• Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity (Nature comm.)

• Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation (Cell Reports Methods)

• Inferring single-cell transcriptomic dynamics with structured latent gene expression dynamics (Cell Reports)

• petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker’s yeast (BMC Bioinformatics)

• N Leibovich, J Rothschild, S Goyal, A Zilman - "Phenomenology and dynamics of competitive ecosystems beyond the niche-neutral regimes" (PNAS, arxiv)

• CJ Nunn, S Goyal - "Contingency and selection in mitochondrial genome dynamics" (eLife)

• C Nunn, S Goyal - " Population dynamics of mitochondrial genomes in Saccharomyces cerevisiae reveal tightly constrained mutational trajectories and a simple relationship between genome content and replicative fitness" (APS)

• S Goyal, S Rehman, C O'Brien - "Statistical dynamics of tumor initiation and progression" (APS)

• M Bonsma-Fisher, S Goyal - "Diversity-generating host-disease coevolution with adaptive immunity" (APS)

• S Freedman, A Howe, S Goyal, M Mani - "Inferring the molecular mechanisms that guide developmental bifurcations" (APS)

• MA Qazi, SK Salim, KR Brown, et al. - "Characterization of the minimal residual disease state reveals distinct evolutionary trajectories of human glioblastoma" (NCBI, bioRxiv)

• SL Freedman, B Xu, S Goyal, M Mani - "A dynamical systems treatment of transcriptomic trajectories in hematopoiesis" (bioRxiv)

• UY Pen, CJ Nunn, S Goyal - "An automated tabletop continuous culturing system with multicolor fluorescence monitoring for microbial gene expression and long-term population dynamics" (ACS Synth. Biol.)

• M Smart, S Goyal, A Zilman - "Roles of phenotypic heterogeneity and microenvironment feedback in early tumor development" (Phys Rev. E)

• SK Rehman, J Haynes, E Collignon, et al. - "Colorectal cancer cells enter a diapause-like DTP state to survive chemotherapy" (Cell)

• SL Freedman, B Xu, S Goyal, M Mani - "Revealing cell-fate bifurcations from transcriptomic trajectories of hematopoiesis" (bioRxiv)

• J Rothschild, N Leibovich, A Zilman, S Goyal - "Abundance transitions in multispecies stochastic Lotka-Volterra" (APS)

• S Freedman, B Xu, S Goyal, M Mani - "Detecting bifurcations in tissue development" (APS)

• S Bradde, A Nourmohammad, S Goyal, V Balasubramanian - "The size of the immune repertoire of bacteria"

• C Nunn, S Goyal - "A model to explain the propagation of small dysfunctional mitochondrial DNAs in budding yeast"

• S Jatav, S Malhotra, FD Miller, A Jha, S Goyal - "Inferring metabolic rewiring in embryonic neural development using single cell data"

• N Shakiba, A Fahmy, G Jayakumaran, et al. - "Cell competition during reprogramming gives rise to dominant clones"

• H Tao, M Zhu, K Lau, OKW Whitley, et al. - "Oscillatory cortical forces promote three dimensional cell intercalations that shape the murine mandibular arch"

• S Goyal, M Bonsma-Fisher - "How adaptive immunity constrains the composition and fate of large bacterial populations"

• GC Lui, S Goyal - "What do metabolic constraints inform us about the emergence of early stable bacterial communities?"

• SG Madeleine Bonsma-Fisher, "How Adaptive Immunity Constrains the Composition and Fate of Large Bacterial Populations"

• S Dasgupta, GD Bader, "Single-cell RNA Sequencing: A New Window into Cell Scale Dynamics"

• H Tao, M Zhu, K Lau, "Oscillatory cortical forces promote three dimensional mesenchymal cell intercalations to shape the mandibular arch"

• N Shakiba, A Fahmy, G Jayakumaran, "Competition During Reprogramming Gives Rise to Deterministically Elite Clones"

• S McGibbon-Gardner, N Shakiba, P Zandstra, "Competition During Reprogramming Gives Rise to Deterministically Elite Clones"

• T Chou, S Goyal, S Kim, ISY Chen. "Lineage-tracking of stem cell differentiation: a neutral model of hematopoiesis in rhesus macaque" (2016)

• S Goyal, S Kim, ISY Chen, T Chou. "Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques" (2015)

• S Goyal, PW Zandstra. "Chasing blood" (2015)

• M Mani, S Goyal, KD Irvine, BI Shraiman. "Collective polarization model for gradient sensing via Dachsous-Fat intercellular signaling" (2013)