About

Paul S. Katz is a professor involved in neuroscience research at UMass Amherst, with a focus on understanding neural circuits and behavior. His lab, Katz Lab, explores various aspects of neurobiology, including connectomics, neurogenesis, transcriptomics, and the neural basis of behavior in different organisms such as Berghia and other model systems. His work emphasizes collaborative discovery, teaching, and learning within a team environment, contributing to the broader scientific understanding of neural function and organization.

Research topics

• Biology
• Artificial Intelligence
• Neuroscience
• Computer Science
• Biophysics
• Pathology
• Medicine
• Chemistry
• Physics
• Optics
• Genetics
• Evolutionary biology
• Biomedical engineering

Selected publications

• MolluscaGenes v0.1 — preliminary release

  Open MIND · 2026-01-01

  datasetOpen accessSenior author

  MolluscaGenes v0.1 — preliminary release. A taxonomically comprehensive mollusc transcriptome and proteome resource consolidating de-novo and previously published transcriptomes for ~300 species spanning all eight molluscan classes (Gastropoda, Bivalvia, Cephalopoda, Polyplacophora, Scaphopoda, Solenogastres, Caudofoveata, Monoplacophora). The release is paired with the TIAMMAt mollusc-revised Pfam HMMs (190 domains across 50 biological categories) for sensitive detection of divergent homologs across the phylum. Contents. BLAST and DIAMOND databases (protein), BLAST nucleotide database, raw protein and mRNA FASTA (gzipped), TIAMMAt-revised HMMs with hmmpress indices, per-species and per-HMM metadata tables, manifest with SHA256 checksums. Code. Command-line wrappers and reproducibility scripts ship in the companion GitHub repository invertome/molluscagenes (GPL-3.0). The wrapper mg_fetch.sh downloads every artifact in this deposit, verifies SHA256 against the manifest, extracts the tarballs, and writes a populated configuration file. Versioning. v0.1 is the database used in the accompanying biorxiv preprint. A full HPC rebuild (v1.0) is in progress and will supersede v0.1 under the same Zenodo concept DOI.

  PublisherDOI

• MolluscaGenes: A Transcriptomic Database for the Mollusca

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-08

  articleOpen accessSenior author

  The phylum Mollusca constitutes one of the most taxonomically and morphologically diverse animal clades; however, the genomic exploration of this group has been hampered by fragmented and taxonomically incomplete transcriptomic resources. To address this fundamental limitation, we present MolluscaGenes, a centralized database that unifies transcriptomes from 299 molluscan species spanning all eight recognized classes, encompassing a broad array of tissues and developmental stages. MolluscaGenes provides searchable databases via BLAST and DIAMOND alongside a suite of 196 molluscan-optimized Hidden Markov Models (HMMs) for sensitive protein family identification. To demonstrate the utility of this resource, we performed a comprehensive phylum-wide characterization of the nicotinic acetylcholine receptor (nAChR) superfamily, recovering 3,586 sequences from over 190 species and resolving 15 distinct phylogenetic clades. This analysis revealed substantial lineage-specific expansions across multiple molluscan classes, the identification of novel clades with substitutions in canonical ligand-binding residues, and the evolutionary placement of chemotactile receptors (CRs) and CR-like sequences as predominantly cephalopod clades within the broader nAChR phylogeny. MolluscaGenes constitutes a foundational resource that will accelerate the elucidation of the unique biology and evolutionary history of Mollusca.

  PublisherDOI

• Hunger modulates behavioral responses to olfactory and chemotactile cues in the specialist predator of dangerous prey, Berghia stephanieae

