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Research Output 1999 2019

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Article
2019
4 Citations (Scopus)

IDH3α regulates one-carbon metabolism in glioblastoma

May, J. L., Kouri, F., Hurley, L. A., Liu, J., Tommasini-Ghelfi, S., Ji, Y., Gao, P., Calvert, A. E., Lee, A., Chandel, N., Davuluri, R. V., Horbinski, C. M., Locasale, J. W. & Stegh, A. H., Jan 1 2019, In : Science Advances. 5, 1, eaat0456.

Research output: Contribution to journalArticle

Glioblastoma
Glycine Hydroxymethyltransferase
Carbon
Methionine
Activity Cycles

Platform-independent classification system for predicting high-grade serous ovarian carcinoma molecular subtypes

Shilpi, A., Kandpal, M., Ji, Y., Seagle, BL. & Davuluri, RV., Apr 3 2019, In : JCO Clinical Cancer Informatics. 3, 1, p. 1-9 9 p.

Research output: Contribution to journalArticle

Open Access
RNA Sequence Analysis
Cystic Fibrosis
MicroRNAs
Phenotype
Blood Cells
2018
2 Citations (Scopus)

Characterization of brain tumor initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors

Malchenko, S., Sredni, S. T., Boyineni, J., Bi, Y., Margaryan, N. V., Guda, M. R., Kostenko, Y., Tomita, T., Davuluri, R. V., Velpula, K., Hendrix, M. J. C. & Soares, M. B., Jan 1 2018, In : Oncotarget. 9, 17, p. 13733-13747 15 p.

Research output: Contribution to journalArticle

Primitive Neuroectodermal Tumors
Neoplastic Stem Cells
Brain Neoplasms
Animal Models
Carcinogenesis
14 Citations (Scopus)

Metastatic cancers promote cachexia through ZIP14 upregulation in skeletal muscle

Wang, G., Biswas, AK., Ma, W., Kandpal, M., Coker, C., Grandgenett, PM., Hollingsworth, MA., Jain, R., Tanji, K., Lomicronpez-Pintado, S., Borczuk, A., Hebert, D., Jenkitkasemwong, S., Hojyo, S., Davuluri, RV., Knutson, MD., Fukada, T. & Acharyya, S., Jun 8 2018, In : Nature Medicine. 24, 6, p. 770-781 12 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Radiomic MRI signature reveals three distinct subtypes of glioblastoma with different clinical and molecular characteristics, offering prognostic value beyond IDH1

Rathore, S., Akbari, H., Rozycki, M., Abdullah, K. G., Nasrallah, M. P., Binder, Z. A., Davuluri, R. V., Lustig, R. A., Dahmane, N., Bilello, M., O'Rourke, D. M. & Davatzikos, C., Dec 1 2018, In : Scientific reports. 8, 1, 5087.

Research output: Contribution to journalArticle

Isocitrate Dehydrogenase
Glioblastoma
Epidermal Growth Factor Receptor
Molecular Imaging
Methyltransferases
2017
29 Citations (Scopus)

Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation

Calvert, A. E., Chalastanis, A., Wu, Y., Hurley, L. A., Kouri, F., Bi, Y., Kachman, M., May, J. L., Bartom, E. T., Hua, Y., Mishra, R. K., Schiltz, G. E., Dubrovskyi, O., Mazar, A. P., Peter, M. E., Zheng, H., James, C. D., Burant, C. F., Chandel, N., Davuluri, R. V. & 2 others, Horbinski, C. M. & Stegh, A. H., May 30 2017, In : Cell reports. 19, 9, p. 1858-1873 16 p.

Research output: Contribution to journalArticle

Bearings (structural)
Isocitrate Dehydrogenase
Gene encoding
Methylation
Differentiation Antigens
47 Citations (Scopus)

Combining anti-miR-155 with chemotherapy for the treatment of lung cancers

Van Roosbroeck, K., Fanini, F., Setoyama, T., Ivan, C., Rodriguez-Aguayo, C., Fuentes-Mattei, E., Xiao, L., Vannini, I., Redis, R. S., D'Abundo, L., Zhang, X., Nicoloso, M. S., Rossi, S., Gonzalez-Villasana, V., Rupaimoole, R., Ferracin, M., Morabito, F., Neri, A., Ruvolo, P. P., Ruvolo, V. R. & 20 others, Pecot, C. V., Amadori, D., Abruzzo, L., Calin, S., Wang, X., You, M. J., Ferrajoli, A., Orlowski, R., Plunkett, W., Lichtenberg, T. M., Davuluri, R. V., Berindan-Neagoe, I., Negrini, M., Wistuba, I. I., Kantarjian, H. M., Sood, A. K., Lopez-Berestein, G., Keating, M. J., Fabbri, M. & Calin, G. A., Jun 1 2017, In : Clinical Cancer Research. 23, 11, p. 2891-2904 14 p.

