Statistical and Computational Analysis of Biological Data Benchmarking, Data Simulation Transcriptomics, Gene Expression Analysis Translational Medicine, Pharmacogenomics, NSAIDs, Chronobiology Genomic Database Development

Publications

• my bibliography at pubmed
• my publons publication summary

---

  2024  

---

• Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms. Jessica E Schwarz, Antonijo Mrčela, Nicholas F Lahens,Yongjun Li, Cynthia Hsu, Gregory R. Grant, Carsten Skarke, Shirley L Zhang, Amita Sehgal. Elife (2024) Nov 1:12:RP88322. doi: 10.7554/eLife.88322.

• BEERS2: RNA-Seq simulation through high fidelity in silico modeling Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, Dimitra Sarantopoulou, Soumyashant Nayak, Amruta Naik, Shaon Sengupta, Peter S Choi, Gregory R. Grant. Briefings Bioinform (2024) Mar 27;25(3):bbae164. doi: 10.1093/bib/bbae164.

• Circadian regulation of lung repair and regeneration Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Greory R. Grant, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. JCI Insight (2024) Mar 8;9(5):e179745. doi: 10.1172/jci.insight.179745

• Differential Impact of In Vivo of Pf4-deltaCre-Mediated and GP1ba-delta-Cre-Mediated Depletion of Cyclooxygenase-1 in Platelets in Mice Soon Yew Tang, Ronan Lordan, Hu Meng, Benjamin J Auerbach, Elizabeth J Hennessy, Arjun Sengupta, Ujjalkumar S Das, Robin Joshi, Oscar A Marcos-Contreras, Ryan McConnell, Gregory R Grant, Emanuela Ricciotti, Vladimir R Muzykantov, Tilo Grosser, Aalim M Weiljie, Garret A FitzGerald. Arterioscler Thromb Vasc Biol. 2024 Jun;44(6):1393-1406.

• Challenges and best practices in omics benchmarking Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, Gregory R. Grant. Nature Reviews Genetics (2024) May;25(5):326-339. doi: 10.1038/s41576-023-00679-6.

  ---

    2023  

  ---

• Deep Phenotyping of the Lipidomic Response in COVID-19 and non-COVID-19 Sepsis Hu Meng, Arjun Sengupta, Emanuela Ricciotti, Antonijo Mrčela, Divij Matthew, Liudmila Mazaleuskaya, Soumita Ghosh, Tom Brooks, Ariel R. Weisman, Alessa Soares Schanoski, Nick Lahens, Gregory R. Grant, Katalin Susztak, Stuart Sealfon, Krzysztof Laudanski, Aalim Weljiek, Nuala B. Meyer, Garret A. FitzGerald Clinical and Translational Medicine (2023) Nov;13(11)

• Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank Thomas G. Brooks, Nicholas F. Lahens, Gregory R. Grant, Yvette I. Sheline, Garret A. FitzGerald, Carsten Skarke Nature Communications (2023) Aug 24;14(1):5172.

• Modulation of the immune response to SARS-CoV-2 vaccination by NSAIDs Skarke C, Lordan R, Barekat K, Naik A, Mathew D, Ohtani T, Greenplate AR, Gregory R. Grant, Lahens NF, Gouma S, Troisi E, Sengupta A, Weljie AM, Meng W, Luning Prak ET, Lundgreen K, Bates P, Meng H, FitzGerald GA Pharmacol Exp Ther. (2023) Aug;386(2):198-204

• Circadian regulation of lung repair and regneration Amruta Naik, Kaitlyn Forrest, Oindrila Paul, Yasmine Issah, Utham Valekunja, Soon Y Tang, Akhilesh B Reddy, Elizabeth Hennessy, Thomas G. Brooks, Fatima Chaudhry, Apoorva Babu, Michael Morley, Jarod Zepp, Gregory R. Grant, Garret A. FitzGerald, Amita Sehgal, G. Scott Worthen, David B. Frank, Edward E Morrisey, Shaon Sengupta JCI Insight (2023) Aug 22;8(16).

