Biology subjects

Lin, J. J.

Publications and source records attributed to Lin, J. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Single molecule Grb2 dynamics reveal spatiomechanical modulation of RTK signaling across length scales

Extracellular matrix (ECM)-mediated cell adhesion and tension regulate development and disease through crosstalk with Receptor Tyrosine Kinases (RTKs). RTKs stimulate proliferation, survival, and metabolic reprogramming via Ras/ERK and PI3K/Akt signaling. Emerging evidence identify the biophysical and biochemical integration of integrin-mediated adhesions with RTK signaling, however, the molecular mechanisms regulating this phenotype remain poorly understood. Here, we demonstrate that ECM stiffness potentiates ligand-mediated epidermal growth factor receptor (EGFR) signaling at scales ranging from the single adaptor protein, Grb2 upward to multicellular spheroids and tissues. We show that ECM stiffness-driven RTK signaling is mediated by integrin adhesions that reshape the membrane to induce the formation of RTK signaling hotspots distributed globally across the cell membrane. A parsimonious computational model and biochemical membrane perturbations causally implicate membrane curvature and topography in tension-dependent integrin-EGFR crosstalk. The results demonstrate how the mechanical properties of the ECM direct molecular recruitment and confinement of signaling molecules to regulate growth factor-dependent RTK signaling. Given that many RTK-driven solid tumors develop a stiff stroma, the findings could explain why many therapeutic tyrosine kinase inhibitors develop clinical resistance. The findings suggest clarifying how tension regulates transmembrane receptor signaling could identify unique force-dependent molecular regulators towards which new antitumor therapies could be applied.

biophysics↗

bioRxiv2026

Self-guided search in immersive VR reveals active hierarchical planning

Despite the ubiquitous nature of visual search in our daily lives, our knowledge of the underlying mechanisms is almost entirely derived from studies using simple, synthetic stimuli briefly flashed on a computer monitor. In real life, however, visual search occurs in three-dimensional environments over much longer timescales and involves the dynamic coordination of attention, memory, and action planning, generating novel predictions that cannot be tested with traditional approaches. Here, we examined how self-guided visual search unfolds under naturalistic conditions that extend over space and time. We asked participants (N=80) to find specific objects (e.g., a green lamp, an orange shelf) in an immersive, visually rich virtual reality environment using range-limited teleportation (2 m steps). Consistent with our hypotheses, we found that self-guided search engaged a hierarchical information-seeking policy characterized at each stage by recurring plan-and-execute cycles paired with subgoal-specific attentional priorities. Subgoal priorities progressed from wayfinding to identification of clusters of target-similar objects, and then to specific target features. These search priorities progressively narrowed the search space through coordinated eye, head, and body movements that recurred throughout the task. We conclude that naturalistic search is hierarchical, built from sequential subgoals with shifting attentional priorities that single-level tasks cannot capture. Moreover, immersive VR with eye-head-body tracking dissociates motor planning from execution moments and reveals how looking content shifts with each task subgoal while the person moves through space, something desktop tasks cannot capture.

animal behavior and cognition↗

bioRxiv2026

A single cortical circuit implements fast and slow visual search

How the brain produces different behaviors from a fixed anatomical substrate is a foundational question in neuroscience. The dominant account holds that behavioral flexibility requires distinct neural circuits: dedicated systems selectively recruited for different processing modes. An alternative proposes that flexibility arises not from switching between circuits, but from dynamically controlling the speed at which a shared circuit operates. Here, we test this account directly using intracranial EEG recordings from nineteen human patients performing two visual search tasks of markedly different difficulty: an easy color-singleton search and a difficult orientation search, a fast vs. slow dissociation attributed for four decades to distinct anatomical and oscillatory neural systems. We show that both search tasks recruit the same cortical regions, oscillatory frequencies, and processing hierarchy. Dynamic time warping reveals that the two neural trajectories are time-stretched versions of one another; the same temporal scaling appears within each condition between faster and slower trials, indexing response speed rather than the distinction between tasks. Alpha-band oscillations (~8-10 Hz) support this temporal scaling through two coordinated mechanisms: synchronizing activity across a posterior cortical network and phase-gating local high-frequency activity (70-150 Hz) within those regions at the same preferred phase in both conditions. These findings establish that, for the two tasks studied here, fast and slow visual search are not implemented by selecting between distinct dedicated circuits, but by adjusting the speed of a single alpha-coordinated architecture. The same principle may apply to other search tasks, and to other domains in which dual-process architectures have been invoked, a testable prediction for future studies.

