Valentin Guignon

17 papers C 1Journal 14Unranked 2
YearRankTypeTitle / Venue / Authors
2025 conf
SWAT4HCLS
Pierre Larmande, Bertrand Pitollat, Ndomassi Tando, Yann Pomie, Bill Gates Happi Happi, Valentin Guignon
2025 J jnl
Database J. Biol. Databases Curation
Peter Selby, Rafael Abbeloos, Anne-Françoise Adam-Blondon, Francisco J. Agosto-Perez, Michael Alaux, Isabelle Alic, Khaled Al-Shamaa, Johan Steven Aparicio, Jan Erik Backlund, Aldrin Batac, Sebastian Beier, Gabriel Besombes, Alice Boizet, Matthijs Brouwer, Terry M. Casstevens, Arnaud Charleroy, Keo Corak, Chaney Courtney, Mariano Crimi, Gouripriya Davuluri, Kauê de Sousa, Jeremy Destin, Stijn Dhondt, Ajay Dhungana, Bert Droesbeke, Manuel Feser, Mirella Flores-Gonzalez, Valentin Guignon, Corina Habito, Asis Hallab, Jenna Hershberger, Puthick Hok, Amanda M. Hulse-Kemp, Lynn Carol Johnson, Sook Jung, Paul Kersey, Andrzej Kilian, Patrick König, Suman Kumar, Josh Lamos-Sweeney, Laszlo Lang, Matthias Lange, Marie-Angélique Laporte, Taein Lee, Erwan Le floch, Francisco López, Brandon Madriz, Dorrie Main, Marco Marsella, Maud Marty, Célia Michotey, Zachary Miller, Iain Milne, Lukas A. Mueller, Moses Nderitu, Pascal Neveu, Nick Palladino, Tim Parsons, Cyril Pommier, Jean-François Rami, Sebastian Raubach, Trevor Rife, Kelly Robbins, Mathieu Rouard, Joseph Ruff, Guilhem Sempéré, Romil Mayank Shah, Paul D. Shaw, Becky Smith, Nahuel Soldevilla, Anne Tireau, Clarysabel Tovar, Grzegorz Uszynski, Vivian Bass Vega, Stephan Weise, Shawn C. Yarnes, BrAPI Consortium
2024 J jnl
Database J. Biol. Databases Curation
Christophe Jenny, Valentin Guignon, Felip Manyer I Ballester, Max Ruas, Mathieu Rouard
2023 conf
SWAT4HCLS
Pierre Larmande, Bertrand Pitollat, Ndomassi Tando, Yann Pomie, Bill Happi, Valentin Guignon, Manuel Ruiz
2021 J jnl
Nucleic Acids Res.
Valentin Guignon, Abdel Toure, Gaëtan Droc, Jean-François Dufayard, Matthieu G. Conte, Mathieu Rouard
2021 J jnl
PLoS Comput. Biol.
Valentin Guignon, Catherine Breton, Jérôme Mariette, François Sabot, Julien Fumey, Vincent Lefort, Anna-Sophie Fiston-Lavier
2021 J jnl
Briefings Bioinform.
Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill L. Wegrzyn, Tavis K. Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily S. Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter, Joe West, Stephen P. Ficklin
2019 J jnl
Database J. Biol. Databases Curation
Yaw Nti-Addae, Dave Matthews, Victor Jun M. Ulat, Raza Syed, Guilhem Sempéré, Adrien Pétel, Jon Renner, Pierre Larmande, Valentin Guignon, Elizabeth Jones, Kelly Robbins
2019 J jnl
Bioinform.
Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar E. Benites-Alfaro, Clayton L. Birkett, Viana C. Calaminos, Pierre Carceller, Guillaume Cornut, Bruno Vasques Costa, Jeremy D. Edwards, Richard Finkers, Star Yanxin Gao, Mehmood Ghaffar, Philip Glaser, Valentin Guignon, Puthick Hok, Andrzej Kilian, Patrick König, Jack Elendil B. Lagare, Matthias Lange, Marie-Angélique Laporte, Pierre Larmande, David S. LeBauer, David A. Lyon, David F. Marshall, Dave Matthews, Iain Milne, Naymesh Mistry, Nicolas Morales, Lukas A. Mueller, Pascal Neveu, Evangelia Papoutsoglou, Brian Pearce, Ivan Perez-Masias, Cyril Pommier, Ricardo H. Ramirez-Gonzalez, Abhishek Rathore, Angel Manica Raquel, Sebastian Raubach, Trevor Rife, Kelly Robbins, Mathieu Rouard, Chaitanya Sarma, Uwe Scholz, Guilhem Sempéré, Paul D. Shaw, Reinhard Simon, Nahuel Soldevilla, Gordon Stephen, Qi Sun, Clarysabel Tovar, Grzegorz Uszynski, Maikel Verouden, BrAPI Consortium
2017 J jnl
Database J. Biol. Databases Curation
