S., Young, P. R., Parker, A. S. & Goodison, S., Feb 1 2009, In : Cancer Epidemiology Biomarkers and Prevention. 18, 2, p. 444-453 10 p.

Research output: Contribution to journalArticle

53 Scopus citations

Comparative interactomics: Analysis of Arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants

Paul, A. L., Liu, L., McClung, S., Laughner, B., Chen, S. & Ferl, R. J., Apr 3 2009, In : Journal of Proteome Research. 8, 4, p. 1913-1924 12 p.

Research output: Contribution to journalArticle

32 Scopus citations

Complete genome sequence of citrus huanglongbing bacterium, 'candidatus liberibacter asiaticus' obtained through metagenomics

Duan, Y., Zhou, L., Hall, D. G., Li, W., Doddapaneni, H., Lin, H., Liu, L., Vahling, C. M., Gabriel, D. W., Williams, K. P., Dickerman, A., Sun, Y. & Gottwald, T., Aug 1 2009, In : Molecular Plant-Microbe Interactions. 22, 8, p. 1011-1020 10 p.

Research output: Contribution to journalArticle

297 Scopus citations

ESPRIT: Estimating species richness using large collections of 16S rRNA pyrosequences

Sun, Y., Cai, Y., Liu, L., Yu, F., Farrell, M. L., Mckendree, W. & Farmerie, W., Jun 22 2009, In : Nucleic acids research. 37, 10, e76.

Research output: Contribution to journalArticle

207 Scopus citations

Expression signatures for a model androgen and antiandrogen in the fathead minnow (Pimephales promelas) ovary

Garcia-Reyero, N., Villeneuve, D. L., Kroll, K. J., Liu, L., Orlando, E. F., Watanabe, K. H., Sepulveda, M. S., Ankley, G. T. & Denslow, N. D., Apr 1 2009, In : Environmental Science and Technology. 43, 7, p. 2614-2619 6 p.

Research output: Contribution to journalArticle

42 Scopus citations

Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen

Garcia-Reyero, N., Kroll, K. J., Liu, L., Orlando, E. F., Watanabe, K. H., Sepúlveda, M. S., Villeneuve, D. L., Perkins, E. J., Ankley, G. T. & Denslow, N. D., Jul 13 2009, In : BMC Genomics. 10, 308.

Research output: Contribution to journalArticle

58 Scopus citations

Site-specific impacts on gene expression and behavior in fathead minnows (Pimephales promelas) exposed in situ to streams adjacent to sewage treatment plants

Garcia-Reyero, N., Adelman, I. R., Martinović, D., Liu, L. & Denslow, N. D., Oct 8 2009, In : BMC bioinformatics. 10, SUPPL. 11, p. S11 1471.

Research output: Contribution to journalArticle

Open Access
32 Scopus citations
2008

Construction of a robust microarray from a non-model species largemouth bass, Micropterus salmoides (Lacèpede), using pyrosequencing technology

Garcia-Reyero, N., Griffitt, R. J., Liu, L., Kroll, K. J., Farmerie, W. G., Barber, D. S. & Denslow, N. D., Jun 1 2008, In : Journal of Fish Biology. 72, 9, p. 2354-2376 23 p.

Research output: Contribution to journalArticle

68 Scopus citations

Gene expression profiles of fathead minnows exposed to surface waters above and below a sewage treatment plant in Minnesota

Garcia-Reyero, N., Adelman, I., Liu, L. & Denslow, N., Jul 1 2008, In : Marine Environmental Research. 66, 1, p. 134-136 3 p.

Research output: Contribution to journalArticle

22 Scopus citations

Microarray analysis of host gene expression for comparison between naïve and HSV-1 latent rabbit trigeminal ganglia

Clement, C., Popp, M. P., Bloom, D. C., Schultz, G., Liu, L., Neumann, D. M., Bhattachrjee, P. S. & Hill, J. M., Jul 3 2008, In : Molecular Vision. 14, p. 1209-1221 13 p.