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-21

  articleOpen accessSenior author

  Animals continuously evaluate environmental cues to guide approach-avoidance decisions, with internal states like hunger dynamically shaping how stimuli are acted upon. While most studies examine the valence-switching of stimuli from appetitive to aversive using simplified or ambiguous stimuli, we leveraged a system in which a single prey contains both appetitive and aversive features. The nudibranch Berghia stephanieae, is a specialist predator of the sea anemone, Exaiptasia diaphana. These nudibranchs must resolve conflicting signals where chemical cues signal food, while contact can result in injury or death. The danger posed by Exaiptasia was described and quantified through direct counts of nematocysts fired into Berghia and multiple instances where the Berghia was captured and consumed by its prey. To test how internal state influenced the perception of stimuli from prey we recorded predatory behavior of Berghia after different periods of food deprivation. We found that the olfactory cues from prey were attractive to Berghia, even when animals were sated, and usually led to a contact-mediated investigation of prey. Hunger independently modulated olfactory and contact cue valence at different internal states and time scales of food deprivation. Hunger specifically altered the threshold for avoidance following contact with prey, indicating that somatosensory and chemotactile cues are modulated by hunger unlike olfactory cues. Our results highlight how internal state and sensory modality interact to shape decision making in a biologically relevant, high-risk predation context.

  PublisherDOI

• MolluscaGenes v0.1 — preliminary release

  Zenodo (CERN European Organization for Nuclear Research) · 2026-01-01

  datasetOpen accessSenior author

  MolluscaGenes v0.1 — preliminary release. A taxonomically comprehensive mollusc transcriptome and proteome resource consolidating de-novo and previously published transcriptomes for ~300 species spanning all eight molluscan classes (Gastropoda, Bivalvia, Cephalopoda, Polyplacophora, Scaphopoda, Solenogastres, Caudofoveata, Monoplacophora). The release is paired with the TIAMMAt mollusc-revised Pfam HMMs (190 domains across 50 biological categories) for sensitive detection of divergent homologs across the phylum. Contents. BLAST and DIAMOND databases (protein), BLAST nucleotide database, raw protein and mRNA FASTA (gzipped), TIAMMAt-revised HMMs with hmmpress indices, per-species and per-HMM metadata tables, manifest with SHA256 checksums. Code. Command-line wrappers and reproducibility scripts ship in the companion GitHub repository invertome/molluscagenes (GPL-3.0). The wrapper mg_fetch.sh downloads every artifact in this deposit, verifies SHA256 against the manifest, extracts the tarballs, and writes a populated configuration file. Versioning. v0.1 is the database used in the accompanying biorxiv preprint. A full HPC rebuild (v1.0) is in progress and will supersede v0.1 under the same Zenodo concept DOI.

  PublisherDOI

• Social Predation by a Nudibranch Mollusc

  Integrative Organismal Biology · 2025-01-01

  articleOpen accessSenior author

  Abstract Synopsis Social predation is a common strategy used by predators to subdue and consume prey. Animals that use this strategy have diverse methods of finding each other, organizing behaviors, and capturing prey. There is wide variation in the extent to which these behaviors are coordinated and in the stability of individual roles. This study characterizes social predation by the nudibranch mollusc, Berghia stephanieae, which is a specialist predator that eats only the sea anemone, Exaiptasia diaphana. A combination of experimental and modeling approaches established that Berghia consistently preys upon E. diaphana in groups, even when resources are abundant. However, this preference for social foraging does not appear to be a fixed personality trait, as individuals did not exhibit stable roles such as leader or follower. Instead, the population exhibited fission–fusion dynamics with temporary roles during predation. The extent of this social feeding was not altered by length of food deprivation, suggesting that animals are not shifting strategies based on hunger state. Furthermore, classic gastropod cues—such as slime trails, attraction to injured anemones, or preference for conspecifics feeding—did not facilitate group formation. Thus, Berghia provides an example of a specialist predator of dangerous prey that loosely organizes social feeding, independent of hunger state and fixed individual roles, while the mechanism of aggregation remains unknown. Significance Statement Social predation is an adaptive strategy that enables predators to subdue dangerous prey while minimizing injury. Many nudibranchs specialize to predate upon cnidarians, which pose unique challenges due to their potent defenses. Although nudibranchs are often characterized as solitary hunters, our study reveals that Berghia stephanieae exhibits social predation behaviors, forming temporary, fluid groups to feed on sea anemones. These groups lack stable social structures, with individuals adopting temporary roles such as joining or initiating feeding. Interestingly, we found no evidence that aggregation is driven by simple cues such as slime trails, conspecific activity, or prey injury, suggesting that group formation may depend on more complex or context-specific mechanisms. This work highlights the need for further research into the ecological and sensory factors underlying social predation in nudibranchs and other marine predators.

