The Axes of Life: A Roadmap for Understanding Dynamic Multiscale Systems

A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs

(2021) Joseph M. Cicchese et al.   Scientific Reports

Deep learning methods in protein structure prediction

(2020) Mirko Torrisi et al.   Computational and Structural Biotechnology Journal

Common biochemical properties of metabolic genes recurrently dysregulated in tumors

(2020) Krishnadev Oruganty et al.   Cancer & Metabolism

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks

(2020) Beryl M Jones et al.   eLife

Conserving stream fishes with changing climate: Assessing fish responses to changes in habitat over a large region

(2020) Yinphan Tsang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Identifying high value areas for conservation: Accounting for connections among terrestrial, freshwater, and marine habitats in a tropical island system

(2019) Yin-Phan Tsang et al.   JOURNAL FOR NATURE CONSERVATION

Perspective: Dimensions of the scientific method

(2019) Eberhard O. Voit   PLoS Computational Biology

Visible Machine Learning for Biomedicine

(2018) Michael K. Yu et al.   CELL

The effects of lateral line ablation and regeneration in schooling giant danios

(2018) Prasong J. Mekdara et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Physical foundations of biological complexity

(2018) Yuri I. Wolf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The background puzzle: how identical mutations in the same gene lead to different disease symptoms

(2017) Jan E. Kammenga   FEBS Journal

Characterization of the encoding properties of intraspinal mechanosensory neurons in the lamprey

(2017) Nicole Massarelli et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY A-NEUROETHOLOGY SENSORY NEURAL AND BEHAVIORAL PHYSIOLOGY

On the origin of biological construction, with a focus on multicellularity

(2017) Jordi van Gestel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

The effect of intrinsic muscular nonlinearities on the energetics of locomotion in a computational model of an anguilliform swimmer

(2015) Christina Hamlet et al.   JOURNAL OF THEORETICAL BIOLOGY

Quantifying stretch and secretion in the embryonic lung: Implications for morphogenesis

(2015) Uduak Z. George et al.   MECHANISMS OF DEVELOPMENT

Putting big data to good use in neuroscience

(2014) Terrence J Sejnowski et al.   NATURE NEUROSCIENCE

Multiscale Computational Models of Complex Biological Systems

(2013) Joseph Walpole et al.   Annual Review of Biomedical Engineering

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

(2013) Sriram Chandrasekaran et al.   PLoS Computational Biology

Molecular signatures from omics data: From chaos to consensus

(2012) Jaeyun Sung et al.   Biotechnology Journal

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Interplay between gene expression noise and regulatory network architecture

(2012) Guilhem Chalancon et al.   TRENDS IN GENETICS

A method for characterizing the biodiversity in bat pinnae as a basis for engineering analysis

(2011) Jianguo Ma et al.   Bioinspiration & Biomimetics

Ear Deformations Give Bats a Physical Mechanism for Fast Adaptation of Ultrasonic Beam Patterns

(2011) Li Gao et al.   PHYSICAL REVIEW LETTERS

Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states

(2011) S. Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Numerical analysis of biosonar beamforming mechanisms and strategies in bats

(2010) Rolf Müller   JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Strong Inference for Systems Biology

(2009) Daniel A. Beard et al.   PLoS Computational Biology

Complexity in biology. Exceeding the limits of reductionism and determinism using complexity theory

(2008) Fulvio Mazzocchi   EMBO REPORTS