ID Genomics (United States)

dicast: a machine learning method for accurate structural variant detection from short-read sequencing data

Abstract Structural variants are a common cause of human diseases, but their detection from short-read sequencing remains challenging, despite being the technology underlying most clinical workflows. We present dicast , a machine-learning method that scores SV calls from short-re...

Integrated Multi-Omics Analysis Reveals Candidate Serum Biomarkers Linked to Cancer-Associated Fibroblast-Mediated Extracellular Matrix Remodeling in Metastatic Gastric Cancer

Abstract Metastatic gastric cancer remains a major cause of cancer-related mortality, while currently available serum biomarkers have limited performance for metastatic risk assessment. This study aimed to identify candidate serum biomarkers associated with gastric cancer progres...

Genomic Fit and Environmental Mismatch: The Tradeoff Model of Polygenic Operating Range

Why do "harmless" common genetic variants trigger catastrophic failures under specific environmental stress? Moving beyond reductionist "one-variant-one-disease" paradigms, this monograph introduces the Tradeoff Model of Polygenic Operating Range. It reframes common polymorphisms...

Cancer as Coherence Rescaling: A Terrain–Timing Model of Multicellular Constraint, Tumor-Level Cooperation, and Metastatic State Propagation

What if carcinogenesis is not a descent into chaotic entropy, but a survival shift to an entirely alternate layer of biological organization? This series finale applies the Terrain–Timing Model to oncology through the mechanism of coherence rescaling. It proposes that as organism...

Schizophrenia as Terrain Fragility: A Terrain–Timing Model of Developmental State-Transition Vulnerability

Why does schizophrenia aggressively cluster around specific developmental windows like late adolescence? Rejecting single-cause neurochemical paradigms, this paper applies the framework of Terrain Fragility—a state of compressed adaptive reserve where networks function normally u...

Schizophrenia as Terrain Fragility: A Terrain–Timing Model of Developmental State-Transition Vulnerability

Why does schizophrenia aggressively cluster around specific developmental windows like late adolescence? Rejecting single-cause neurochemical paradigms, this paper applies the framework of Terrain Fragility—a state of compressed adaptive reserve where networks function normally u...

The Endocrine-Chronobiological Axis: Hormones, Lifespan Transitions, and Biological Operating Range

How do major lifespan transitions unmask hidden genetic vulnerabilities? This paper introduces the Endocrine-Chronobiological Axis, establishing hormone profiles as time-varying, internal modifiers of an organism's biological operating range. It reframes hormones from static cros...

Genomic Fit and Environmental Mismatch: The Tradeoff Model of Polygenic Operating Range

Why do "harmless" common genetic variants trigger catastrophic failures under specific environmental stress?Moving beyond reductionist "one-variant-one-disease" paradigms, this monograph introduces the Tradeoff Model of Polygenic Operating Range. It reframes common polymorphisms...

Amyotrophic Lateral Sclerosis as Declining Recovery Capacity

What if ALS progression is driven by a collapse in network recovery kinetics rather than a binary cellular trigger? This paper applies the Terrain–Timing Model to motor-neuron degeneration, operationalizing ALS as a progressive, non-linear collapse in the capacity of vulnerable m...

Cancer as Coherence Rescaling: A Terrain–Timing Model of Multicellular Constraint, Tumor-Level Cooperation, and Metastatic State Propagation

What if carcinogenesis is not a descent into chaotic entropy, but a survival shift to an entirely alternate layer of biological organization? This series finale applies the Terrain–Timing Model to oncology through the mechanism of coherence rescaling. It proposes that as organism...

The Endocrine-Chronobiological Axis: Hormones, Lifespan Transitions, and Biological Operating Range

How do major lifespan transitions unmask hidden genetic vulnerabilities? This paper introduces the Endocrine-Chronobiological Axis, establishing hormone profiles as time-varying, internal modifiers of an organism's biological operating range. It reframes hormones from static cros...

Modes of Temporal Incoherence

Core Systems Focus: Provides the functional taxonomy for timing failures across biological signaling and recovery tracks.Synopsis: This monograph distinguishes Phase Incoherence, Kinetic Incoherence, and Continuity Incoherence, shifting attention from whether a biological event o...

The Biological Event Horizon: A Terrain–Timing Theory of Reversibility

Core Systems Focus: Characterizes system execution thresholds, hysteresis, and the transition from recoverable perturbation to state-maintained dysfunction. Synopsis: This paper operationalizes the Biological Event Horizon as the transition at which removing an initiating perturb...

The Terrain–Timing Model: A Systems Framework for Biological Coherence

Core Systems Focus: Establishes the universal conceptual and relational architecture of the model, independent of any single disease state. Synopsis: Paper 1 argues that biological function depends on more than the presence or normal abundance of molecular components. It proposes...

Genetic etiology associated with post‑transplant outcomes in a retrospective cohort of pediatric kidney transplant recipients based on genomics analysis

To determine whether genetic etiology, as determined by whole-exome sequencing (WES) and copy-number variant (CNV) analysis, is associated with graft survival and early injury profiles in pediatric kidney transplant recipients. We conducted a single-center, retrospective cohort s...

The comprehensive detection of hemoglobinopathy variants via long-read sequencing

ABSTRACT BACKGROUND The genetic complexity of hemoglobin genes, characterized by high GC content and homologous sequences, poses significant challenges for detecting hemoglobin variants in clinical settings. METHODS A long-read indexed PCR method utilizing the novel CycloneSEQ na...

Cancer of unknown primary: the evolution of tissue of origin identification in the artificial intelligence era

Cancer of Unknown Primary (CUP) presents substantial diagnostic and therapeutic challenges owing to its heterogeneous nature and the absence of an identifiable primary tumor site. This review provides a structured search of the pathogenesis, epidemiological characteristics, and l...

Unravelling the genetic structure and genetic relationships of indigenous Greek sheep breeds using SNP markers

Abstract Background Indigenous sheep of Greece represent important genetic resources shaped by long-term adaptation to diverse environments. However, many populations face demographic decline, genetic erosion, and their genomic diversity remains inadequately characterized. This s...