• Sexual dimorphism in the response to chronic circadian misalignment Sean T. Anderson, Hu Meng, Thomas G. Brooks, Soon Yew Tang, Ronan Lordan, Arjun Sengupta, Soumyashant Nayak, Antonijo Mrcela, Dimitra Sarantopoulou, Aalim Weljie, Gregory R. Grant, Frederic D. Bushman, Garret A. FitzGerald Science Translational Medicine (2023) May 17;15(696).

• Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses Thomas G. Brooks, Aditi Manjrekar, Gregory R. Grant Journal of Biological Rhythms (2023) Dec;38(6):556-570.

• The genetic and evolutionary basis of gene expression variation in East Africans Derek E. Kelly, Shweta Ramdas, Rong Ma, Renata A. Rawlings-Goss, Gregory R. Grant, Alessia Ranciaro, Jibril B. Hirbo, William Beggs, Meredith Yeager, Stephen Chanock, Thomas B. Nyambo, Sabah A Omar, Dawit Wolde Meskel, Gurja Belay, Hongzhe Li, Christopher D. Brown, Sarah A. Tishkoff Genome Biology (2023) Feb 24;24(1).

• RNA splicing analysis using heterogeneous and large RNA-seq datasets Jorge Vaquero-Garcia, Joseph Aicher, Matthew Gazzara, San Jewell, Caleb Radens, Anupama Jha, Scott Norton, Nicholas Lahens, Gregory Grant, and Yoseph Barash. Nature Communications (2023) Mar 3;14(1).

  ---

    2022  

  ---

• Time-Specific Associations of Wearable Sensor-Based Cardiovascular and Behavioral Readouts with Disease Phenotypes in the Outpatient Setting of the Chronic Renal Insufficiency Cohort (CRIC) Nicholas F. Lahens, Mahboob Rahman, Jordana B. Cohen, Debbie L. Cohen, Jing Chen, Matthew R. Weir, Harold I. Feldman, Gregory R. Grant, Raymond R. Townsend, Carsten Skarke. Digit Health (2022) Jun 16;8:20552076221107903. doi: 10.1177/20552076221107903

• Nitecap: an exploratory circadian analysis web application Thomas G. Brooks, Antonijo Mrcela, Nicholas F. Lahens, Georgios K. Paschos, Tilo Grosser, Carsten C. Skarke, Garret FitzGerald, Gregory R. Grant J Biol Rhythms 2022 Feb;37(1):43-52. doi: 10.1177/0748730421105440

  ---

    2021  

  ---

• Considerations for the Safe Operation of Schools During the Coronavirus Pandemic Ronan Lordan, Samantha Prior, Elizabeth Hennessy, Amruta Naik, ..., Gregory R Grant ... Garret A. FitzGerald, Tilo Grosser Frontiers in Public Health (2021)

• CAMPAREE: A robust and configurable RNA expression simulator Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Anand Srinivasan, Jonathan Schug, John B. Hogenesch, Yoseph Barash, Gregory R. Grant. BMC Genomics (2021) Sep 25;22(1):692

• MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis. Barry Slaff, Caleb M. Radens, Paul Jewell, Anupama Jha, Nichlas F. Lahens, Gregory R. Grant, Andrei Thomas-Tikhonenko, Kristen W. Lynch & Yoseph Barash. Nature Communications (2021) Jun 7;12(1):3353

• Sex dependent compensatory mechanisms to preserve blood pressure homeostasis in PGI2 receptor deficient mice. Soon Tang, Meng Hu, Sean Anderson, Dimitra Sarantopoulou, Soumita Ghosh, Nicholas Lahens, Katherine Theken, Emanuela Ricciotti, Elizabeth Hennessy, Vincent Tu, Kyle Bittinger, Aalim Weljie, Gregory R. Grant, Garret FitzGerald. Journal of Clinical Investigation (JCI). (2021) Jun 8;136310

• Comparative evaluation of full-length isoform quantification from RNA-Seq. Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrcela, Nicholas F. Lahens, Gregory R. Grant. BMC Bioinformatics (2021) May 25;22(1):266

• Accounting for Time: Circadian Rhythms in the Time of COVID-19. Sengupta S, Brooks TG, Gregory R. Grant, FitzGerald GA J Biol Rhythms (2021) Feb;36(1):4-8

