Brenner ED, Scheid PE, DeGrazia J, Geltzeiler AR, Katari MS. Using the Integrated Genome Viewer to reveal amplicon-derived polymorphism enriched at the phenylthiocarbamide locus in the teaching lab. Biochem Mol Biol Educ. 2021 Jan 11. doi: 10.1002/bmb.21479

Matthew D Brooks, Che-Lun Juang, Manpreet Singh Katari, José M Alvarez, Angelo Pasquino, Hung-Jui Shih, Ji Huang, Carly Shanks, Jacopo Cirrone, Gloria M Coruzzi, ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks, Plant Physiology,Nov 2020 , kiaa012, https://doi.org/10.1093/plphys/kiaa012

Garcia-Oliveira AL, Kimata B, Kasele S, Kapinga F, Masumba E, Mkamilo G, Sichalwe C, Bredeson JV, Lyons JB, Shah T, Muranaka S, Katari MS, Ferguson ME. Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava. PLoSOne. 2020;15(8):e0236674. doi:10.1371/journal.pone.0236674. eCollection 2020. PubMed PMID: 32756600; PubMed Central PMCID: PMC7406056.

Heerah S, Katari MS, Penjor R, Coruzzi GM, Marshall-Colon A.   WRKY1 mediates transcriptional regulation of light and nitrogen signaling pathways. Plant Physiol. 2019 Aug 13. pii: pp.00685.2019. doi: 10.1104/pp.19.00685.  PubMed PMID: 31409699.

Tripathi L, Tripathi JN, Shah T, Muiruri KS, Katari MMolecular Basis of Disease Resistance in Banana Progenitor Musa balbisiana against Xanthomonas campestris pv. musacearum. Sci Rep. 2019 May 7;9(1):7007. doi: 10.1038/s41598-019-43421-1. PubMed PMID: 31065041; PubMed Central PMCID: PMC6504851.

Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME.QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert. Theor Appl Genet. 2017 Oct;130(10):2069-2090. doi: 10.1007/s00122-017-2943-z. Epub 2017 Jul 13. PubMed PMID: 28707249; PubMed Central PMCID: PMC5606945

Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Sci Rep. 2017 Aug 29;7(1):9747. doi: 10.1038/s41598-017-09617-z. PubMed PMID: 28852026; PubMed Central PMCID: PMC5575035.

Nzuki I, Katari MS, Bredeson JV, Masumba E, Kapinga F, Salum K, Mkamilo GS, Shah T, Lyons JB, Rokhsar DS, Rounsley S, Myburg AA, Ferguson ME. QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glazioviiFront Plant Sci. 2017;8:1168. doi: 10.3389/fpls.2017.01168. eCollection 2017. PubMed PMID: 28785268; PubMed Central PMCID: PMC5519584.

Murphy M, Chatterjee SS, Jain S, Katari M, DasGupta R. TCF7L1 Modulates Colorectal Cancer Growth by Inhibiting Expression of the Tumor-Suppressor Gene EPHB3. Sci Rep. 2016 Jun 23;6:28299. doi: 10.1038/srep28299. PubMed PMID: 27333864; PubMed Central PMCID: PMC4917863.

Obertello M, Shrivastava S, Katari MS, Coruzzi GM. Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice. Plant Physiol. 2015 Aug;168(4):1830-43. doi: 10.1104/pp.114.255877. Epub 2015 Jun 4. PubMed PMID: 26045464; PubMed Central PMCID: PMC4528727

Li Y, Mukherjee I, Thum KE, Tanurdzic M, Katari MS, Obertello M, Edwards MB, McCombie WR, Martienssen RA, Coruzzi GM. The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.Genome Biol. 2015 Apr 19;16:79. doi: 10.1186/s13059-015-0640-2. PubMed PMID: 25928034; PubMed Central PMCID: PMC4464704.

Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutiérrez RA. Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics. 2013 Oct 11;14:701. doi: 10.1186/1471-2164-14-701. PubMed PMID: 24119003; PubMed Central PMCID: PMC3906980.

Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD. Plasticity regulators modulate specific root traits in discrete nitrogen environments. PLoS Genet. 2013;9(9):e1003760. doi: 10.1371/journal.pgen.1003760. Epub 2013 Sep 5. PubMed PMID: 24039603; PubMed Central PMCID: PMC3764102.

Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R. A functional phylogenomic view of the seed plants. PLoS Genet. 2011 Dec;7(12):e1002411. doi: 10.1371/journal.pgen.1002411. Epub 2011 Dec 15. PubMed PMID: 22194700; PubMed Central PMCID: PMC3240601.

