About

Dr. James Knierim is a professor of neuroscience at the Johns Hopkins University School of Medicine and a researcher at the Zanvyl Krieger Mind/Brain Institute. His research focuses on the neurophysiology of memory within the hippocampal formation. His work investigates how the hippocampus processes information, including the flow of signals through its subregions and the role of inputs from the entorhinal cortex. He uses multi-electrode arrays to record extracellular action potentials from hippocampal neurons in freely moving rats, with a particular interest in place cells that activate when the animal occupies specific locations, forming a cognitive map crucial for navigation and memory formation. His research explores how objects and landmarks are incorporated into this map and how these processes underpin episodic memory formation. Dr. Knierim's background includes a BA in psychology from Haverford College, a PhD in neurobiology from Caltech where he studied the primate visual system, and a postdoctoral fellowship at the University of Arizona focusing on spatial firing characteristics of hippocampal cells. He has held faculty positions at the University of Texas Medical School at Houston before joining Johns Hopkins in 2009.

Research topics

• Artificial Intelligence
• Computer Science
• Psychology
• Neuroscience
• Evolutionary biology
• Cognitive science
• Cognitive psychology
• Biology

Selected publications

• SCREWx: A Screwless, Chronic, Recoverable, and Lightweight Neuropixels fixture for freely-moving rodents

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-06

  articleOpen access

  Summary High-density Neuropixels probes enable the study of large neural populations with single-cell and sub-millisecond resolution. While single-probe and acute head-fixed experiments have yielded critical scientific insights, understanding the neural mechanisms underlying many complex behaviors requires simultaneous multi-region recordings in freely moving, chronically implanted animals. Various probe fixtures have been developed to enable high-density recording, but existing designs impose critical limitations: their substantial weight restricts the maximum probe count that smaller animals can support, their bulky dimensions constrain the proximity of targeted brain regions, and their complex assembly risks damaging the probe during insertion and recovery. In this paper, we present a lightweight, fully 3D-printable, compact, and screwless fixture for chronic Neuropixels implants in freely moving rodents that features simple mechanisms for stable implantation and safe extraction. Our fixture design enables stable, high-yield single-unit recordings for months-long experiments, along with an 83% successful probe extraction rate. This fixture design provides a robust and accessible solution for long-term, multi-probe chronic Neuropixels recordings, increasing experimental throughput and enabling more complex experimental designs to investigate brain-wide neural dynamics.

  PublisherOA PDFDOI

• Three-dimensional spatial selectivity of hippocampal neurons during space flight

  DANDI Archive · 2026-02-27

  datasetOpen access1st authorCorresponding

  This dataset contains extracellular recordings from hippocampal place cells in three freely moving rats during the Neurolab Space Shuttle mission (STS-90) in April 1998. The experiment investigated whether the hippocampus can maintain stable spatial representations during three-dimensional navigation in microgravity. Rats were implanted with multi-electrode recording arrays and trained to traverse a three-dimensional track called the "Escher staircase," in which three 90-degree yaw turns were interleaved with three 90-degree pitch turns, creating a closed loop after only 270 degrees of total yaw rotation. This design placed the spatial information from external landmarks in conflict with the expected input from the head-direction system, which normally requires 360 degrees of yaw to signal a return to the starting direction. The dataset includes both preflight recordings on a flat rectangular track and in-flight recordings on the Escher staircase track from flight days 4 and 9. Place cells eventually demonstrated normal spatially specific firing, with spatial information content comparable to preflight levels, though initial exposures on flight day 4 showed abnormal spatial selectivity patterns. Hippocampal EEG was also recorded, showing normal theta rhythm during locomotion and normal sharp waves and ripples during quiet rest. Rats received medial forebrain bundle stimulation as a reward for traversing the track.

  PublisherDOI

• Using Anatomy and Computational Theory to Inspire Neurophysiological Experiments on Information Processing Through the Hippocampus

  Hippocampus · 2026-01-01 · 1 citations

  article1st authorCorresponding

  This article is a personal history of the background, ideas, and motivations behind the major discoveries from my lab in the past 27 years. Tracing the main themes back to my training as a graduate student and a postdoc, I discuss how all of our work has been influenced by a desire to use anatomical and computational literature to inspire and constrain the experimental questions we have addressed. The backstory of two fundamental discoveries made in the early days on my independent research program are described: (a) differences between DG, CA3, and CA1 population dynamics in relation to computational theories of pattern separation and pattern completion and (b) differences in the types of information conveyed to the hippocampus from its lateral and medial entorhinal cortex inputs. Also described are how these initial findings set the foundation for numerous subsequent discoveries as we followed the data from one experiment to the next, with the goals of understanding how information is represented and transformed through the hippocampal formation in support of spatial learning and episodic memory.

  PublisherDOI

• Simultaneous path-integration recalibration in head direction and place cells

  Current Biology · 2026-03-17

  articleOpen access

  Accurate spatial navigation relies on path integration, a process of tracking one's location by integrating self-motion cues. Path integration uses a gain factor relating self-motion signals to displacement on the cognitive map. This gain is plastic, recalibrating rapidly to match perceived displacements relative to external cues. To elucidate the mechanism of recalibration, we simultaneously recorded from place cells, which instantiate the cognitive map, and head direction (HD) cells, thought to orient the map. Persistent conflict between self-motion and visual feedback induced functionally identical recalibration of path-integration gain in the two neural populations during forward locomotion; however, during locomotor immobility accompanied by head scanning, HD cells did not exhibit recalibration. Moreover, the two populations manifested differential field-shifting dynamics relative to landmarks during recalibration. These results uncover a tightly coordinated yet behavior-dependent recalibration process across the navigation circuit that achieves robust yet flexible coupling of the internal sense of position and direction.