neuroscience↗

bioRxiv2026

TORC1 integrates metabolic state transitions during aging

Target of rapamycin complex 1 (TORC1) coordinates nutrient availability with anabolic metabolism, yet how TORC1-linked metabolic states influence cellular aging remains unclear. Using genetic, transcriptomic, metabolomic, and pharmacological analyses in prototrophic Saccharomyces cerevisiae, we identify context-dependent metabolic state transitions that uncouple cellular proliferation from long-term survival during aging. Loss of the SEACIT complex, conserved with mammalian GATOR1, establishes a low-flux metabolic state characterized by coordinated remodeling of nitrogen, nucleotide, and central carbon metabolism during stationary phase. Pharmacological restraint of nucleotide, glycolytic, or sterol metabolism converges on similar adaptive metabolic programs, whereas perturbations that impair mitochondrial respiratory capacity destabilize these states and reduce survival. Integrative analyses in human cancer and primary cells further reveal that diverse metabolic perturbations converge on mTORC1 suppression but generate distinct mitochondrial and stress responses depending on nutrient availability. Together, these findings demonstrate that TORC1 integrates metabolic state transitions in which nutrient availability and mitochondrial function determine cellular survival during aging.

systems biology↗

bioRxiv2026

Copper modulates iron-dependent survival through distinct TORC1 and AMPK signaling pathways

Copper and iron are redox-active micronutrients with tightly coupled homeostasis, yet how copper modulates iron-dependent stress responses remains unclear. Using Saccharomyces cerevisiae under nutrient-limited conditions, we uncoupled proliferative growth from long-term survival to dissect metal-dependent adaptation. Copper selectively preserved survival without affecting growth, whereas iron showed similar effects. Iron chelation impaired growth and suppressed electron transport chain gene expression; copper partially rescued these defects but required iron for its pro-survival activity. Despite this interdependence, copper and iron engaged distinct signaling programs. Iron-dependent survival required a Target of Rapamycin complex 1 (TORC1)-permissive state and was attenuated by rapamycin, whereas copper remained active under TORC1 inhibition. In contrast, copper promoted survival through AMP-activated protein kinase (AMPK) and antioxidant pathways, while iron exhibited context-dependent AMPK reliance. Together, these findings identify copper and iron as state-dependent regulators of cellular survival.

