*: Equal Contribution
#: Corresponding/Senior Author
Bold: Goyal lab members

Preprints/Forthcoming Manuscripts

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning
Niu Z., O'Farrell A., Li J., Reffsin S., Jain N., Dardani I., Goyal Y., and #Raj A.
bioRxiv (in revision)
data | code

Metastatic potential in clonal melanoma cells is driven by a rare, early-invading subpopulation
Kaur A., …, Goyal Y., Weeraratna A.T., Herlyn M., and #Raj A.
bioRxiv (in revision)

2024

Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms
*Zhang Z., *Melzer M.E., Arun K., Sun H., Eriksson C.J., Fabian I., Shaashua S., Kiani K., Oren Y., and #Goyal Y.
Cell Genomics
data | code | wesbite | package | meme
Media coverage: Northwestern University, Phys.org

Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells
Mellis I.A., Melzer M.E., Bodkin N., and #Goyal Y.
Genome Biology
data | code | meme

Navigating non-genetic plasticity in cancer drug resistance
Sun H., Kumari N., Melzer M., Backman V., and #Goyal Y.
Annual Review of Cancer Biology (accepted for the forcoming issue)

Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists
#Karim A., …, Goyal Y., …, and #Lucks J.
Nature Communications
pdf

TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo
Kim J., …, Grody E., Goyal Y., …, and #Martinelli E.
Nature Communications
pdf | data | code

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells
Jain N., Goyal Y., Dunagin M.C., Cote C.C., Mellis I.A., Emert B., Jiang C.L., Dardani I.P., Reffsin S., and #Raj A.
Cell Systems
pdf | data | code

2023

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells
#Goyal Y., Busch G.T., Pillai M., Li J., Boe R., Grody E.I., Chelvanambi M., Dardani I.P., Emert B., Bodkin N., Braun J., Fingerman D., Kaur A., Jain N., Ravindran P.T., Mellis I.A., Kiani K., Alicea G., Fane M.E., Ahmed S.S., Li H., Chen Y., Chai C., …, and #Raj A.
Nature
pdf | code | data | meme
Previewed by: Cancer Discovery, Nature Genetics
Media coverage: STAT News, Schmidt Science Fellows, Northwestern University, Breakthrough Podcast

Theory and computation of non-genetic heterogeneity in cancer
Pillai M., Hojel E., #Jolly M.K., and #Goyal Y.
Nature Computational Science
pdf | meme

Towards a systems-level probing of tumor clonality
*Grody E.I., *Abraham A., #Shukla V., and #Goyal Y.
iScience
pdf | meme

ClonoCluster: a method for using clonal origin to inform transcriptome clustering
Richman L.P., Goyal Y., Jiang C.L., and Raj A.
Cell Genomics
pdf | code | data

Dynamical hallmarks of cancer: phenotypic switching in melanoma and epithelial-mesenchymal plasticity
Jain P., Pillai M., Duddu A.S., Somarelli J.A., Goyal Y., Jolly M.K.
Seminars in Cancer Biology
pdf

Modeling Diabetic Endothelial Dysfunction with Patient-Specific Induced Pluripotent Stem Cells
Gorashi R., Bolanos N.R., Dang C., Chai C., Kovacs B., Alharbi S., Ahmed S.S., Goyal Y., Ameer G., and Jinag B.
Bioengineering & Translational Medicine
pdf | code | data

ERK hyperactivation serves as a unified mechanism of escape in intrinsic and acquired CDK4/6 inhibitor resistance in acral lentiginous melanoma
Jagirdar K., …, Goyal Y., Ji H., Liu Q., and Rebecca V.
Oncogene

2022

High-throughput and multiplexed RNA detection in situ with clampFISH 2.0
Dardani I.P., Emert B., Goyal Y., Jiang C.L., Kaur A., Rouhanifard S.H., Alicea G.M., Fane M.E., Xiao M., Herlyn M., Weeraratna A.T., and Raj A.
Nature Methods
pdf | code | data

Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
Kiani K., Sanford E.M., Goyal Y., and Raj A.
Molecular Systems Biology
pdf | code | data

Cell type determination for cardiac differentiation occurs soon after seeding of hiPS cell
Jiang C.L., Goyal Y., Jain N., Wang Q., Truitt R.E., Cote A.J., Emert B., Mellis I.A., Kiani K., Yang W., Jain R., and Raj A.
Genome Biology
pdf | code | data

Preformation and epigenesis converge to specify primordial germ cell fate in the early Drosophila embryo
Colonnetta M., Goyal Y., Johnson H.E., Syal S., Schedl P., and Deshpande G.
PLoS Genetics
pdf | code | data