An international bioinformatics infrastructure to underpin the Arabidopsis community. Plant Cell. 2010 Aug;22(8):2530-6. doi: 10.1105/tpc.110.078519. Epub 2010 Aug 31. PubMed PMID: 20807877; PubMed Central PMCID: PMC2947164.

Obertello M, Krouk G, Katari MS, Runko SJ, Coruzzi GM. Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. BMC Syst Biol. 2010 Aug 12;4:111. doi: 10.1186/1752-0509-4-111. PubMed PMID: 20704717; PubMed Central PMCID: PMC2933594.

Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol. 2010 Jul 12;2:225-39. doi: 10.1093/gbe/evq012. PubMed PMID: 20624728; PubMed Central PMCID: PMC2997538.

Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA. VirtualPlant: a software platform to support systems biology research. Plant Physiol. 2010 Feb;152(2):500-15. doi: 10.1104/pp.109.147025. Epub 2009 Dec 9. PubMed PMID: 20007449; PubMed Central PMCID: PMC2815851.

Nero D, Katari MS, Kelfer J, Tranchina D, Coruzzi GM. In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana. BMC Bioinformatics. 2009 Dec 21;10:435. doi: 10.1186/1471-2105-10-435. PubMed PMID: 20025756; PubMed Central PMCID: PMC2803859.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One. 2009 Jun 2;4(6):e5764. doi: 10.1371/journal.pone.0005764. PubMed PMID: 19503618; PubMed Central PMCID: PMC2685480.

Thum KE, Shin MJ, Gutiérrez RA, Mukherjee I, Katari MS, Nero D, Shasha D, Coruzzi GM.An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.BMC Syst Biol. 2008 Apr 4;2:31. doi: 10.1186/1752-0509-2-31. PubMed PMID: 18387196; PubMed Central PMCID: PMC2335094.

Gutiérrez RA, Stokes TL, Thum K, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero DC, McClung CR, Coruzzi GM. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1.Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4939-44. doi: 10.1073/pnas.0800211105. Epub 2008 Mar 14. PubMed PMID: 18344319; PubMed Central PMCID: PMC2290744.

Poultney CS, Gutiérrez RA, Katari MS, Gifford ML, Paley WB, Coruzzi GM, Shasha DE.Sungear: interactive visualization and functional analysis of genomic datasets.Bioinformatics. 2007 Jan 15;23(2):259-61. doi: 10.1093/bioinformatics/btl496. Epub 2006 Oct 2. PubMed PMID: 17018536.

de la Torre JE, Egan MG, Katari MS, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R.ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol. 2006 Jun 15;6:48. doi: 10.1186/1471-2148-6-48. PubMed PMID: 16776834; PubMed Central PMCID: PMC1564041.

Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes.BMC Genomics. 2005 Oct 15;6:143. doi: 10.1186/1471-2164-6-143. PubMed PMID: 16225698; PubMed Central PMCID: PMC1285361.

Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR. Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana.Genome Res. 2005 Apr;15(4):496-504. doi: 10.1101/gr.3239105. PubMed PMID: 15805491; PubMed Central PMCID: PMC1074364.

Cannon SB, McCombie WR, Sato S, Tabata S, Denny R, Palmer L, Katari M, Young ND, Stacey G. Evolution and microsynteny of the apyrase gene family in three legume genomes. Mol Genet Genomics. 2003 Dec;270(4):347-61. doi: 10.1007/s00438-003-0928-x. Epub 2003 Nov 4. PubMed PMID: 14598165.

Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM. Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol.2003;4(12):R78. doi: 10.1186/gb-2003-4-12-r78. Epub 2003 Nov 18. PubMed PMID: 14659015; PubMed Central PMCID: PMC329417.

Wines ME, Lee L, Katari MS, Zhang L, DeRossi C, Shi Y, Perkins S, Feldman M, McCombie WR, Holdener BC. Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis. Genomics.2001 Feb 15;72(1):88-98. doi: 10.1006/geno.2000.6466. PubMed PMID: 11247670.

Berenson CS, Gallery MA, Katari MS, Foster EW, Pattoli MA. Gangliosides of monocyte-derived macrophages of adults with advanced HIV infection show reduced surface accessibility. J Leukoc Biol. 1998 Sep;64(3):311-21. doi: 10.1002/jlb.64.3.311. PubMed PMID: 9738657.