Andreas Pfenning

Associate Professor, Ray and Stephanie Lane Computational Biology Department Carnegie Mellon University

  • Pittsburgh PA

Andreas Pfenning has published a number of high-impact papers on genomic tools to study sequence differences.

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Carnegie Mellon University

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Biography

Over the last several decades, the genetic revolution has showed us that much of human biology, even complex behavior, is encoded in our genome. Most of the variation in genome sequence that influences neurological disease predisposition and behavioral ability occurs in the vast regulatory regions between genes. The goal of the Pfenning laboratory is to build a set of computational and experimental genomic tools to study how sequence differences in those regions influence neurons, neural circuits, disease predisposition, and behavior. By understanding the genetic mechanisms underlying neural function, we seek to uncover the cell type-specific basis of Alzheimer’s disease and addiction, as well as gain insights into how speech production ability evolved in the human lineage.

Areas of Expertise

Computational Biology
Neural Function
Human Biology
Genomics
Disease Predisposition
Speech Production‎

Media Appearances

Similar genetic elements underlie vocal learning in mammals

Phys.org  online

2024-02-29

"New artificial intelligence methods were needed to help find evolutionary signals in regulatory elements across hundreds of genomes," said Pfenning, a corresponding author on the new study and an associate professor in CMU's Ray and Stephanie Lane Computational Biology Department affiliated with the Neuroscience Institute and Department of Biological Sciences. "We're entering an exciting era where AI is improving our ability to trace human evolutionary history. Studying the gene regulatory elements requires building a map of which ones are active in the relevant brain region of species with vocal learning behavior."

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What bats can teach us about the evolution of human speech

UC Berkeley News  online

2024-02-29

“We found that the types of cells that form long range connections in the human and bat brain are the same ones that we discovered as most relevant to vocal learning based on the genetic analysis,” Pfenning said. “The anatomy and genetics are both pointing to the same mechanism underlying the evolution of vocal learning across mammals and speech production in humans.”

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New Technique Isolates Brain Cells Associated With Parkinson's Disease

CMU News  online

2020-11-30

"Even a small portion of the brain can have dozens of different cell types," said Andreas Pfenning, an assistant professor in CMU's Computational Biology Department. "Each of these cell types has different roles in the behavior of an animal and also in disease." Separating cells of a certain type from their neighbors is thus a critical first step for researchers who want to study them.

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Media

Social

Industry Expertise

Biotechnology

Education

Duke University

Ph.D.

Computational Biology

2012

Carnegie Mellon University

B.S.

Computer Science

2006

Languages

  • English
  • German

Articles

Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition

Cell Reports

2024

Key mechanisms underlying chronic pain occur within the dorsal horn. Genome-wide association studies (GWASs) have identified genetic variants predisposed to chronic pain. However, most of these variants lie within regulatory non-coding regions that have not been linked to spinal cord biology. Here, we take a multi-species approach to determine whether chronic pain variants impact the regulatory genomics of dorsal horn neurons. First, we generate a large rhesus macaque single-nucleus RNA sequencing (snRNA-seq) atlas and integrate it with available human and mouse datasets to produce a single unified, species-conserved atlas of neuron subtypes.

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RERconverge expansion: using relative evolutionary rates to study complex categorical trait evolution

Molecular Biology and Evolution

2024

Comparative genomics approaches seek to associate molecular evolution with the evolution of phenotypes across a phylogeny. Many of these methods lack the ability to analyze non-ordinal categorical traits with more than two categories. To address this limitation, we introduce an expansion to RERconverge that associates shifts in evolutionary rates with the convergent evolution of categorical traits. The categorical RERconverge expansion includes methods for performing categorical ancestral state reconstruction, statistical tests for associating relative evolutionary rates with categorical variables, and a new method for performing phylogeny-aware permutations, “permulations”, on categorical traits.

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AI-designed DNA sequences regulate cell-type-specific gene expression

Nature

2024

Different parts of a cell’s genome can be active or inactive depending on the cell’s function in the body, and whether it is in a disease state. The instructions for activating or repressing a gene are encoded in the genome, and each type of cell has its own genomic ‘language’ that is based on highly complex patterns of nucleotides that describe whether a gene will be expressed. Writing in Nature, Gosai et al.1 apply artificial intelligence (AI) methods to learn the ‘regulatory grammar’ of that language — that is, the patterns of nucleotides in the genome that relate to gene-regulatory activity — for different cell types. The authors then apply those models, along with experimental genomics techniques, to create synthetic DNA sequences that can drive gene expression in specific cell types, which has implications for targeted cell and gene therapy.

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