  ---

    2020 (COVID year)  

  ---

• RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake Guo X, Gao X, Keenan BT, Zhu J, Sarantopoulou D, Lian J, Galante RJ, Gregory R. Grant, Pack AI. BMC Genomics (2020) Sep 14;21(1):633

  ---

    2019  

  ---

• Age attenuates the transcriptional changes that occur with sleep in the medial prefrontal cortex Xiaofeng Guo, Brendan T. Keenan, Dimitra Sarantopoulou, Diane C. Lim, Gregory R. Grant, Allan I. Pack. Aging Cell (2019) Dec;18(6):e13021

• Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input Dimitra Sarantopoulou, Soon Yew Tang, Emanuela Ricciotti, Nicholas F. Lahens, Damien Lekkas, Jonathan Schug, Xiaofeng S. Guo, Georgios K. Paschos, Garret A. FitzGerald, Allan I. Pack, Gregory R. Grant. Scientific Reports (2019) Sep 17;9(1):13477.

• Circadian control of lung inflammation in influenza infection. Shaon Sengupta, Soon Tang, Jill Devine, Sean Anderson, Soumyashant Nayak, Shirley Zhang, Alex Valenzuela, Devin Fisher, Gregory R Grant, Carolina Lopez, and Garret FitzGerald. Nature Communications (2019) Sep 11;10(1):4107

• Variability in the Analgesic Response to Ibuprofen is Associated with Cyclooxygenase Activation in Inflammatory Pain. Katherine Theken, Elliot Hersh, Nicholas Lahens, Hyo-Min Lee, Xuanwen Li, Eric Granquist, Helen Giannakopoulos, Lawrence Levin, Stacey Secreto-Dankanich, Grant GR, John Detre, Garret FitzGerald, Tilo Grosser, and John Farrar. Clinical Pharmacology & Therapeutics (2019) Mar 31

• A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. Yan Sun, Eun Ji Kim, Sebastien Felt, Louis J. Taylor, Divyansh Agarwal, Grant GR, Carolina B. Lopez. PLOS Pathogens (2019) PLoS Pathog. Apr 17;15(4)

• Distinct vascular genomic response of proton and gamma radiation-A pilot investigation. Ricciotti E, Sarantopoulou D, Grant GR, Sanzari JK, Krigsfeld GS, Kiliti AJ, Kennedy AR, Grosser T. PLoS One (2019) Feb 11;14(2)

  ---

    2018  

  ---

• Spliceosome factors target timeless (tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila. Shakhmantsir I, Nayak S, Grant GR, Sehgal A. Elife (2018) Dec 5;7

• Lipocalin-Like Prostaglandin D Synthase but Not Hemopoietic Prostaglandin D Synthase Deletion Causes Hypertension and Accelerates Thrombogenesis in Mice. Song WL, Ricciotti E, Liang X, Grosser T, Grant GR, FitzGerald GA. J Pharmacol Exp Ther (2018) Dec;367(3):425-432

• SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus. Gupta P, Guluner O, Nayak S, Grant GR, Kalb R PlOS One (2018) July 11;13

• Transgenerational inheritance of chronic adolescent stress: Effects of stress response and the amygdala transcriptome. Manners MT, Yohn NL, Lahens NF, Grant GR, Bartolomei MS, Blendy JA Genes Brain Behav. (2018) Jun 13

• Overlap in signaling between Smoothened and the α subunit of the heterotrimeric G protein G13. Guo X, Riobo-Del Galdo NA, Kim EJ, Grant GR, Manning DR. PLoS One (2018) May 15:13(5)

• Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Scott Norton, Jorge Vaquero-Garcia, Nicholas F. Lahens, Grant GR, Yoseph Barash. Bioinformatics. 2018 May 1;34(9):1488-1497

• Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription. Eun Ji Kim, Grant GR, Anita S. Bowman, Naqi Haider, Harini V. Gudiseva, Venkata Ramana Murthy Chavali. Scientific Reports (2018) Feb 14;8(1):3040

  ---

    2017  

  ---

• A Pilot Characterization of the Human Chronobiome. Carsten Skarke, Nicholas Lahens, Seth Rhoades, Amy Campbell, Kyle Bittinger, Aubrey Bailey, Christian Hoffmann, Randal Olson, Lihong Chen, Guangrui Yang, Thomas Price, Jason Moore, Frederic Bushman, Casey Greene, Gregory R Grant, Aalim Weljie, and Garret FitzGerald. Scientific Reports. 2017 Dec 7;7(1):17141. doi: 10.1038/s41598-017-17362-6.

