「ploi」の検索結果

Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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Classify constitutional (germline) copy number variants for clinical reporting using the 2019 ACMG/ClinGen technical standards points-based framework, with ClassifyCNV and AnnotSV for semi-automated scoring. Covers the separate copy-number-loss and copy-number-gain rubrics, the five-tier classification, ClinGen haploinsufficiency/triplosensitivity and dosage-sensitive regions, de novo and segregation evidence, and population-frequency benign evidence. Use when assigning pathogenic/likely-pathogenic/VUS/likely-benign/benign to a constitutional CNV, scoring a CNV against ACMG/ClinGen criteria, or distinguishing the automatable evidence from the case-specific evidence requiring manual input.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Identify and exploit authentication and session management vulnerabilities in web applications. Broken authentication consistently ranks in the OWASP Top 10 and can lead to account takeover, identity theft, and unauthorized access to sensitive systems.

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Provide comprehensive techniques for penetration testing AWS cloud environments. Covers IAM enumeration, privilege escalation, SSRF to metadata endpoint, S3 bucket exploitation, Lambda code extraction, and persistence techniques for red team operations.

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Provide comprehensive techniques for testing REST, SOAP, and GraphQL APIs during bug bounty hunting and penetration testing engagements. Covers vulnerability discovery, authentication bypass, IDOR exploitation, and API-specific attack vectors.

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Testing WebSocket implementations for authentication bypass, cross-site hijacking, injection attacks, and insecure message handling during authorized security assessments.

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Tests APIs for excessive data exposure where endpoints return more data than the client application needs, relying on the frontend to filter sensitive fields. The tester intercepts API responses and analyzes them for leaked PII, internal identifiers, debug information, or sensitive business data that the UI does not display but the API transmits. This maps to OWASP API3:2023 Broken Object Property Level Authorization. Activates for requests involving API data leakage testing, excessive data exposure, response filtering bypass, or API over-fetching.

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Tests APIs for Broken Function Level Authorization (BFLA) vulnerabilities where regular users can invoke administrative functions or access privileged API endpoints by directly calling them. The tester identifies admin and privileged endpoints, then attempts to access them with regular user credentials by manipulating HTTP methods, URL paths, and request parameters. Maps to OWASP API5:2023 Broken Function Level Authorization. Activates for requests involving BFLA testing, admin endpoint bypass, function-level access control testing, or API privilege escalation.

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Perform Kerberoasting attacks using Impacket's GetUserSPNs to extract and crack Kerberos TGS tickets for Active Directory service accounts.

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Analyzes and simulates BGP hijacking scenarios in authorized lab environments to assess route origin validation, RPKI deployment, and BGP monitoring defenses against prefix hijacking and route leak attacks on internet routing infrastructure.

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Detect abuse of elevation control mechanisms including UAC bypass, sudo exploitation, and setuid/setgid manipulation by monitoring registry modifications, process elevation flags, and unusual parent-child process relationships.

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Executes authorized attack simulations against Active Directory environments to identify misconfigurations, weak credentials, dangerous privilege paths, and exploitable trust relationships that could lead to domain compromise. The tester uses BloodHound for attack path analysis, Mimikatz for credential extraction, and Impacket for protocol-level attacks including Kerberoasting, AS-REP Roasting, and delegation abuse. Activates for requests involving Active Directory pentest, AD attack simulation, domain compromise testing, or Kerberos attack assessment.

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Tests APIs for injection vulnerabilities including SQL injection, NoSQL injection, OS command injection, LDAP injection, and Server-Side Request Forgery (SSRF) through API parameters, headers, and request bodies. The tester crafts malicious payloads targeting different backend technologies and injection contexts to extract data, execute commands, or access internal services. Maps to OWASP API8:2023 Security Misconfiguration and API7:2023 SSRF. Activates for requests involving API injection testing, SQLi in APIs, NoSQL injection, SSRF testing, or API input validation assessment.

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Detect privilege escalation attempts including token manipulation, UAC bypass, unquoted service paths, kernel exploits, and sudo/doas abuse across Windows and Linux.

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Detects fileless malware and in-memory attacks that execute entirely in RAM without writing persistent files to disk, evading traditional antivirus. Use when building detections for PowerShell-based attacks, reflective DLL injection, WMI persistence, and registry-resident malware. Activates for requests involving fileless malware detection, in-memory attacks, PowerShell exploitation, or living-off-the-land techniques.

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Detect and prevent API enumeration attacks including BOLA and IDOR exploitation by monitoring sequential identifier access patterns and authorization failures.

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Detect cyber attacks targeting OT historian servers (OSIsoft PI, Ignition, Wonderware) that sit at the IT/OT boundary and serve as pivot points for lateral movement between enterprise and control networks, including data manipulation, unauthorized queries, and exploitation of historian-specific vulnerabilities.

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Plan and execute a comprehensive red team engagement covering reconnaissance through post-exploitation using MITRE ATT&CK-aligned TTPs to evaluate an organization's detection and response capabilities.

日本語の概要は準備中です。原文の説明を表示しています。