Research output: Contribution to journalArticle

11 Scopus citations
2007

Development and validation of a 2,000-gene microarray for the fathead minnow (Pimephales promelas)

Larkin, P., Villeneuve, D. L., Knoebl, I., Miracle, A. L., Carter, B. J., Liu, L., Denslow, N. D. & Ankley, G. T., Jul 1 2007, In : Environmental Toxicology and Chemistry. 26, 7, p. 1497-1506 10 p.

Research output: Contribution to journalArticle

33 Scopus citations

Development of a microarray chip for gene expression in rabbit ocular research

Popp, M. P., Liu, L., Timmers, A., Esson, D. W., Shiroma, L., Meyers, C., Berceli, S., Tao, M., Wistow, G., Schultz, G. S. & Sherwood, M. B., Feb 27 2007, In : Molecular Vision. 13, p. 164-173 10 p.

Research output: Contribution to journalArticle

14 Scopus citations
28 Scopus citations

Improved breast cancer prognosis through the combination of clinical and genetic markers

Sun, Y., Goodison, S., Li, J., Liu, L. & Farmerie, W., Jan 1 2007, In : Bioinformatics. 23, 1, p. 30-37 8 p.

Research output: Contribution to journalArticle

109 Scopus citations
2006
70 Scopus citations

Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2

Gabriel, D. W., Allen, C., Schell, M., Denny, T. P., Greenberg, J. T., Duan, Y. P., Flores-Cruz, Z., Huang, Q., Clifford, J. M., Presting, G., González, E. T., Reddy, J., Elphinstone, J., Swanson, J., Yao, J., Mulholland, V., Liu, L., Farmerie, W., Patnaikuni, M., Balogh, B. & 8 others, Norman, D., Alvarez, A., Castillo, J. A., Jones, J., Saddler, G., Walunas, T., Zhukov, A. & Mikhailova, N., Jan 2006, In : Molecular Plant-Microbe Interactions. 19, 1, p. 69-79 11 p.

Research output: Contribution to journalArticle

Open Access
89 Scopus citations

Neuronal Transcriptome of Aplysia: Neuronal Compartments and Circuitry

Moroz, L. L., Edwards, J. R., Puthanveettil, S. V., Kohn, A. B., Ha, T., Heyland, A., Knudsen, B., Sahni, A., Yu, F., Liu, L., Jezzini, S., Lovell, P., Iannucculli, W., Chen, M., Nguyen, T., Sheng, H., Shaw, R., Kalachikov, S., Panchin, Y. V., Farmerie, W. & 3 others, Russo, J. J., Ju, J. & Kandel, E. R., Dec 29 2006, In : Cell. 127, 7, p. 1453-1467 15 p.

Research output: Contribution to journalArticle

222 Scopus citations
2005

Biological workflow with BlastQuest

Farmerie, W. G., Hammer, J., Liu, L., Sahni, A. & Schneider, M., Apr 2005, In : Data and Knowledge Engineering. 53, 1, p. 75-97 23 p.

Research output: Contribution to journalArticle

11 Scopus citations
2004

Microarray analysis of the failure of filtering blebs in a rat model of glaucoma filtering surgery

Esson, D. W., Popp, M. P., Liu, L., Schultz, G. S. & Sherwood, M. B., Dec 1 2004, In : Investigative Ophthalmology and Visual Science. 45, 12, p. 4450-4462 13 p.

Research output: Contribution to journalArticle

30 Scopus citations
2003

A global view of the selectivity of zinc deprivation and excess on genes expressed in human THP-1 mononuclear cells

Cousins, R. J., Blanchard, R. K., Popp, M. P., Liu, L., Cao, J., Moore, J. B. & Green, C. L., Jun 10 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 12, p. 6952-6957 6 p.

Research output: Contribution to journalArticle

134 Scopus citations