• Mitotic Transcription and Waves of Gene Reactivation During Mitotic Exit. Katherine C. Palozola, Greg Donahue, Gregory R. Grant, Justin S. Becker, Allison Cote, Hong Liu, Hongtao Yu, Arjun Raj, Kenneth S. Zaret. Science (2017) Oct 6;358(6359):119-122.

• Sleep restriction induced energy, methylation and lipogenesis metabolic switches in rat liver. Arjun Sengupta, Seth D Rhoades, Eun Ji Kim, Soumyashant Nayak, Gregory R Grant, Peter Meerlo, Aalim M Weljie. The International Journal of Biochemistry & Cell Biology Int J Biochem Cell Biol. (2017) Aug 30. PMID 28860003

• A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Eun Ji Kim, Giacomo Baruzzo, Katharina E. Hayer, Tapan Ganguly, Jonathan Schug, Gregory R. Grant. BMC Genomics. (2017) Aug 10;18(1):602

• Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R. Grant, Elizabeth A. Heller. PLoS Comput Biol. (2017) Jun 13;13(6)

• Characterizing the 'POAGome': a bioinformatics-driven approach to primary open-angle glaucoma. Ian D. Danford, Lana D. Verkuil, Daniel J. Choi, David W. Collins, Harini V. Gudiseva, Katherine E. Uyhazi, Marisa K. Lau, Levi N. Kanu, Gregory R. Grant, Venkata R.M. Chavali, Joan M. O'Brien Prog Retin Eye Res. (2017) Feb 18

• Transcriptional and Cell Cycle Alterations Mark Aging of Primary Human Adipose-Derived Stem Cells. Xiaoyin Shan, Cleresa Roberts, Eun Ji Kim, Arianna Brenner, Gregory Grant, Ivona Percec. Stem Cells (2017) Feb 17

• Simulation-based comprehensive benchmarking of RNA-seq aligners. Giacomo Baruzzo, Katharina E. Hayer, Eun Ji Kim, Barbara Di Camillo, Garret A. FitzGerald, Gregory Grant. Nature Methods (2017) Feb;14(2):135-139

  ---

    2016  

  ---

• A broad-spectrum lipidomics screen of anti-inflammatory drug combinations in human blood. Liudmila Mazaleuskaya, John Lawson, Xuanwen Li, Gregory Grant, Clementina Mesaros, Tilo Grosser, Ian Blair, Emanuela Ricciotti, Garret Fitzgerald. JCI Insight. (2016) Aug 4;1(12)

• Investigation of the functional role of human Interleukin-8 gene haplotypes by CRISPR/Cas9 mediated genome editing Manjunatha R. Benakanakere, Livia S. Finoti, Urara Tanaka, Gregory R. Grant, Raquel M. Scarel-Caminaga, Denis F. Kinane. Scientific Reports (2016) Aug 8;6:31180

• Cardiovascular Consequences of Prostanoid I Receptor Deletion in Microsomal Prostaglandin E Synthase-1 Deficient Hyperlipidemic Mice Soon Yew Tang, James Monslow, Gregory R. Grant, Leslie Todd, Sven-Christian Pawelzik, Lihong Chen, John Lawson, Ellen Pure, Garret A. FitzGerald Circulation. (2016) Jul 26;134(4)

• Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Guangrui Yang, Lihong Chen, Grant GR, Georgios Paschos, Wenliang Song, Erik S. Musiek, Vivian Lee, Sarah C. McLoughlin, Tilo Grosser, George Cotsarelis, and Garret A. FitzGerald. Science Translational Medicine (2016) Feb 3;8(324)

  ---

    2015  

  ---

• Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Bioinformatics (Oxford, England). (2015);

• Considerations for RNA-seq analysis of circadian rhythms. Li J, Grant GR, Hogenesch JB, Hughes ME. Methods in enzymology. (2015); 551:349-67.