2021

Art as a Toolkit for Data Science
*Zhu L., and *Goyal Y.
Marg

Molecular mechanisms underlying cellular effects of human MEK1 mutations
*Marmion R.A., *Yang L., Goyal Y., Jindal G.A., Wetzel J.L., Singh M., Schupbach T., and Shvartsman S.Y.
Molecular Biology of the Cell 

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity
Mellis I.A., Edelstein H.I., Truitt R., Goyal Y., Beck L.E., Symmons O., Dunagin M.C., Saldana R.A.L., Shah P.P., Pérez-Bermejo J.A., Padmanabhan A., Yang W., Jain R., and Raj A.
Cell Systems

2020

Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancer
Schuh L., Saint-Antoine M., Sanford E.M., Emert B.L., Singh A., Marr C., Raj A., and #Goyal Y.
Cell Systems
article pdf | code | data
Media coverage: Schmidt Science Fellows

Activation induced substrate engagement in Erk signaling
Paul S., Yang L., Mattingly H.H., Goyal Y., Shvartsman S.Y., and Veraksa A.
Molecular Biology of the Cell

2018

A quantitative model of developmental Erk signaling
Goyal Y., Schupbach T., and Shvartsman S.Y.
Developmental Biology

2017

How activating mutations affect MEK1 regulation and function
*Jindal G.A., *Goyal Y., Humphreys J.M., Yeung E., Tian K., Patterson V.L., He H., Burdine R.D., Goldsmith E.J., and Shvartsman S.Y.
Journal of Biological Chemistry
Highlighted by: Virtual Issue: Signaling through space and time, Journal of Biological Chemistry

Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia
Cuellar T. L., Herzner A-M., Zhang X., Goyal Y., Watanabe C., Friedman B.A., Janakiraman V., Durink S., Stinson J., Arnott D., Cheung T.K., Chaudhuri S., Modrusan Z., Doerr J.M., Classon M., and Haley B.
Journal of Cell Biology
Previewed by: Robbez M.L., Tie H.C., and Rowe H.M., Cancer cells, on your histone marks, get SETDB1, silence retrotransposons, and go!, Journal of Cell Biology

Parallel imaging of Drosophila embryos for quantitative analysis of genetic perturbations of the Ras pathway
*Goyal Y., *Levario T.J., Mattingly H.H., Holmes S., Shvartsman S.Y., and Lu H.
Disease Models & Mechanisms
Highlighted by: The Node

Uncoupling neurogenic gene networks in the Drosophila embryo
*Rogers W.A., *Goyal Y., Yamaya K., Shvartsman S.Y., and Levine M.S.
Genes & Development
Previewed by: Crews S., Creating cell type-specific mutants by enhancer mutagenesis, Genes & Development

Divergent effects of intrinsically active MEK variants on developmental Ras signaling
*Goyal Y., *Jindal G.A., Pelliccia J.L., Yamaya K., Yeung E., Futran A.S., Burdine R.D., Schupbach T., and Shvartsman S.Y. 
Nature Genetics
Highlighted by: F1000Prime
Media coverage: MedicalXpress, EurekAlert, Technology Org, Medical News

In vivo severity ranking of Ras pathway mutations associated with developmental disorders
*Jindal G.A., *Goyal Y., Yamaya K., Futran A.S., Kountouridis J., Schupbach T., Burdine R.D., and Shvartsman S.Y.
PNAS

The spatiotemporal limits of developmental Erk signaling
*Johnson H.E., *Goyal Y., Pannucci N., Schupbach T., Shvartsman S.Y., and Toettcher J.E.
Developmental Cell
Awarded: Best of 2017, Developmental Cell
Journal cover: January 23, 2017 issue
Previewed by: Shilo B. and Barkai N., Lighting up Erk activity, Developmental Cell
Highlighted by: F1000Prime

2015

Rasopathies: unraveling mechanisms with animal models
*Jindal G.A., *Goyal Y., Burdine R.D., Rauen K.A., and Shvartsman S.Y.
Disease Models & Mechanisms

Structural basis of neurohormone perception by the receptor tyrosine kinase torso
Jenni S., Goyal Y., Grotthuss M.V., Shvartsman S.Y., and Klein D.E.
Molecular Cell

2013

Metabolic engineering for enhanced hydrogen production: a review
Goyal Y., Kumar M., and Gayen K.
Canadian Journal of Microbiology

2011

Evaluating factors that influence microbial synthesis yields by linear regression with numerical and ordinal variables
*Colletti P. F., *Goyal Y., Varman A. M., Feng X., Wu B., and Tang Y.J.
Biotechnology and Bioengineering
Highlighted by: Two year metabolic engineering issue, Biotechnology and Bioengineering

Role of dopant concentration, crystal phase, and particle size on microbial inactivation of Cu-doped TiO2 nanoparticles
Sahu M., Wu B., Zhu L., Jacobson C., Wang W., Jones K., Goyal Y., Tang Y.J., and Biswas P.
Nanotechnology