Max Ruas, Valentin Guignon, Guilhem Sempéré, Julie Sardos, Yann Hueber, H. Duvergey, Alain Andrieu, Richard Chase, Christophe Jenny, Tom Hazekamp, Brian M. Irish, K. Jelali, J. Adeka, Tomás Ayala-Silva, C. P. Chao, Jeff W. Daniells, B. Dowiya, B. Effa effa, L. Gueco, L. Herradura, L. Ibobondji, E. Kempenaers, J. Kilangi, S. Muhangi, P. Ngo Xuan, J. Paofa, Claudie Pavis, Deless Thiémélé, Colette Tossou, Jeffrey Sandoval, Asti Sutanto, G. Vangu Paka, Guilian Yi, Ines van den houwe, Nicolas Roux, Mathieu Rouard
2015 J jnl
Nucleic Acids Res.
Alexis Dereeper, Stéphanie Bocs, Mathieu Rouard, Valentin Guignon, Sébastien Ravel, Christine Tranchant-Dubreuil, Valérie Poncet, Olivier Garsmeur, Philippe Lashermes, Gaëtan Droc
2013 J jnl
Database J. Biol. Databases Curation
Gaëtan Droc, Delphine Larivière, Valentin Guignon, Nabila Yahiaoui, Dominique This, Olivier Garsmeur, Alexis Dereeper, Chantal Hamelin, Xavier Argout, Jean-François Dufayard, Juliette Lengelle, Franc-Christophe Baurens, Alberto Cenci, Bertrand Pitollat, Angélique D'Hont, Manuel Ruiz, Mathieu Rouard, Stéphanie Bocs
2012 J jnl
Bioinform.
Valentin Guignon, Gaëtan Droc, Michael Alaux, Franc-Christophe Baurens, Olivier Garsmeur, Claire Poiron, Tim Carver, Mathieu Rouard, Stéphanie Bocs
2011 J jnl
Theor. Comput. Sci.
Aïda Ouangraoua, Valentin Guignon, Sylvie Hamel, Cédric Chauve
2011 J jnl
Nucleic Acids Res.
Mathieu Rouard, Valentin Guignon, Christelle Aluome, Marie-Angélique Laporte, Gaëtan Droc, Christian Walde, Christian M. Zmasek, Christophe Périn, Matthieu G. Conte
2008 J jnl
Nucleic Acids Res.
Alexis Dereeper, Valentin Guignon, Guillaume Blanc, Stéphane Audic, S. Buffet, François Chevenet, Jean-François Dufayard, Stéphane Guindon, Vincent Lefort, Magali Lescot, Jean-Michel Claverie, Olivier Gascuel
2005 C conf
SPIRE
Valentin Guignon, Cédric Chauve, Sylvie Hamel
sql/redb_js_tables.sql
← Index sql/redb_js_tables.sql sql
-- JavaScript malware analysis tables
-- Engine: ReplacingMergeTree(analysis_date) — latest analysis wins on re-processing
--
-- File order:
--   1. redb_js_features
--   2. redb_js_suspicious_apis
--   3. redb_js_deobfuscation
--   4. code_text_content              (generic text-content table; JS today,
--                                      PowerShell / Python / email / extracted
--                                      PDF / Office text in the future)
--   5. redb_iocs source_type ALTER    (extends Enum8 with text_raw/text_normalized
--                                      so JS — and any future text-based pipeline —
--                                      can distinguish IOCs found in the raw vs
--                                      normalised surface)
--   6. redb_iocs ioc_type ALTER       (adds registry_key=42 so HKLM/HKCU/HKEY_*
--                                      keys are extracted alongside file paths)
--
-- Decoded strings from JS still go into the shared code_binja_strings_raw
-- table (same schema used by DecompileBinja and DecompileAPK). JS
-- string_encoding values: hex, unicode, charcode, base64, concat. Plain long
-- literals are not extracted here — they're already in code_text_content and
-- scraped by the IOC pipeline over text_raw/text_normalized.
-- string_offset is the line number in the source file.
--
-- redb_js_features.script_type values (file format / container, first match):
--   jse, wsf, hta, embedded_html, wscript, esm, node_module, standalone, unknown
-- redb_js_features.detected_environment values (runtime by API surface, first
-- match):
--   wscript, browser_extension, service_worker, deno, node, browser, unknown