  ---

    2014  

  ---

• Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. Toung JM, Lahens N, Hogenesch JB, Grant G. PLoS One. (2014) Nov 14;9(11)

• IVT-seq reveals extreme bias in RNA-sequencing. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. Genome Biol (2014) June 30; 15(6)

• Erythropoietin upregulation in pulmonary arterial hypertension. Karamanian VA, Harhay M, Grant GR, Palevsky HI, Grizzle WE, et al. Pulmonary circulation. (2014); 4(2):269-79.

• Myeloid cell microsomal prostaglandin E synthase-1 fosters atherogenesis in mice. Chen L, Yang G, Monslow J, Todd L, Cormode DP, Tang J, Grant GR, Delong JH, Tang SY, Lawson JA, Pure E, Fitzgerald GA. PNAS (2014) May 6;111(18):6828-33

• Myeloid COX-2 deletion reduces mammary tumor growth through enhanced cytotoxic T lymphocyte function Edward P. Chen, Nune Markosyan, Emma Connolly, John A. Lawson, Xuanwen Li, Gregory R. Grant, Tilo Grosser, Garret A. FitzGerald and Emer M. Smyth Carcinogenesis (2014) published online March 3rd.

  ---

    2013  

  ---

• Systematic evaluation of spliced aligners for RNA-Seq. Par G. Engstron, Tamara Stejger, Botond Sipos, Gregory R Grant, RGASP Consortium, Nick Goldman, Tim J. Hubbard, Jennifer Harrow, Roderic Guigo, Paul Bertone. Nature Methods (2013) 10, 1185-1191.

• Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. Michael H Farkas, Gregory R Grant, Joseph A White, Maria E Sousa, Mark B Consugar and Eric A Pierce. BMC Genomics (2013), 14:486

• Cell Selective Cardiovascular Biology of Microsomal Prostaglandin E Synthase-1. Lihong Chen, Guangrui Yang, Xiufeng Xu, Gregory Grant, John A. Lawson, Mohammad Bohlooly-Y, and Garret A. FitzGerald. Circulation (2013), 127: 233-243

• Drug Resistance and pseudoresistance; and unintended consequence of Enteric Coated Aspirin. Tilo Grosser, Susanne Fries, John Lawson, Shiv Kapoor, Gregory Grant, Garret A. FitzGerald. Circulation (2013), 127: 377-385

• EuPathDB: The Eukaryotic Pathogen Database. Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Shon Cade, Ryan Doherty, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Gregory Grant, Omar S. Harb, Mark Heiges, Sufen Hu, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, Deborah F. Pinney, Brian Pitts, David S. Roos, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Haiming Wang, Susanne Warrenfeltz. Nucleic Acids Research (2013), January; 41(D1): D684b

  ---

    2012  

  ---

• Obesity in mice with adipocyte-specific deletion of clock component Bmal1. Georgios K. Paschos, Salam Ibrahim, Wen-Liang Song, Takeshige Kunieda, Gregory Grant, Teresa M. Reyes, Christopher A. Bradfield, Cheryl H. Vaughan, Michael Eiden, Mojgan Masoodi, Julian L. Griffin, Fenfen Wang, John A. Lawson and Garret A. FitzGerald. Nature Medicine (2012) Nov 11

• Transcriptome Analyses to Investigate the Pathogenesis of RNA Splicing Factor Retinitis Pigmentosa. Michael H. Farkas, Greg R. Grant, Eric A. Pierce. Advances in Experimental Medicine and Biology (2012), Volume 723, pp 519-525

• Transcriptional Pausing Controls. A Rapid Antiviral Innate Immune Response In Drosophila. Jie Xu, Gregory Grant, Leah R. Sabin, Beth Gordesky-Gold, Ari Yasunaga, Mathew Tudor, Sara Cherry. Cell: Host & Microbe (2012) Oct 18;12(4):531-43.

• Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. Genome Research (2012) Jul;22(7):1266-81.