  PublisherDOI

• Hippocampal theta frequency as a readout of path-integration recalibration

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-11

  articleOpen accessSenior authorCorresponding

  Abstract Understanding how the brain represents hidden variables is a fundamental challenge. In navigation, the internal path-integration gain is often masked by external landmarks that override the path integrator. Path integration can recalibrate its gain when allothetic and idiothetic cues conflict, but the real-time dynamics of this process are hidden to direct observation. Here, we demonstrate that theta frequency provides an error signal between the observable hippocampal gain and the internal path-integration gain. Theta frequency decreased as conflict between landmark-driven hippocampal gain and path-integration gain increased and recovered as the path-integration gain recalibrated to the new gain. A continuous attractor model replicated these dynamics, suggesting that the theta-frequency drop is driven by the misalignment of allothetic and idiothetic inputs, reducing the excitatory drive to the network. Thus, theta frequency provides a real-time readout of internal gain-error signals, offering a novel methodology to estimate hidden cognitive variables through observable physiological oscillations.

  PublisherOA PDFDOI

• Three-dimensional spatial selectivity of hippocampal neurons during space flight

  DANDI Archive · 2026-02-27

  datasetOpen access1st authorCorresponding

  This dataset contains extracellular recordings from hippocampal place cells in three freely moving rats during the Neurolab Space Shuttle mission (STS-90) in April 1998. The experiment investigated whether the hippocampus can maintain stable spatial representations during three-dimensional navigation in microgravity. Rats were implanted with multi-electrode recording arrays and trained to traverse a three-dimensional track called the "Escher staircase," in which three 90-degree yaw turns were interleaved with three 90-degree pitch turns, creating a closed loop after only 270 degrees of total yaw rotation. This design placed the spatial information from external landmarks in conflict with the expected input from the head-direction system, which normally requires 360 degrees of yaw to signal a return to the starting direction. The dataset includes both preflight recordings on a flat rectangular track and in-flight recordings on the Escher staircase track from flight days 4 and 9. Place cells eventually demonstrated normal spatially specific firing, with spatial information content comparable to preflight levels, though initial exposures on flight day 4 showed abnormal spatial selectivity patterns. Hippocampal EEG was also recorded, showing normal theta rhythm during locomotion and normal sharp waves and ripples during quiet rest. Rats received medial forebrain bundle stimulation as a reward for traversing the track.

  PublisherDOI

• Allothetic and idiothetic spatial cues control the multiplexed theta phase coding of place cells

  Nature Neuroscience · 2025-08-26 · 3 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Data and code associated with the publication: Landmark vector cells in the absence of visual input

  Open MIND · 2025-11-01

  datasetOpen accessSenior author

  This repository includes the dataset and code used to generate the figures for the study published in Puliyadi et al. 2025 describing the presence of landmark vector activity in darkness. This dataset includes neuronal spiking activity from CA1, along with code to run a simulation of allocentric field generation using vector computations.

  OA PDFDOI

• Dynamic coupling between visual landmark processing in area 29e and parahippocampal path integration circuits of the rodent cortex

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-12 · 1 citations

  preprintSenior author

  The brain relies on external landmarks to anchor internal spatial representations. The neural mechanisms underlying this process and the sources of landmark signals remain unknown in mammals. Here, we simultaneously recorded single neurons across five parahippocampal regions in rats navigating a virtual reality environment that preserved natural locomotion. Area 29e, an understudied parahippocampal field, displayed strong locking to visual landmarks under conditions in which neurons in the other regions, such as the medial entorhinal cortex, decoupled their spatial firing from the landmarks. Compared to the other regions, area 29e neurons also displayed weaker theta modulation, stronger gamma rhythmicity, stronger egocentric head-direction tuning, and enhanced landmark contrast sensitivity. The loss of landmark anchoring in non-29e parahippocampal neurons was preceded by a decline of gamma-band influence from 29e to medial entorhinal cortex. Together, these findings position 29e as a specialized visuospatial hub that may carry landmark signals for anchoring parahippocampal representations of space to the external world.

  PublisherDOI

• Neural compass in the sky

  Science · 2025-10-16

  letterSenior author

  Head-direction neurons maintain stable directional signals during large-scale navigation in the wild.

  PublisherDOI

Recent grants

• A Control Theoretic Approach to Addressing Hippocampal Function

  NIH · $3.6M · 2017–2028

• NIH Grant K02MH063297

  NIH · $395k · 2006

• PROJECT 1-Neural encoding based on lateral and medial entorhinal information processing streams in behaviorally-characterized aged rats

  NIH · $72.5M · 1997–2027

• CRCNS: Path Intergration by the Grid Cell Network

  NIH · $3.0M · 2006–2017

• NIH Grant P01NS038310

  NIH · $17.2M · 2011

Frequent coauthors

• Douglas GoodSmith

  Johns Hopkins University

  79 shared

• Francesco Savelli

  Johns Hopkins University

  73 shared

• Heekyung Lee

  Nongwoo Bio (South Korea)

  59 shared

• Sachin S. Deshmukh

  47 shared

• Manu S. Madhav

  Johns Hopkins University

  40 shared

• Guo‐li Ming

  39 shared

• Cheng Wang

  Chinese Academy of Sciences

  37 shared

• Hongjun Song

  36 shared

Labs

• Krieger Mind/Brain Institute - James Knierim LabPI

Education

• Ph.D., Biology

  California Institute of Technology

  1991

• B.A., Psychology

  Haverford College

  1983