cell biology↗

bioRxiv2026

Prevalence and Actionability of MTAP Loss in Oncogene-Driven Lung Cancer

BackgroundMethylthioadenosine phosphorylase (MTAP) loss co-occurs with actionable genomic alterations in non-small cell lung cancer (NSCLC) and creates vulnerability to protein arginine methyltransferase 5 (PRMT5) inhibition. Estimates of prevalence of MTAP loss rely on next-generation sequencing which can underestimate copy losses. Moreover, the activity of PRMT5 inhibitors in oncogene-driven NSCLC is not well established. MethodsWe assessed MTAP expression by immunohistochemistry (IHC) in 243 NSCLCs (n=132 early stage, n=111 metastatic), including 33 specimens with paired lymph nodes. Antiproliferative activity of PRMT5 inhibitor monotherapy and in combination with tyrosine kinase inhibitors (TKIs) was evaluated in MTAP-deleted NSCLC cell lines harboring EGFR or KRAS mutations or ALK rearrangements. ResultsAmong 243 NSCLC specimens from 240 patients (72% with driver alterations, 90% adenocarcinoma), MTAP loss was identified in 43 (18%) specimens from 40 (17%) patients, including 18 (14%) early-stage and 22 (20%) metastatic tumors. MTAP loss occurred in 24% of stage 4 driver-positive NSCLCs versus 14% of driver-negative tumors (p=0.314). Twenty (61%) lung-nodal pairs demonstrated concordance; eight cases only exhibited decreased MTAP expression in nodes. Variable sensitivity to PRMT5 inhibitors was observed in 22 MTAP-deleted NSCLC cell lines (9 EGFR-mutant, 7 KRAS-mutant, 6 ALK-rearranged), with responses seen in TKI-sensitive and TKI-resistant lines. SDMA (symmetric dimethylarginine) expression did not predict PRMT5 inhibitor sensitivity. TKI + PRMT5 inhibitor combos had greater activity than monotherapy. ConclusionsMTAP loss occurs in 1-in-5 oncogene-driven metastatic NSCLCs. PRMT5 inhibitor activity is independent of TKI exposure, driver alteration, and SDMA expression and enhanced by addition of TKI. These findings support clinical evaluation of PRMT5 inhibitor + TKI combinations for advanced NSCLC.

cancer biology↗

bioRxiv2026

The bromodomain protein Bdf3 is sufficient to activate expression of a procyclin gene in bloodstream stage African trypanosomes

The early branching eukaryotic parasite, Trypanosoma brucei, lives extracellularly in the mammalian host, where it expresses variant surface glycoprotein (VSG). Antigenic variation of VSGs allows the parasite to evade the host immune response while in the bloodstream. Upon transition to the tsetse fly vector, the parasite remodels its surface to express procyclin protein from a limited set of EP and GPEET genes. While the environmental signals that trigger the switch from expressing VSG genes to expressing EP and GPEET genes are known, the molecular mechanism that initiates transcription of the EP and GPEET genes during parasite differentiation to the procyclic stage within the tsetse is not well understood. Previous work has shown that the chromatin interacting bromodomain protein Bdf3 is absent from the pol I promoter of the EP locus in bloodstream parasites, but appears there shortly after initiation of differentiation from the bloodstream to the procyclic stage. Here, we show that tethering of Bdf3 to the EP promoter using a dCas9-Bdf3 fusion protein and a guide RNA is sufficient to increase transcript levels of EP1 in bloodstream parasites, where the gene is normally silenced. This result supports the model that Bdf3 appears at the EP locus during differentiation to facilitate initiation of transcription, which is consistent with the role for Bdf3 as a transcriptional activator in other systems. Understanding gene regulatory mechanisms in this early branching eukaryote may help build a more complete picture for the conserved and unique features of gene regulatory proteins across diverse biological systems. ImportanceThe Trypanosoma brucei parasite is transmitted to a mammalian host via the tsetse fly vector, where it causes African trypanosomiasis, a fatal disease that causes a severe human and economic burden for people living in in areas of sub-Saharan African. While drug treatments have improved for some strains, some infections still require treatment with drugs that have serious side effects. One avenue for drug development is to try and manipulate the lifecycle of the parasite to make it poorly adapted to the mammalian host. However, this requires detailed knowledge of the mechanisms by which parasites regulate their genes as they progress through the lifecycle. Here, we show that the DNA interacting bromodomain protein Bdf3 may be a key driver for turning on insect-specific genes that code for insect-stage surface proteins. This finding could aid in the development of lifecycle manipulating drugs, and shed light on how gene regulatory mechanisms evolved.