• Vascular COX-2 modulates blood pressure and thrombosis in mice. Yu Y, Ricciotti E, Scalia R, Tang SY, Grant G, Yu Z, Landesberg G, Crichton I, Wu W, Puri E, Funk CD, FitzGerald GA. Sci Transl Med (2012) May 2;4(132)

  ---

    2011  

  ---

• Discovery Approaches to UPR in Athero-Susceptible Endothelium in vivo Mete Civelek, Elisabetta Manduchi, Gregory R. Grant, Christian J. Stoeckert Jr., Peter F. Davies. Methods Enzymol. (2011); 489;109-26

• Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce. Bioinformatics (2011) 2011 Sep 15;27(18):2518-28.

• Side-Specific Expression of Activated Leukocyte Adhesion Molecule (ALCAM; CD166) in Pathosusceptible Regions of Swine Aortic Valve Endothelium Marie A. Guerraty, Gregory R. Grant, John W. Karanian, Oscar A. Chiesa, William F. Pritchard, Peter F. Davies. The Journal of Heart Valve Disease (2011);20:165-167

• Microsomal Prostaglandin E₂Synthase-1 Modulates the Response to Vascular Injury. Miao Wang, Kaori Ihida-Stansbury, Devashish Kothapalli, Mathieu C. Tamby, Zhou Yu, Lihong Chen, Gregory Grant, Yan Cheng, John A. Lawson, Richard K. Assoian, Peter L. Jones, PhD; Garret A. FitzGerald, MD Cicrulation (2011) (123:631-639)

  ---

    2010  

  ---

• Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor gamma Function in Adipocytes and Macrophages Martina I Lefterova 1, David J Steger, David Zhuo, Mohammed Qatanani, Shannon E Mullican, Geetu Tuteja, Elisabetta Manduchi, Gregory R Grant, Mitchell A Lazar. Mol Cell Biol . 2010 May;30(9):2078-89f

• Propagation of adipogenic signals through an epigenomic transition state.. David J. Steger, Gregory R. Grant, Michael Schupp, Takuya Tomaru, Martina I. Lefterova, Jonathan Schug, Elisabetta Manduchi, Christian J. Stoeckert Jr., and Mitchell A. Lazar Genes & Dev (2010) 24(10)

• Cell-Specific Determinants of PPARgamma Function in Adipocytes and Macrophages. Martina I. Lefterova, David J. Steger, David Zhuo, Mohammed Qatanani, Shannon E. Mullican, Geetu Tuteja, Elisabetta Manduchi, Gregory R. Grant, and Mitchell A. Lazar Molecular and Cellular Biology (2010) 30(9):2078-89

• Hypercholesterolemia induces side-specific phenotype changes and PPARgamma pathway activation in swine aortic valve endothelium. Marie A. Guerraty, Gregory R. Grant, John W. Karanian, Oscar A. Chiesa, William F. Pritchard, and Peter F. Davies. Arteriosclerosis, Thrombosis, and Vascular Biology (2010) Feb;30(2):225-31

  ---

    2009  

  ---

• Pre-lesional arterial endothelial phenotypes in hypercholesterolemia: Universal ABCA1 upregulation contrasts with region-specific gene expression in vivo. Civelek Mete, Gregory R Grant, Irolla CR, Shi C, Riley RJ, Chiesa OA, Stoeckert CJ Jr, Karanian JW, Pritchard WF, Peter F Davies. Am J Physiol Heart Circ Physiol. (2009) Nov 6

• TriTrypDB: A Functional Genomic Resource for the Trypanosomatidae. Mark Aslett, Critina Aurrecoechea, Mathew Berriman, et al. Nucleic Acids Research (2009) Jan;38 (Database issue) :D457-62.

• A Flexible Two Stage Procedure for Identifying Gene Sets that are Differentially Expressed. Ruth Heller, Elisabetta Manduchi, Gregory R. Grant, Warren J. Ewens. Bioinformatics (2009), 25(8): 1019-1025.

• Molecular Karyotype of Sporadic Unilateral Retinoblastoma Tumors. Arupa Ganguly, Kim Nichols, Gregory R. Grant, Eric Rappaport, Carol Shields. RETINA (2009) 29(7): 1002-1012.