Research output: Contribution to journalArticle

Lung Neoplasms
Drug Therapy
Neoplasms
Nude Mice
Therapeutics
9 Citations (Scopus)

Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms

Dapas, M., Kandpal, M., Bi, Y. & Davuluri, R. V., Jan 1 2017, In : Briefings in Bioinformatics. 18, 2, p. 260-269 10 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
RNA
Gene expression
Exons
Protein Isoforms
7 Citations (Scopus)

Identification of genetic and epigenetic variants associated with breast cancer prognosis by integrative bioinformatics analysis

Shilpi, A., Bi, Y., Jung, S., Patra, S. K. & Davuluri, R. V., Jan 9 2017, In : Cancer Informatics. 16

Research output: Contribution to journalArticle

Computational Biology
Epigenomics
Breast Neoplasms
Single Nucleotide Polymorphism
DNA Methylation
15 Citations (Scopus)

Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes

Liu, X., Zhao, B., Sun, L., Bhuripanyo, K., Wang, Y., Bi, Y., Davuluri, R. V., Duong, D. M., Nanavati, D., Yin, J. & Kiyokawa, H., Jan 30 2017, In : Nature communications. 8, 14286.

Research output: Contribution to journalArticle

Ubiquitin-Activating Enzymes
Ubiquitination
Ubiquitin
enzymes
Ubiquitin-Conjugating Enzymes
1 Citation (Scopus)

Stabilization of HIF-1α and HIF-2α, upregulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model

Malchenko, S., Sredni, S. T., Bi, Y., Margaryan, N. V., Boyineni, J., Mohanam, I., Tomita, T., Davuluri, R. V. & Soares, M. B., Mar 2017, In : PloS one. 12, 3, e0173106.

Research output: Contribution to journalArticle

Primitive Neuroectodermal Tumors
Tumors
Animals
Up-Regulation
Animal Models
9 Citations (Scopus)

Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs

Vannini, I., Wise, P. M., Challagundla, K. B., Plousiou, M., Raffini, M., Bandini, E., Fanini, F., Paliaga, G., Crawford, M., Ferracin, M., Ivan, C., Fabris, L., Davuluri, R. V., Guo, Z., Cortez, M. A., Zhang, X., Chen, L., Zhang, S., Fernandez-Cymering, C., Han, L. & 14 others, Carloni, S., Salvi, S., Ling, H., Murtadha, M., Neviani, P., Gitlitz, B. J., Laird-Offringa, I. A., Nana-Sinkam, P., Negrini, M., Liang, H., Amadori, D., Cimmino, A., Fabbri, M. & Calin, G. A., Dec 1 2017, In : Nature communications. 8, 1, 1801.

Research output: Contribution to journalArticle

suppressors
MicroRNAs
Tumors
Carcinogenesis
tumors
2016
14 Citations (Scopus)

Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer

Jin, H. J., Jung, S., DebRoy, A. R. & Davuluri, R. V., Jan 1 2016, In : Oncotarget. 7, 34, p. 54616-54626 11 p.

Research output: Contribution to journalArticle

Chromatin
Single Nucleotide Polymorphism
Prostatic Neoplasms
Transcription Factors
Gene Expression
83 Citations (Scopus)

Imaging patterns predict patient survival and molecular subtype in glioblastoma via machine learning techniques

Macyszyn, L., Akbari, H., Pisapia, J. M., Da, X., Attiah, M., Pigrish, V., Bi, Y., Pal, S., Davuluri, R. V., Roccograndi, L., Dahmane, N., Martinez-Lage, M., Biros, G., Wolf, R. L., Bilello, M., O'Rourke, D. M. & Davatzikos, C., Mar 1 2016, In : Neuro-oncology. 18, 3, p. 417-425 9 p.

