The microbiome and metatranscriptome of a panel from the Sarracenia mapping population reveal complex assembly and function involving host influence

Jiazhang Cai, Iqra Mohsin, Willie Rogers, Mengrui Zhang, Lin Jiang, Russell Malmberg, Magdy Alabady

Front. Plant Sci., vol. 15, 2024

The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic

Jialin Yang, Michael Skaro, Jiani Chen, Duna Zhan, Leke Lyu, Skylar Gay, Ahmed Kandeil, Mohamed A Ali, Ghazi Kayali, Kateryna Stoianova, Pensheng Ji, Magdy Alabady, Justin Bahl, Liang Liu, Jonathan Arnold

Scientific Reports, vol. 13(1), 2023, p. 5571

Genome report: Whole genome sequence and annotation of Penstemon davidsonii

Kate L. Ostevik, Magdy Alabady, Mengrui Zhang, Mark D. Rausher

BioRxiv, 2023, September 3

Whole-genome sequence and annotation of Penstemon davidsonii

Kate L Ostevik, Magdy S. Alabady, Mengrui Zhang, M. Rausher

bioRxiv, 2023

Genome and evolution of Prosopis alba Griseb., a drought and salinity tolerant tree legume crop for arid climates

Wenqian Kong, Min Liu, P. Felker, M. Ewens, C. Bessega, C. Pometti, Jinpeng Wang, Peng Xu, J. Teng, Jinyu Wang, Xiyin Wang, Yuannian Jiao, Magdy S. Alabady, F. Thibaud-Nissen, P. Masterson, Xin Qiao, A. Paterson

Plants, People, Planet, 2023

Diet composition and diversity does not explain fewer, smaller urban nestlings

E. Grabarczyk, S. Gill, M. Vonhof, Magdy S. Alabady, Zeng-Hui Wang, Jason M. Schmidt

PloS one, 2022

Analysis of genes associated with proinflammatory and profibrotic pathways upregulated in ischemia-induced chronic kidney disease in cats.

B. N. Lourenço, C. Schmiedt, Magdy S. Alabady, J. Stanton, A. Coleman, C. Brown, D. Rissi, Scott A. Brown, J. Tarigo

American journal of veterinary research, 2021

Early transcriptome changes induced by the Geminivirus C4 oncoprotein: setting the stage for oncogenesis

C. M. Deom, Magdy S. Alabady, Li Yang

BMC Genomics, 2021

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques

Charlotte Wang, Linda Wu, Zeng-Hui Wang, Magdy S. Alabady, Daniel Parson, Zainab Molumo, Sarah C. Fankhauser

PLoS ONE, 2020

Gapless assembly of maize chromosomes using long-read technologies

Jianing Liu, Arun S. Seetharam, K. Chougule, Shujun Ou, Kyle W. Swentowsky, J. Gent, V. Llaca, M. Woodhouse, N. Manchanda, G. Presting, D. Kudrna, Magdy S. Alabady, C. Hirsch, K. Fengler, D. Ware, T. Michael, M. Hufford, R. Dawe

Genome Biology, 2020

Adapterama I : Universal stubs and primers for 384 1 unique dual-indexed or 147 , 456 combinatorially-2 indexed Illumina libraries ( iTru & iNext ) 3 4

T. Glenn, R. Nilsen, Troy J. Kieran, J. Sanders, -. NataliaJ.Bayona, Vásquez, J. W. Finger, Todd W. Pierson, K. Bentley, Sandra L. Hoffberg, Swarnali Louha, Francisco J. García-De León, M. A. Río-Portilla, K. Reed, Jennifer L. Anderson, J. Meece, S. Aggrey, R. Rekaya, Magdy S. Alabady, Myriam Bélanger, K. Winker, B. Faircloth

2019

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

T. Glenn, R. Nilsen, Troy J. Kieran, J. Sanders, N. Bayona‐Vásquez, J. W. Finger, Todd W. Pierson, K. Bentley, Sandra L. Hoffberg, S. Louha, F. J. García-De León, M. A. del Rio Portilla, K. Reed, Jennifer L. Anderson, J. Meece, S. Aggrey, R. Rekaya, Magdy S. Alabady, Myriam Bélanger, K. Winker, B. Faircloth

PeerJ, 2019

A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize

R. Dawe, E. G. Lowry, J. Gent, Michelle C. Stitzer, Kyle W. Swentowsky, David M. Higgins, J. Ross-Ibarra, J. Wallace, L. Kanizay, Magdy S. Alabady, Weihong Qiu, Kuo-fu Tseng, Na Wang, Zhi Gao, J. Birchler, A. Harkess, Amy L. Hodges, E. N. Hiatt

Cell, 2018

A carnivorous plant genetic map: pitcher/insect-capture QTL on a genetic linkage map of Sarracenia