• PlasmoDB: a functional genomic database for malaria parasites. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H. Nucleic Acids Res. (2009) Jan;37(Database issue):D539-43

• GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Sullivan S, Treatman C, Wang H. Nucleic Acids Res. (2009) Jan;37(Database issue):D526-30.

  ---

    2007  

  ---

• Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays. Mitchell Guttman, Carolyn Mies, Katarzyna Dudycz-Sulicz, Sharon J. Diskin, Don A. Baldwin, Christian J. Stoeckert Jr., Gregory R. Grant. PLoS Genetics Vol. 3, No. 8, e143 doi:10.1371 (2007).

• Human miR-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3'UTR -- a mechanism for functional SNPs related to phenotypes. Praveen Sethupathy, Christelle Borel, Maryline Gagnebin, Gregory R. Grant, Samuel Deutsch, Terry S. Elton, Artemis G. Hatzigeorgiou, Stylianos E. Antonarakis. The American Journal of Human Genetics Am J Hum Genet. (2007) August; 81(2): 405-413.

• Analysis and management of microarray gene expression data, Unit 19.6 in Current Protocols in Molecular Biology. Grant G.R., Manduchi E., Stoeckert C.J. Jr. (2007) John Wiley & Sons.

• Biochemical, molecular and behavioral phenotypes of Rab3A mutations in the mouse. Shuzhang Yang, Michael Farias, David Kapfhamer, John Tobias, Gregory Grant, Ted Abel, Maja Bucan. Genes Brain Behav 6: 77-96 (2007).

  ---

    2006  

  ---

• STAC: A method for testing the significance of DNA copy-number aberrations across multiple array-CGH experiments. Sharon J. Diskin, Thomas Eck, Joel Greshock, Yael P. Mosse, Tara Naylor, Christian J. Stoeckert, Jr., Barbara L. Weber, John M. Maris and Gregory R. Grant. Genome Research (2006). 16: 1149-1158.

• Integrative genomics identifies distinct molecular classes of neuroblastoma and demonstrates that multiple genes are targeted by regional alterations in DNA copy number. Qun Wang, Sharon Diskin, Eric Rappaport, Edward Attiyeh, Yael Mosse, Daniel Shue, Eric Seiser, Jayanti Jagannathan, Suzanne Shusterman, Manisha Bansal, Deepa Khazi, Cynthia Winter, Erin Okowa, Gregory Grant, Avital Cnbaan, Huaqing Zhao, Nai-Kong Cheung, William Gerald, Wendy London, Katherine K. Matthay, Garrett M. Brodeur and John M. Maris. Cancer Research (2006). Cancer Research 66, 6050-6062.

  ---

    2005  

  ---

• Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet Anthony G. Passerini , Congzhu Shi, Nadeene M. Francesco, Peiying Chuan, Elisabetta Manduchi, Gregory R. Grant, Christian J. Stoeckert Jr., John W. Karanian, Diane Wray-Cahen , William F. Pritchard and Peter F. Davies (2005). Biochemical and Biophysical Research Communications, Vol 21 no 11, 2684-2690.

• A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Grant, G.R, Junmin Liu, Stoeckert, C.J.Jr. (2005). Bioinformatics - 2005 21(11):2684-2690

• Spatial heterogeneity of endothelial phenotypes correlates with side-specific vulnerability to calcification in normal porcine aortic valves. (2005). Simmons C.A., Grant G.R., Manduchi E., Davies P.F., Circulation Research, 96(7):792-799

• Textbook: Statistical Methods in Bioinformatics: An Introduction EDITION 2.  W. Ewens, G. Grant, Textbook, Springer-Verlag (2005).