Research output: Contribution to journalArticle

Glioblastoma
Survival
Biomarkers
Machine Learning
Blood-Brain Barrier
14 Citations (Scopus)

MNK inhibition disrupts mesenchymal glioma stem cells and prolongs survival in a mouse model of glioblastoma

Bell, J. B., Eckerdt, F. D., Alley, K., Magnusson, L. P., Hussain, H., Bi, Y., Arslan, A. D., Clymer, J., Alvarez, A. A., Goldman, S., Cheng, S. Y., Nakano, I., Horbinski, C., Davuluri, R. V., David James, C. & Platanias, L. C., Oct 1 2016, In : Molecular Cancer Research. 14, 10, p. 984-993 10 p.

Research output: Contribution to journalArticle

Glioblastoma
Mesenchymal Stromal Cells
Glioma
Cell Survival
Phosphotransferases
2015
3 Citations (Scopus)
Protein Isoforms
Exons
Neoplasms
RNA
Glioblastoma
6 Citations (Scopus)

Gene expression profiling of the human natural killer cell response to Fc receptor activation: Unique enhancement in the presence of interleukin-12

Campbell, A. R., Regan, K., Bhave, N., Pattanayak, A., Parihar, R., Stiff, A. R., Trikha, P., Scoville, S. D., Liyanarachchi, S., Kondadasula, S. V., Lele, O., Davuluri, R. V., Payne, P. R. O. & Carson, W. E., Oct 15 2015, In : BMC Medical Genomics. 8, 1, 66.

Research output: Contribution to journalArticle

Fc Receptors
Gene Expression Profiling
Interleukin-12
Natural Killer Cells
Gene Regulatory Networks
55 Citations (Scopus)

Genetic predisposition to papillary thyroid carcinoma: Involvement of FOXE1, TSHR, and a novel lincRNA Gene, PTCSC2

He, H., Li, W., Liyanarachchi, S., Jendrzejewski, J., Srinivas, M., Davuluri, R. V., Nagy, R. & De La Chapelle, A., Jan 1 2015, In : Journal of Clinical Endocrinology and Metabolism. 100, 1, p. E164-E172

Research output: Contribution to journalArticle

Long Noncoding RNA
Genetic Predisposition to Disease
Gene expression
Lymphocytes
Genes

Genetic predisposition to papillary thyroid carcinoma: involvement of FOXE1, TSHR, and a novel lincRNA gene, PTCSC2

He, H., Li, W., Liyanarachchi, S., Jendrzejewski, J., Srinivas, M., Davuluri, R. V., Nagy, R. & de la Chapelle, A., Jan 1 2015, In : The Journal of clinical endocrinology and metabolism. 100, 1, p. E164-E172

Research output: Contribution to journalArticle

Long Noncoding RNA
Genetic Predisposition to Disease
Gene expression
Genes
Lymphocytes
8 Citations (Scopus)

Identification of reprogrammed myeloid cell transcriptomes in NSCLC

Durrans, A., Gao, D., Gupta, R., Fischer, K. R., Choi, H., El Rayes, T., Ryu, S., Nasar, A., Spinelli, C. F., Andrews, W., Elemento, O., Nolan, D., Stiles, B., Rafii, S., Narula, N., Davuluri, R., Altorki, N. K. & Mittal, V., Jun 5 2015, In : PloS one. 10, 6, e0129123.

Research output: Contribution to journalArticle

Myeloid Cells
lung neoplasms
Transcriptome
transcriptome
Non-Small Cell Lung Carcinoma
9 Citations (Scopus)

Shift in monocyte apoptosis with increasing viral load and change in apoptosis-related ISG/Bcl2 family gene expression in chronically HIV-1-infected subjects

Patro, S. C., Pal, S., Bi, Y., Lynn, K., Mounzer, K. C., Kostman, J. R., Davuluri, R. V. & Montaner, L. J., Jan 1 2015, In : Journal of Virology. 89, 1, p. 799-810 12 p.

Research output: Contribution to journalArticle

interferons
viral load
Human immunodeficiency virus 1
Viral Load
monocytes
9 Citations (Scopus)

Sprouty2 drives drug resistance and proliferation in Glioblastoma

Walsh, A. M., Kapoor, G. S., Buonato, J. M., Mathew, L. K., Bi, Y., Davuluri, R. V., Martinez-Lage, M., Simon, M. C., O'Rourke, D. M. & Lazzara, M. J., Aug 1 2015, In : Molecular Cancer Research. 13, 8, p. 1227-1237 11 p.