molecular biology↗

bioRxiv2025

Sensorimotor dynamics differentiate singing and speaking

Singing and speaking often dissociate clinically--people who stutter can sing fluently, and individuals with aphasia and speech output problems from stroke may express sentences fluently in song--yet the neural mechanisms of this centuries-old clinical phenomenon remain unclear. We recorded intracranial EEG while neurosurgical patients produced matched sentences by singing or speaking, sampling millimeter- and millisecond-scale activity across both hemispheres. During articulation, high-frequency activity (70-150 Hz) lateralized oppositely across behaviors, with right-dominant sensorimotor cortex (SMC) activation for singing and left-dominant activation for speaking. Phase-amplitude coupling revealed that mu-band ([~]10 Hz) phase locally organized HFA in left SMC in a channel-specific, spatially interdigitated architecture preserved across both behaviors. Mu-band synchrony in speaking showed an early left-led pattern, whereas singing exhibited a ramping of synchrony within the left sensorimotor cortex and between the two motor cortices, supporting progressive interhemispheric recruitment. Frequency-domain Granger- Geweke causality revealed that the left primary somatosensory cortex drives both motor cortices at speech onset. In contrast in singing, control over motor cortices relied on both hemispheres. Singing and speaking engage a shared mu-coupled sensorimotor substrate through distinct recruitment dynamics.

neuroscience↗

bioRxiv2025

Fronto-Hippocampal Synchronization in Rapid Spatial Learning in Humans

Achieving goals in real-life situations--from fetching a glass of water to landing a dream job--often requires planning based on experience and executing a sequence of actions. Neurophysiological research in animal models has indicated that the orbitofrontal cortex (OFC) mediates relationships between memory, actions, and outcomes and the hippocampus and other medial temporal lobe (MTL) regions are known to be critical for rapid learning, but little is known about how these areas interact to support rapid learning and retrieval of goal-directed action sequences in humans. Here, we leverage a rare opportunity to investigate human OFC gamma oscillations and examine the coordination between the OFC and MTL during a continuous multi-step task that requires applying recently acquired experience to guide behavior. We used multisite intracranial electroencephalography (iEEG) recordings while participants searched for a hidden goal in an animated game to study neural activity in both brain areas during goal-directed behavior. Hippocampal ripples--brief high-frequency oscillations reflecting synchronized neuronal firing--are known to support memory consolidation during sleep, but their role during active memory retrieval and updating remains unclear. We found that OFC gamma activity was modulated by both memory demands and ripples in the hippocampus and adjacent structures. Notably, ripple-coupled OFC gamma during exploration was associated with subsequent task performance. We propose that hippocampal ripples mark a narrow window, supporting hippocampal-cortical communication required for successful goal encoding for future behaviors.

neuroscience↗

bioRxiv2025

Neural dynamics of proactive and reactive cognitive control in medial and lateral prefrontal cortex

Goal-directed behavior requires adjusting cognitive control to both react to and prepare for conflict. Previous work indicates theta oscillations and population activity in dorsomedial prefrontal cortex (dmPFC) and dorsolateral prefrontal cortex (dlPFC) are critical for reactive control. However, the neural mechanisms supporting proactive control are less clear. Here, we investigated the neural basis of behavioral adaptations when control is prepared in anticipation of conflict using intracranial EEG (iEEG) in dmPFC and dlPFC during a Stroop task where conflict frequency was manipulated across blocks. We observed canonical conflict-driven increases in dmPFC theta and in dmPFC and dlPFC local population activity, as indexed by high frequency activity (HFA). Conflict also suppressed theta power in both regions after the response, accentuated a pre-response beta desynchronization selectively in dlPFC, and increased a post-response beta rebound in both regions. Importantly, we identified a pre-trial marker of proactive control where dmPFC theta power increased before trials when conflict was expected, and theta, beta, and HFA conflict signals in both regions were enhanced when conflict was rare and diminished when conflict was common. These findings reveal shared HFA but dissociable oscillatory dynamics in dmPFC and dlPFC during reactive conflict processing, highlight pre-trial dmPFC theta as a potential substrate for proactive control, and refine the roles of dmPFC and dlPFC in control adaptations.

neuroscience↗

bioRxiv2025

Declarative Memory Through the Lens of Single-Trial Peaks in High-Frequency Power