  ---

    2004  

  ---

• Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta.. Anthony G. Passerini, Denise C. Polacek, Congzhu Shi, Nadeene M. Francesco, Elisabetta Manduchi, Gregory R. Grant, William F. Pritchard, Steven Powell, Gary Y. Chang, Christian J. Stoeckert, Jr. and Peter F. Davies. (2004) PNAS vol. 101, no. 8 2482-2487

• RAD and the RAD Study-Annotator: an approach to collection, organization, and exchange of all relevant information for high-throughput gene expression studies. (2004) Manduchi M., Grant G.R., He H., Liu J., Mailman M.D., Pizarro A.D., Whetzel P.L., Stoeckert C.J. Jr. Bioinformatics, 20(4): 452-459

  ---

    2003  

  ---

• Maintaining data integrity in microarray data management. Grant G.R., Manduchi M., Pizzaro, A., Stoeckert C.J. Jr. (2003), Biotechnology and Bioengineering,

• Comment on 'Resampling-based multiple testing for DNA microarray data analysis' by Ge, Dudoit, and Speed (2003). Test, 12: 1-77.

• Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA. Polacek D.C., Passerini A.G., Shi C., Francesco N.M., Manduchi E., Grant G.R., Powell S., Bischof H., Winkler H., Stoeckert C.J. Jr., Davies P.F. (2003), Physiological Genomics 13: 147-156.

  ---

    2002  

  ---

• The Plasmodium genome database. Kissinger, J.C., Brunk, B.P., Crabtree, J., Fraunholz, M.J., Gajria, B., Milgram, A.J., Pearson, D.S., Schug, J., Bahl, A., Diskin, S.J., Ginsburg, H., Grant, G.R., Gupta, D., Labo, P., Li, L., Mailman, M.D., McWeeney, S.K., Whetzel, P., Stoeckert, C.J. Jr., Roos, D.S. Nature. (2002) Oct 3;419(6906):490-2.

• Comparison of different labeling methods for two-channel high-density microarray experiments. Manduchi, E., Scearce$*, Carolyn Mies2, Katarzyna Dudycz-Sulicz2, Sharon J. Diskin3, Don A. Baldwin4, Christian J. Stoeckert Jr.1,5, Gregory R. Grant1,5 , L.M., Brestelli, J.E., Kaestner, K.H., Stoeckert, C.J. Jr. Physiol Genomics. (2002) Sep 3;10(3):169-179.

• PlasmoDB: The Plasmodium Genome Resource. An integrated database providing tools for accessing and analyzing mapping, expression and sequence data (both finished and unfinished). Bahl, A., Brunk, B., Coppel, R.L., Crabtree, J., Diskin, S.J., Fraunholz, M.J., Grant, G.R., Gupta, D., Huestis, R.L., Kissinger, J.C., Labo, P., Li, L., McWeeney, S.K., Milgram, A.J., Roos, D.S., Schug, J., Stoeckert, C.J. Nucleic Acids Res. 30: 87-90 (2002)

• Using Non-Parametric Methods in the Context of Multiple Testing to Identify Differentially Expressed Genes. G. Grant, E. Manduchi and C. Stoeckert, Critical Assessment of Microarray Data Analysis (CAMDA00) Methods of microarray data analysis, editors S.M. Lin and K.F. Johnson, Kluwer Academic Publishers (Boston, 2002): 37-55. (Winner of the best presentation award.)

  ---

    2001  

  ---

• Textbook: Statistical Methods in Bioinformatics: An Introduction.  W. Ewens, G. Grant, Textbook, Springer-Verlag (2001).

  ---

    2000  

  ---

• Generation of Patterns from Gene Expression Data by Assigning Confidence to Differentially Expressed Genes. E. Manduchi, G. Grant, C. Stoeckert, S. McKenzie, S. Surry, C. Overton, C. Stoeckert, Bioinformatics (2000) 16, 685-698.

  ---

    1999  

  ---

• Significance Testing for Direct Identity-by-descent Mapping. G. Grant, E. Manduchi, V. Cheung, W. Ewens, Annals of Human Genetics (1999) 63, 441-454.

Arithmetic Geometry Number Theory

Publications

• Root Numbers and Algebraic Points on Elliptic Surfaces with Base an Elliptic Curve. G. Grant, E. Manduchi, Duke Mathematical Journal (1998) Vol. 93, No.3, 479-486
  
• Root Numbers and Algebraic Points on Elliptic Surfaces with Base P¹, G. Grant, E. Manduchi, Duke Mathematical Journal (1997) Vol. 89, No.3, 413-422.
  
• Thesis: Galois PSL₂(F_q) extensions, Root Numbers and Elliptic Curves. (1995).