Research output: Contribution to journalArticle

Glioblastoma
Drug Resistance
Neoplasms
Epidermal Growth Factor Receptor
Glioma
2014
33 Citations (Scopus)

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation

Plasschaert, R. N., Vigneau, S., Tempera, I., Gupta, R., Maksimoska, J., Everett, L., Davuluri, R., Mamorstein, R., Lieberman, P. M., Schultz, D., Hannenhalli, S. & Bartolomei, M. S., Jan 1 2014, In : Nucleic acids research. 42, 2, p. 774-789 16 p.

Research output: Contribution to journalArticle

Embryonic Stem Cells
Cell Differentiation
Binding Sites
Genome
Gene Expression
31 Citations (Scopus)

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes

Pal, S., Bi, Y., MacYszyn, L., Showe, L. C., O'Rourke, D. M. & Davuluri, R. V., Apr 2014, In : Nucleic acids research. 42, 8, p. e64

Research output: Contribution to journalArticle

Glioblastoma
Protein Isoforms
Gene Expression
Genes
Reverse Transcriptase Polymerase Chain Reaction
67 Citations (Scopus)

MiR-218 opposes a critical RTK-HIF pathway in mesenchymal glioblastoma

Mathew, L. K., Skuli, N., Mucaj, V., Lee, S. S., Zinn, P. O., Sathyan, P., Imtiyaz, H. Z., Zhang, Z., Davuluri, R. V., Rao, S., Venneti, S., Lal, P., Lathia, J. D., Rich, J. N., Keith, B., Minn, A. J. & Simon, M. C., Jan 16 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 1, p. 291-296 6 p.

Research output: Contribution to journalArticle

Receptor Protein-Tyrosine Kinases
Glioblastoma
MicroRNAs
Neoplasms
Cell Survival
22 Citations (Scopus)

Protein kinase a activation enhances β-catenin transcriptional activity through nuclear localization to PML bodies

Zhang, M., Mahoney, E., Zuo, T., Manchanda, P. K., Davuluri, R. V. & Kirschner, L. S., Oct 9 2014, In : PLoS One. 9, 10, 0109523.

Research output: Contribution to journalArticle

Catenins
cAMP-dependent protein kinase
Cyclic AMP-Dependent Protein Kinases
protein kinases
Protein Kinases
26 Citations (Scopus)

Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline

Stong, N., Deng, Z., Gupta, R., Hu, S., Paul, S., Weiner, A. K., Eichler, E. E., Graves, T., Fronick, C. C., Courtney, L., Wilson, R. K., Lieberman, P. M., Davuluri, R. V. & Riethman, H., Jun 2014, In : Genome research. 24, 6, p. 1039-1050 12 p.

Research output: Contribution to journalArticle

Binding Sites
Terminal Repeat Sequences
Telomere
Computational Biology
Cell Line
2013
152 Citations (Scopus)

ADAR1 forms a complex with dicer to promote MicroRNA processing and RNA-induced gene silencing

Ota, H., Sakurai, M., Gupta, R., Valente, L., Wulff, B. E., Ariyoshi, K., Iizasa, H., Davuluri, R. V. & Nishikura, K., Apr 25 2013, In : Cell. 153, 3, p. 575-589 15 p.

Research output: Contribution to journalArticle

Gene Silencing
RNA Editing
MicroRNAs
RNA Interference
Genes
326 Citations (Scopus)

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

Ling, H., Spizzo, R., Atlasi, Y., Nicoloso, M., Shimizu, M., Redis, R. S., Nishida, N., Gafà, R., Song, J., Guo, Z., Ivan, C., Barbarotto, E., De Vries, I., Zhang, X., Ferracin, M., Churchman, M., Van Galen, J. F., Beverloo, B. H., Shariati, M., Haderk, F. & 33 others, Estecio, M. R., Garcia-Manero, G., Patijn, G. A., Gotley, D. C., Bhardwaj, V., Shureiqi, I., Sen, S., Multani, A. S., Welsh, J., Yamamoto, K., Taniguchi, I., Song, M. A., Gallinger, S., Casey, G., Thibodeau, S. N., Le Marchand, L., Tiirikainen, M., Mani, S. A., Zhang, W., Davuluri, R. V., Mimori, K., Mori, M., Sieuwerts, A. M., Martens, J. W. M., Tomlinson, I., Negrini, M., Berindan-Neagoe, I., Foekens, J. A., Hamilton, S. R., Lanza, G., Kopetz, S., Fodde, R. & Calin, G. A., Sep 1 2013, In : Genome research. 23, 9, p. 1446-1461 16 p.