R. Malmberg, W. L. Rogers, Magdy S. Alabady

Life Science Alliance, 2018

Abundance and Multilocus Sequence Analysis of Vibrio Bacteria Associated with Diseased Elkhorn Coral (Acropora palmata) of the Florida Keys

Keri M Kemp, Jason R. Westrich, Magdy S. Alabady, Martin L. Edwards, E. Lipp

Applied and Environmental Microbiology, 2017

Widespread natural variation of DNA methylation within angiosperms

Chad E. Niederhuth, Adam J. Bewick, L. Ji, Magdy S. Alabady, K. Kim, Qing Li, Nicholas A. Rohr, Aditi Rambani, J. Burke, J. Udall, C. Egesi, J. Schmutz, J. Grimwood, S. Jackson, N. Springer, R. Schmitz

bioRxiv, 2016

Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei

D. Reynolds, Brigitte T. Hofmeister, L. Cliffe, Magdy S. Alabady, T. Siegel, R. Schmitz, R. Sabatini

PLoS Genetics, 2016

Developmental Transcriptional Model Describing Regulated Genes, Qtls And Pathways During The Primary And Secondary Cell Walls Of Pima Fibers

Magdy S. Alabady, B. Arpat

bioRxiv, 2016

Adapterama I: Universal Stubs and Primers for Thousands of Dual-Indexed Illumina Libraries (iTru & iNext)

T. Glenn, R. Nilsen, Troy J. Kieran, J. W. Finger, Todd W. Pierson, K. Bentley, Sandra L. Hoffberg, S. Louha, F. J. García-De León, Miguel Angel del Rio Portilla, K. Reed, Jennifer L. Anderson, J. Meece, Samuel E. Aggery, R. Rekaya, Magdy S. Alabady, Myriam Bélanger, K. Winker, B. Faircloth

bioRxiv, 2016

Universal stubs and primers for thousands of dual-indexed Illumina libraries 1 ( iTru & iNext ) 2 3

T. Glenn, R. Nilsen, Troy J. Kieran, J. W. Finger, Todd W. Pierson, K. Bentley, Sandra L. Hoffberg, S. Louha, F. J. G. León, A. Portilla, K. Reed, Jennifer L. Anderson, J. Meece, E. Samuel, Aggrey, R. Rekaya, Magdy S. Alabady, Myriam Bélanger, K. Winker, B. Faircloth

2016

Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula × alba 717-1B4

Liang-Jiao Xue, Magdy S. Alabady, Mohammad Mohebbi, Chung-Jui Tsai

Tree Genetics & Genomes, 2015

Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq)

Magdy S. Alabady, W. L. Rogers, R. Malmberg

PLoS ONE, 2015

A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

A. Barling, K. Swaminathan, T. Mitros, Brandon T James, J. Morris, Ornella Ngamboma, M. Hall, J. Kirkpatrick, Magdy S. Alabady, Ashley K. Spence, M. Hudson, D. Rokhsar, S. Moose

BMC Genomics, 2013

A detailed gene expression study of the Miscanthusgenus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

Adam R. Barling, Kankshita Swaminathan, T. Mitros, Brandon T James, Juliette Morris, Ornella Ngamboma, M. Hall, J. Kirkpatrick, Magdy S. Alabady, Ashley K. Spence, M. Hudson, D. Rokhsar, S. Moose

BMC Genomics, 2013

Effects of the probiotic Lactobacillus animalis in murine Mycobacterium avium subspecies paratuberculosis infection

E. Karunasena, Paresh C Kurkure, Russell Lackey, K. McMahon, Estevan P Kiernan, S. Graham, Magdy S. Alabady, David L. Campos, O. L. Tatum, M. Brashears

BMC Microbiology, 2013

Serum albumin alters the expression of iron-controlled genes in Pseudomonas aeruginosa.

C. Kruczek, M. Wachtel, Magdy S. Alabady, P. Payton, J. Colmer-Hamood, A. Hamood

Microbiology, 2012

Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses

K. Swaminathan, Magdy S. Alabady, Kranthi Varala, E. De Paoli, Isaac Y. Ho, D. Rokhsar, A. Arumuganathan, R. Ming, P. Green, B. Meyers, S. Moose, M. Hudson

Genome Biology, 2010

Double feature selection and cluster analyses in mining of microarray data from cotton

Magdy S. Alabady, Eunseog Youn, T. Wilkins

BMC Genomics, 2008

Gene-rich islands for fiber development in the cotton genome.

Zhanyou Xu, R. Kohel, G. Song, Jaemin Cho, Magdy S. Alabady, Jing Yu, Pamela K. Koo, J. Chu, Shuxun Yu, T. Wilkins, Yuxian Zhu, John Z. Yu

Genomics, 2008

Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population

Younghoon Park, Magdy S. Alabady, M. Ulloa, Brad Sickler, T. Wilkins, John Z. Yu, D. Stelly, R. Kohel, O. El-Shihy, R. Cantrell

Zeitschrift für Induktive Abstammungs- und Vererbungslehre, 2005