Declarative memory depends on the coordination of local processing, indexed by high-frequency broadband (HFB) activity, with global network organization, indexed by theta oscillations. However, theta and HFB exhibit asynchronous timing, raising the question of how results of local processing are communicated throughout the network. Using intracranial EEG in patients performing a recognition memory task, we examined this coordination across the medial temporal lobe (MTL) and prefrontal cortex (PFC). HFB peak activity was earlier in the MTL than PFC. Anchoring analyses of theta phase clustering and connectivity to HFB peaks revealed strong phase clustering locked to HFB peaks in the PFC, as well as connectivity between the PFC and MTL that predicted individual memory performance. Graph analysis revealed specific connections amidst sparse network connectivity during memory success. This study demonstrates that transient brain states linked to internal physiological events support memory and refines our understanding of local and network-level process interactions. HighlightsO_LIMemory-linked theta activity is time-locked to internal brain events C_LIO_LINetwork connectivity changes dynamically during memory processing C_LIO_LISparse network connectivity supports successful memory C_LIO_LISpecific sequences of transient states may be critical for declarative memory C_LI

neuroscience↗

bioRxiv2025

Circuit dynamics of approach-avoidance conflict in humans

Debilitating anxiety is pervasive in the modern world. Choices to approach or avoid are common in everyday life and excessive avoidance is a cardinal feature of anxiety disorders. Here, we used intracranial EEG to define a distributed prefrontal-limbic circuit supporting approach and avoidance. Presurgical epilepsy patients (n=20) performed a continuous-choice, approach-avoidance conflict decision-making task inspired by the arcade game Pac-Man, where patients trade-off harvesting rewards against potential losses from attack by the ghost. As patients approached increasing rewards and threats, we found evidence of a limbic circuit mediated by increased theta power in the hippocampus, amygdala, orbitofrontal cortex (OFC) and anterior cingulate cortex (ACC), that drops rapidly during avoidance. Theta band connectivity within this circuit and with the lateral prefrontal cortex increases during approach and falls during avoidance, and amygdala and lateral frontal activity granger-caused the theta oscillations in both the OFC and ACC. Importantly, the degree of network connectivity predicted how long patients approach, with enhanced network synchronicity extending approach times. Finally, when threat is imminent, the system dynamically switches to a sustained increase in high-frequency activity (70-150Hz) in the middle frontal gyrus (MFG), tracking the degree of threat. The results provide evidence for a distributed prefrontal-limbic circuit, mediated by theta oscillations and high frequency activity, underlying approach-avoidance conflict in humans.

neuroscience↗

bioRxiv2024

The development of aperiodic neural activity in the human brain

The neurophysiological mechanisms supporting brain maturation are fundamental to attention and memory capacity across the lifespan. Human brain regions develop at different rates, with many regions developing into the third and fourth decades of life. Here, in this preregistered study (https://osf.io/gsru7), we analyzed intracranial EEG (iEEG) recordings from widespread brain regions in a large developmental cohort. Using task-based (i.e., attention to-be-remembered visual stimuli) and task-free (resting-state) data from 101 children and adults (5.93 - 54.00 years, 63 males; n electrodes = 5691), we mapped aperiodic (1/[f]-like) activity, a proxy of neural noise, with steeper slopes indexing less noise and flatter slopes indexing more noise. We reveal that aperiodic slopes flatten with age into young adulthood in both association and sensorimotor cortices, challenging models of early sensorimotor development based on brain structure. In prefrontal cortex (PFC), attentional state modulated age effects, revealing steeper task-based than task-free slopes in adults and the opposite in children, consistent with the development of cognitive control. Age-related differences in task-based slopes also explained age-related gains in memory performance, linking the development of PFC cognitive control to the development of memory. Last, with additional structural imaging measures, we reveal that age-related differences in gray matter volume are similarly associated with aperiodic slopes in association and sensorimotor cortices. Our findings establish developmental trajectories of aperiodic activity in localized brain regions and illuminate the development of PFC control during adolescence in the development of attention and memory.