Research output: Contribution to journalArticle

Untranslated RNA
Chromosomal Instability
Colonic Neoplasms
Single Nucleotide Polymorphism
Long Noncoding RNA
28 Citations (Scopus)

Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia

Glass, C., Wuertzer, C., Cui, X., Bi, Y., Davuluri, R., Xiao, Y. Y., Wilson, M., Owens, K., Zhang, Y. & Perkins, A., Jun 27 2013, In : PloS one. 8, 6, e67134.

Research output: Contribution to journalArticle

Virus Integration
myeloid leukemia
Viruses
Acute Myeloid Leukemia
Genes
57 Citations (Scopus)

HINCUTs in cancer: Hypoxia-induced noncoding ultraconserved transcripts

Ferdin, J., Nishida, N., Wu, X., Nicoloso, M. S., Shah, M. Y., Devlin, C., Ling, H., Shimizu, M., Kumar, K., Cortez, M. A., Ferracin, M., Bi, Y., Yang, D., Czerniak, B., Zhang, W., Schmittgen, T. D., Voorhoeve, M. P., Reginato, M. J., Negrini, M., Davuluri, R. V. & 3 others, Kunej, T., Ivan, M. & Calin, G. A., Dec 1 2013, In : Cell Death and Differentiation. 20, 12, p. 1675-1687 13 p.

Research output: Contribution to journalArticle

Neoplasms
Inteins
Oxygen
Untranslated RNA
Proteins
32 Citations (Scopus)

Isoform level expression profiles provide better cancer signatures than gene level expression profiles

Zhang, Z., Pal, S., Bi, Y., Tchou, J. & Davuluri, R. V., Apr 17 2013, In : Genome Medicine. 5, 4, 33.

Research output: Contribution to journalArticle

Neoplasm Genes
Transcriptome
Protein Isoforms
Genes
Cell Line
17 Citations (Scopus)
Differential Expression
RNA
Genes
Exons
Gene
2012
76 Citations (Scopus)

A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection

Deng, Z., Wang, Z., Stong, N., Plasschaert, R., Moczan, A., Chen, H. S., Hu, S., Wikramasinghe, P., Davuluri, R. V., Bartolomei, M. S., Riethman, H. & Lieberman, P. M., Oct 31 2012, In : EMBO Journal. 31, 21, p. 4165-4178 14 p.

Research output: Contribution to journalArticle

Telomere
Transcription
Chromatin
RNA Polymerase II
DNA

Estimation of gene expression at isoform level from mRNA-seq data by Bayesian hierarchical modeling

Bhattacharjee, M., Gupta, R. & Davuluri, R. V., Dec 1 2012, In : Frontiers in Genetics. 3, NOV, Article 239.

Research output: Contribution to journalArticle

RNA Isoforms
Protein Isoforms
Gene Expression
Messenger RNA
Genes
42 Citations (Scopus)

Identification of host-chromosome binding sites and candidate gene targets for Kaposi's sarcoma-associated herpesvirus LANA

Lu, F., Tsai, K., Chen, H. S., Wikramasinghe, P., Davuluri, R. V., Showe, L., Domsic, J., Marmorstein, R. & Lieberman, P. M., May 1 2012, In : Journal of virology. 86, 10, p. 5752-5762 11 p.

Research output: Contribution to journalArticle

Human herpesvirus 8
Human Herpesvirus 8
binding sites
Chromosomes
Binding Sites
35 Citations (Scopus)

RP58/ZNF238 directly modulates proneurogenic gene levels and is required for neuronal differentiation and brain expansion

Xiang, C., Baubet, V., Pal, S., Holderbaum, L., Tatard, V., Jiang, P., Davuluri, R. V. & Dahmane, N., Apr 1 2012, In : Cell Death and Differentiation. 19, 4, p. 692-702 11 p.

Research output: Contribution to journalArticle

Agenesis of Corpus Callosum
Microcephaly
Neocortex
Brain
Growth
19 Citations (Scopus)

Sequencing and analysis of a South Asian-Indian personal genome

Gupta, R., Ratan, A., Rajesh, C., Chen, R., Kim, H. L., Burhans, R., Miller, W., Santhosh, S., Davuluri, R. V., Butte, A. J., Schuster, S. C., Seshagiri, S. & Thomas, G., Aug 31 2012, In : BMC Genomics. 13, 1, 440.

