Publications

Selected highlights

Nature 2018

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

Shahid S, Kim G, Johnson NR, Wafula EK, Wang F, Coruh C, Bernal-Galeano V, Phifer T, dePamphilis CW, Westwood JH and Axtell MJ

DOI

— First evidence that a parasitic plant deploys mobile small RNAs as virulence factors to silence host genes, establishing interspecies RNAi as a mechanism of plant–plant communication.

Nature Plants 2019

Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants

Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu WB, Kelly EA, Zhang H, Person TN

DOI

— Shows that horizontally acquired genes in Cuscuta are frequent sources of small RNAs, linking foreign DNA acquisition with the evolution of new regulatory functions.

The Plant Cell 2019

The RNA export factor ALY1 enables genome-wide RNA-directed DNA methylation

Choudury S, Shahid S, Cuerda-Gil D, Panda K, Cullen A, Ashraf QUA, Sigman MJ, McCue AD, Slotkin RK

DOI

— Connects nuclear RNA export to genome-wide RdDM, revealing an unexpected layer of control over transposon silencing and DNA methylation.

Annual Review of Genetics 2022

The epigenetic control of the transposable element lifecycle in plant genomes and beyond

Liu P, Cuerda-Gil D, Shahid S, Slotkin RK

DOI

— Reviews how epigenetic and small RNA pathways regulate transposons and shape genome stability, plasticity and evolution.

All publications

Full list of publications in Google Scholar (opens in new tab)

2026

Thumbnail for "Adaptation to plant defence in an agricultural insect pest: Integrating genome scans and gene expression in the soybean aphid reveals multi-genic pathways
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Adaptation to plant defence in an agricultural insect pest: Integrating genome scans and gene expression in the soybean aphid reveals multi-genic pathways

Pavinato VAC, Penton-Michel EH, Shahid S, Wenger JA, Slotkin RK, Michel A

Molecular Ecology

DOI

2025

miRScore: a rapid and precise microRNA validation tool

Vanek A, Griffiths-Jones S, Meyers B, Shahid S, Axtell MJ

PLoS Computational Biology

DOI

2025

Experimental warming alters free-living nitrogen fixation in a humid tropical forest

Bartz P, Grullón-Penkova I, Cavaleri M, Reed S, Shahid S, Wood T, Bachelot B

New Phytologist

DOI

2022

The epigenetic control of the transposable element lifecycle in plant genomes and beyond

Liu P, Cuerda-Gil D, Shahid S, Slotkin RK

Annual Review of Genetics

DOI

2020

The current revolution in transposable element biology enabled by long reads

Shahid S, Slotkin RK

Current Opinion in Plant Biology

DOI

2020

Thumbnail for "Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements
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Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements

Yates-Stewart AD, Daron J, Wijeratne S, Shahid S, Edgington HA, Slotkin RK, Michel A

Insect Biochemistry and Molecular Biology

DOI

2019

Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants

Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu WB, Kelly EA, Zhang H, Person TN

Nature Plants

DOI

2019

The RNA export factor ALY1 enables genome-wide RNA-directed DNA methylation

Choudury S, Shahid S, Cuerda-Gil D, Panda K, Cullen A, Ashraf QUA, Sigman MJ, McCue AD, Slotkin RK

The Plant Cell

DOI

2018

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

Shahid S, Kim G, Johnson NR, Wafula EK, Wang F, Coruh C, Bernal-Galeano V, Phifer T, dePamphilis CW, Westwood JH and Axtell MJ

Nature

DOI

Highlighted in

NCRI (opens in new tab) Molecular Plant (opens in new tab) Nature Reviews Genetics (opens in new tab)

2017

Comparative genomics of two jute species and insight into fiber biogenesis

Islam MS et al. (including Shahid S and Alam M)

Nature Plants

DOI

2016

Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele

Shahid S*, Begum R*, Razzaque S, Jesmin, Seraj ZI * Equal contribution

Journal of Cereal Science

DOI

2015

Thumbnail for "Comprehensive annotation of Physcomitrella patens small RNA loci reveals that the heterochromatic short interfering RNA pathway is largely conserved in land plants
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Comprehensive annotation of Physcomitrella patens small RNA loci reveals that the heterochromatic short interfering RNA pathway is largely conserved in land plants

Coruh C, Cho SH, Shahid S, Liu Q, Wierzbicki A, Axtell MJ

The Plant Cell

DOI

2015

A stable RNA G-quadruplex within the 5′-UTR of Arabidopsis thaliana ATR mRNA inhibits translation

Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC

Biochemical Journal

DOI

2014

Seeing the forest for the trees: annotating small RNA producing genes in plants

Coruh C, Shahid S, Axtell MJ

Current Opinion in Plant Biology

DOI

2013

Identification and annotation of small RNA genes using ShortStack

Shahid S, Axtell MJ

Methods

DOI

2013

The Amborella genome and the evolution of flowering plants

Amborella Genome Project

Science

DOI

2011

Prediction of plant promoters based on hexamers and random triplet pair analysis

Azad A, Shahid S, Noman N, Lee H

Algorithms for Molecular Biology

DOI

2011

Physiology and gene expression of the rice landrace Horkuch under salt stress

Lisa LA, Elias SM, Rahman MS, Shahid S, Iwasaki T, Hasan AM, Kosuge K, Fukami Y, Seraj ZI

Functional Plant Biology

DOI

2010

READS - a resource for plant non-coding regulatory sequence analysis

Shahid S, Elias SM, Biswas S, Seraj ZI

Plant Tissue Culture and Biotechnology

DOI