-- 1. Core features & obfuscation metrics (1 row per sample)
CREATE TABLE IF NOT EXISTS redb_js_features (
    sha256 FixedString(64),
    line_count UInt32,
    char_count UInt64,
    text_entropy Float64,
    max_line_length UInt32,
    avg_line_length Float64,
    is_minified UInt8,
    is_likely_obfuscated UInt8,
    obfuscator_name LowCardinality(String),
    obfuscation_score UInt8,
    obfuscation_techniques Array(String),
    eval_count UInt32,
    function_constructor_count UInt32,
    settimeout_setinterval_count UInt32,
    document_write_count UInt32,
    innerhtml_count UInt32,
    unescape_count UInt32,
    fromcharcode_count UInt32,
    atob_count UInt32,
    decodeuri_count UInt32,
    total_function_count UInt32,
    total_variable_count UInt32,
    max_nesting_depth UInt16,
    avg_identifier_length Float64,
    hex_string_count UInt32,
    unicode_escape_count UInt32,
    long_string_count UInt32,
    base64_string_count UInt32,
    comment_ratio Float64,
    script_type LowCardinality(String),
    detected_environment LowCardinality(String),
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY sha256;

-- 2. Suspicious API calls (multi-row per sample)
--
-- `revealed_by_deobf` is 1 when the API only appears after the deobfuscation
-- pass (i.e. the call site is hidden in the raw artefact and surfaces only in
-- text_normalized). Useful for filtering "what did normalisation actually
-- buy us" without re-running the diff.
CREATE TABLE IF NOT EXISTS redb_js_suspicious_apis (
    sha256 FixedString(64),
    api_name String,
    api_category LowCardinality(String),
    call_count UInt32,
    line_numbers Array(UInt32),
    context_snippet String,
    revealed_by_deobf UInt8,
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY (sha256, api_name);

-- 3. Deobfuscation results (1 row per sample)
CREATE TABLE IF NOT EXISTS redb_js_deobfuscation (
    sha256 FixedString(64),
    deobfuscator_used LowCardinality(String),
    deobfuscation_successful UInt8,
    original_size UInt64,
    deobfuscated_size UInt64,
    size_change_ratio Float64,
    original_entropy Float64,
    deobfuscated_entropy Float64,
    new_strings_found UInt32,
    new_apis_found UInt32,
    deobfuscated_sha256 FixedString(64),
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY sha256;