Research output: Contribution to journalArticle

Genome
Single Nucleotide Polymorphism
Warfarin
India
Mitochondrial Genome
161 Citations (Scopus)

The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type

Jendrzejewski, J., He, H., Radomska, H. S., Li, W., Tomsic, J., Liyanarachchi, S., Davuluri, R. V., Nagy, R. & De La Chapelle, A., May 29 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 22, p. 8646-8651 6 p.

Research output: Contribution to journalArticle

Untranslated RNA
Tumor Suppressor Genes
Thyroid Gland
Alleles
Genotype
2011
109 Citations (Scopus)

Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development

Pal, S., Gupta, R., Kim, H., Wickramasinghe, P., Baubet, V., Showe, L. C., Dahmane, N. & Davuluri, R. V., Aug 1 2011, In : Genome Research. 21, 8, p. 1260-1272 13 p.

Research output: Contribution to journalArticle

Alternative Splicing
Transcriptome
Genes
Cerebellum
Protein Isoforms
216 Citations (Scopus)

Association of a microRNA/TP53 feedback circuitry with pathogenesis and outcome of b-cell chronic lymphocytic leukemia

Fabbri, M., Bottoni, A., Shimizu, M., Spizzo, R., Nicoloso, M. S., Rossi, S., Barbarotto, E., Cimmino, A., Adair, B., Wojcik, S. E., Valeri, N., Calore, F., Sampath, D., Fanini, F., Vannini, I., Musuraca, G., Dell'Aquila, M., Alder, H., Davuluri, R. V., Rassenti, L. Z. & 9 others, Negrini, M., Nakamura, T., Amadori, D., Kay, N. E., Rai, K. R., Keating, M. J., Kipps, T. J., Calin, G. A. & Croce, C. M., Jan 5 2011, In : JAMA - Journal of the American Medical Association. 305, 1, p. 59-67 9 p.

Research output: Contribution to journalArticle

B-Cell Chronic Lymphocytic Leukemia
MicroRNAs
Chromosome Aberrations
Confidence Intervals
Light
37 Citations (Scopus)

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

Sun, H., Wu, J., Wickramasinghe, P., Pal, S., Gupta, R., Bhattacharyya, A., Agosto-Perez, F. J., Showe, L. C., Huang, T. H. M. & Davuluri, R. V., Jan 17 2011, In : Nucleic acids research. 39, 1, p. 190-201 12 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Chromosome Mapping
Genes
Genome
Nucleic Acid Regulatory Sequences
19 Citations (Scopus)

IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

Kim, H., Bi, Y., Pal, S., Gupta, R. & Davuluri, R. V., Jul 27 2011, In : BMC bioinformatics. 12, 305.

Research output: Contribution to journalArticle

Least-Squares Analysis
Gene expression
Messenger RNA
Gene Expression
Least Squares
32 Citations (Scopus)

MPromDb update 2010: An integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data

Gupta, R., Bhattacharyya, A., Agosto-Perez, F. J., Wickramasinghe, P. & Davuluri, R. V., Jan 1 2011, In : Nucleic Acids Research. 39, SUPPL. 1

Research output: Contribution to journalArticle

Databases
Genes
Messenger RNA
Organ Specificity
Expressed Sequence Tags
14 Citations (Scopus)

Tree-based position weight matrix approach to model transcription factor binding site profiles

Bi, Y., Kim, H., Gupta, R. & Davuluri, R. V., Sep 2 2011, In : PLoS One. 6, 9, e24210.

Research output: Contribution to journalArticle

Position-Specific Scoring Matrices
binding sites
Transcription Factors
transcription factors
Pulse width modulation
2010
21 Citations (Scopus)

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data

Gupta, R., Wikramasinghe, P., Bhattacharyya, A., Perez, F. A., Pal, S. & Davuluri, R. V., Jan 18 2010, In : BMC bioinformatics. 11, SUPPLL.1, S65.

Research output: Contribution to journalArticle

Molecular Sequence Annotation
Data Mining
Promoter
Sequencing
Data mining
50 Citations (Scopus)

Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)

Lu, F., Wikramasinghe, P., Norseen, J., Tsai, K., Wang, P., Showe, L., Davuluri, R. V. & Lieberman, P. M., Oct 11 2010, In : Virology Journal. 7, 262.

Research output: Contribution to journalArticle

Epstein-Barr Virus Nuclear Antigens
Chromosomes
Binding Sites
Genome
Chromatin Immunoprecipitation