  PublisherOA PDFDOI

• The wiring diagram of an entire animal

  eLife · 2025-08-27

  editorialOpen accessSenior author

  A digital atlas of every cell in a developing marine worm reveals how networks across the body coordinate sensing and movement, and provides insights into the evolution of the nervous system.

  PublisherDOI

• Expression patterns and behavioral effects of conopressin and APGWamide in the nudibranch Berghia stephanieae

  Peptides · 2024-05-29

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Cellular‐resolution gene expression mapping reveals organization in the head ganglia of the gastropod, <i>Berghia stephanieae</i>

  The Journal of Comparative Neurology · 2024-06-01 · 6 citations

  articleOpen accessSenior author

  Gastropod molluscs such as Aplysia, Lymnaea, and Tritonia have been important for determining fundamental rules of motor control, learning, and memory because of their large, individually identifiable neurons. Yet only a small number of gastropod neurons have known molecular markers, limiting the ability to establish brain-wide structure-function relations. Here we combine high-throughput, single-cell RNA sequencing with in situ hybridization chain reaction in the nudibranch Berghia stephanieae to identify and visualize the expression of markers for cell types. Broad neuronal classes were characterized by genes associated with neurotransmitters, like acetylcholine, glutamate, serotonin, and GABA, as well as neuropeptides. These classes were subdivided by other genes including transcriptional regulators and unannotated genes. Marker genes expressed by neurons and glia formed discrete, previously unrecognized regions within and between ganglia. This study provides the foundation for understanding the fundamental cellular organization of gastropod nervous systems.

  PublisherOA PDFDOI

• Sample preparation methods for volume electron microscopy in mollusc <i>Berghia stephanieae</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-02-28 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Creating a high-resolution brain atlas in diverse species offers crucial insights into general principles underlying brain function and development. A volume electron microscopy approach to generate such neural maps has been gaining importance due to advances in imaging, data storage capabilities, and data analysis protocols. Sample preparation remains challenging and is a crucial step to accelerate the imaging and data processing pipeline. Here, we introduce several replicable methods for processing the brains of the gastropod mollusc, Berghia stephanieae for volume electron microscopy. Although high-pressure freezing is the most reliable method, the depth of cryopreservation is a severe limitation for large tissue samples. We introduce a BROPA-based method using pyrogallol and methods to rapidly process samples that can save hours at the bench. This is the first report on sample preparation and imaging pipeline for volume electron microscopy in a gastropod mollusc, opening up the potential for connectomic analysis and comparisons with other phyla.

  PublisherOA PDFDOI

• Author response for "Cellular‐resolution gene expression mapping reveals organization in the head ganglia of the gastropod, &lt;i&gt;Berghia stephanieae&lt;/i&gt;"

  2024-04-04

  peer-reviewSenior author
  PublisherDOI

Recent grants

• Evolution of Neural Circuits for Locomotion

  NSF · $526k · 2005–2008

• CRCNS data sharing: Comparative Neuromics of Gastropod Molluscs

  NSF · $223k · 2008–2011

• Evolution of Neural Circuits for Locomotion

  NSF · $523k · 2008–2013

• NIH Grant F32MH009748

  NIH · $69k

• NIH Grant R01MH049563

  NIH · $436k · 1995

Frequent coauthors

• Akira Sakurai

  Georgia State University

  27 shared

• Sweden Jessen

  Malmö University

  25 shared

• M. Desmond Ramirez

  University of Massachusetts Amherst

  13 shared

• Robert Calin‐Jageman

  11 shared

• James M. Newcomb

  10 shared

• Arianna N. Tamvacakis

  University of Arkansas at Fayetteville

  9 shared

• William N. Frost

  Rosalind Franklin University of Medicine and Science

  9 shared

• Adriano Senatore

  University of Toronto

  8 shared

Labs

• Paul S. Katz's LabPI

  The lab focuses on the structure, function, development, and evolution of nervous systems.

Education

• PhD, Neurobiology and Behavior

  Cornell University

  1989