neuroscience↗

bioRxiv2024

Attentional Information Routing in The Human Brain

Brain-wide communication supporting flexible behavior requires coordination between sensory and associative regions but how brain networks route sensory information at fast timescales to guide action remains unclear. Using human intracranial electrophysiology and spiking neural networks during spatial attention tasks, where participants detected targets at cued locations, we show that high-frequency activity bursts (HFAb) mark temporal windows of elevated population firing that enable fast, long-range communications. HFAbs were evoked by sensory cues and targets, dynamically coupled to low-frequency rhythms. Notably, both the strength of cue-evoked HFAbs and their decoupling from slow rhythms predicted behavioral accuracy. HFAbs synchronized across the brain, revealing distinct cue- and target-activated subnetworks. These subnetworks exhibited lead-lag dynamics following target onset, with cue-activated subnetworks preceding target-activated subnetworks when cues were informative. Computational modeling suggested that HFAbs reflect transitions to population spiking, denoting temporal windows for network communications supporting attentional performance. These findings establish HFAbs as signatures of population state transitions, supporting information routing across distributed brain networks.

neuroscience↗

bioRxiv2024

Modeling Cortical Versus Hippocampal Network Dysfunction in a Human Brain Assembloid Model of Epilepsy and Intellectual Disability

Neurodevelopmental disorders often impair multiple cognitive domains. For instance, a genetic epilepsy syndrome might cause seizures due to cortical hyperexcitability and present with memory impairments arising from hippocampal dysfunction. This study examines how a single disorder differentially affects distinct brain regions by using human patient iPSC-derived cortical- and hippocampal-ganglionic eminence assembloids to model Developmental and Epileptic Encephalopathy 13 (DEE-13), a condition arising from gain-of-function mutations in the SCN8A gene. While cortical assembloids showed network hyperexcitability akin to epileptogenic tissue, hippocampal assembloids did not, and instead displayed network dysregulation patterns similar to in vivo hippocampal recordings from epilepsy patients. Predictive computational modeling, immunohistochemistry, and single-nucleus RNA sequencing revealed changes in excitatory and inhibitory neuron organization that were specific to hippocampal assembloids. These findings highlight the unique impacts of a single pathogenic variant across brain regions and establish hippocampal assembloids as a platform for studying neurodevelopmental disorders.

neuroscience↗

bioRxiv2023

Systematic transcriptomics analysis of calorie restriction and rapamycin unveils their synergistic interaction in prolonging cellular lifespan

Aging is a multifaceted biological process marked by the decline in both mitotic and postmitotic cellular function, often central to the development of age-related diseases. In the pursuit of slowing or even reversing the aging process, a prominent strategy of significant interest is calorie restriction (CR), also known as dietary restriction, and the potential influence of a drug called rapamycin (RM). Both CR and RM have demonstrated the capacity to extend healthspan and lifespan across a diverse array of species, including yeast, worms, flies, and mice. Nevertheless, their individual and combined effects on mitotic and postmitotic cells, as well as their comparative analysis, remain areas that demand a thorough investigation. In this study, we employ RNA-sequencing methodologies to comprehensively analyze the impact of CR, RM, and their combination (CR+RM) on gene expression in yeast cells. Our analysis uncovers distinctive, overlapping, and even contrasting patterns of gene regulation, illuminating the unique and shared effects of CR and RM. Most notably, our findings reveal a synergistic effect of CR+RM in extending the lifespan of postmitotic cells, a result validated in both yeast and human cells. This research offers valuable insights into the processes of aging and presents potential strategies for enhancing healthspan and delaying the onset of age-related diseases. These findings have the potential to revolutionize our approach to implementing these interventions under specific conditions and within the context of age-related diseases.

genomics↗

bioRxiv2023

Dynamics of endogenous and water cortisol release in Asian Seabass Lates calcarifer after acute stress in a farm scale recirculating aquaculture system

Stress in farmed fish is associated with poor feeding, slow growth, disease, and mortality. Therefore, it is essential to closely monitor the stress levels in fish to optimize farming practices which could then enhance productivity and welfare in aquaculture operations. Cortisol, a stress hormone that can be found in the blood, is a reliable biomarker for evaluating fish stress. As blood sampling is highly invasive, alternative cortisol sampling methods such as fin, mucus, and the surrounding water which contains released cortisol, have been proposed as less invasive or non-invasive sampling methods. However, a comprehensive understanding of their temporal dynamics and associations with plasma cortisol levels is still lacking. In this study, we subjected Lates calcarifer, Asian sea bass within a farm-scale (3,000 L tank, 9,000 L system) high-flow rate (8,000 L/hour) Recirculating Aquaculture System (RAS) to an acute handling stress challenge specifically involving chasing and air exposure, and quantified cortisol dynamics both within different biological samples including blood, fin, and mucus and in tank water from multiple sampling points. We showed that handling stress induced an expected increase in plasma and mucosal cortisol, peaking at 1 hour and 24-48 hours, respectively, and that plasma and mucus cortisol were moderately correlated, especially during the stress period. Fin cortisol did not show consistent dynamics. Water cortisol similarly rose, but peaked within 40 minutes from the start of the stressor, in a pattern that was dependent on the site of sampling within the RAS system, likely due to RAS circulation dynamics. Our study is the first to examine the impact of stress on cortisol accumulation and release in Asian Sea bass in a farm-scale RAS, thus complementing existing research on the efficacy of fin, mucus, and water cortisol as stress indicators that could help optimize aquaculture productivity and welfare.

physiology↗

bioRxiv2023

Anatomical registration of intracranial electrodes. Robust model-based localization and deformable smooth brain-shift compensation methods

Precise electrode localization is important for maximizing the utility of intracranial EEG data. Electrodes are typically localized from post-implantation CT artifacts, but algorithms can fail due to low signal-to-noise ratio, unrelated artifacts, or high-density electrode arrays. Minimizing these errors usually requires time-consuming visual localization and can still result in inaccurate localizations. In addition, surgical implantation of grids and strips typically introduces non-linear brain deformations, which result in anatomical registration errors when post-implantation CT images are fused with the pre-implantation MRI images. Several projection methods are currently available, but they either fail to produce smooth solutions or do not account for brain deformations. To address these shortcomings, we propose two novel algorithms for the anatomical registration of intracranial electrodes that are almost fully automatic and provide highly accurate results. We first present GridFit, an algorithm that simultaneously localizes all contacts in grids, strips, or depth arrays by fitting flexible models to the electrodes CT artifacts. We observed localization errors of less than one millimeter (below 8% relative to the inter-electrode distance) and robust performance under the presence of noise, unrelated artifacts, and high-density implants when we ran [~]6000 simulated scenarios. Furthermore, we validated the method with real data from 20 intracranial patients. As a second registration step, we introduce CEPA, a brain-shift compensation algorithm that combines orthogonal-based projections, spring-mesh models, and spatial regularization constraints. When tested with real data from 15 patients, anatomical registration errors were smaller than those obtained for well-established alternatives. Additionally, CEPA accounted simultaneously for simple mechanical deformation principles, which is not possible with other available methods. Inter-electrode distances of projected coordinates smoothly changed across neighbor electrodes, while changes in inter-electrode distances linearly increased with projection distance. Moreover, in an additional validation procedure, we found that modeling resting-state high-frequency activity (75-145 Hz) in five patients further supported our new algorithm. Together, GridFit and CEPA constitute a versatile set of tools for the registration of subdural grid, strip, and depth electrode coordinates that provide highly accurate results even in the most challenging implantation scenarios. The methods presented here are implemented in the iElectrodes open-source toolbox, making their use simple, accessible, and straightforward to integrate with other popular toolboxes used for analyzing electrophysiological data.

bioinformatics↗