-- 4. Generic text-content table for any text-based artefact (JS today;
--    PowerShell, Python, plain text, email bodies, extracted PDF/Office text
--    in the future). One row per sha256. content_type carries the magika
--    label so callers can filter without joining other tables.
CREATE TABLE IF NOT EXISTS code_text_content (
    sha256 FixedString(64),
    content_type LowCardinality(String),
    text_raw String CODEC(ZSTD(3)),
    text_normalized Nullable(String) CODEC(ZSTD(3)),
    normalizer_used Nullable(String),
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY sha256;

-- 5. Extend redb_iocs.source_type Enum8 with two universal text-content
--    surfaces: text_raw (the artefact's original text) and text_normalized
--    (a deobfuscated/canonicalised form). Used by the JS IOC extraction
--    pipeline today; any future text-based pipeline (PowerShell, PDF, etc.)
--    plugs into the same two values.
--
-- Existing rows keep their stored integer values; only newly-inserted rows
-- can use 4/5. The MODIFY COLUMN must list the full final enum, including
-- the existing values (1/2/3) — ClickHouse rejects partial alters.
ALTER TABLE redb_iocs
    MODIFY COLUMN source_type
    Enum8('decompiled_function'=1, 'disassembled_function'=2, 'string'=3,
          'text_raw'=4, 'text_normalized'=5);

-- 6. Extend redb_iocs.ioc_type Enum8 with registry_key=42. Windows registry
--    paths (HKLM\..., HKCU\..., HKEY_LOCAL_MACHINE\...) are a distinct class
--    of IOC from filesystem paths and were previously extracted by nothing.
--    Same MODIFY COLUMN constraint as the source_type alter — the full final
--    enum must be listed.
ALTER TABLE redb_iocs
    MODIFY COLUMN ioc_type
    Enum8('ipv4'=1, 'ipv6'=2, 'fqdn'=3, 'url'=4, 'email'=5, 'server'=6,
          'hash_md5'=10, 'hash_sha1'=11, 'hash_sha256'=12,
          'cve'=20, 'cwe'=21, 'cpe'=22,
          'crypto_btc'=30, 'crypto_eth'=31, 'crypto_xrp'=32, 'crypto_bch'=33,
          'crypto_ada'=34, 'crypto_substrate'=35,
          'path_linux'=40, 'path_windows'=41, 'registry_key'=42,
          'onion'=50);

-- 7. Migrate redb_js_features to the two-tier obfuscation verdict.
--    `is_obfuscated` (binary heuristic at score >=40) is renamed to
--    `is_likely_obfuscated` (heuristic at >=60 + ≥1 strong signal, OR
--    js-x-ray flagged the obfuscator family). `obfuscator_name` is the
--    family name reported by @nodesecure/js-x-ray (jsfuck, obfuscator.io,
--    morse, jjencode, freejsobfuscator, ...) or empty when not detected.
--
--    Run once against an existing deployment. The CREATE TABLE above
--    already reflects the post-migration shape, so fresh installs skip this.
ALTER TABLE redb_js_features
    RENAME COLUMN is_obfuscated TO is_likely_obfuscated;
ALTER TABLE redb_js_features
    ADD COLUMN IF NOT EXISTS obfuscator_name LowCardinality(String) AFTER is_likely_obfuscated;

-- 8. Harmonise code_text_content column names with redb_iocs.source_type
--    enum values. The enum already uses `text_raw` / `text_normalized` for
--    the surface labels; the table previously stored the same data under
--    `content_raw` / `content_normalized`, forcing every join across the two
--    to translate names. Renaming the columns produces a self-documenting
--    schema where `redb_iocs.source_type='text_raw'` points directly at
--    `code_text_content.text_raw`.
--
--    Run once against an existing deployment. The CREATE TABLE above
--    already reflects the post-migration shape, so fresh installs skip this.
ALTER TABLE code_text_content
    RENAME COLUMN content_raw TO text_raw;
ALTER TABLE code_text_content
    RENAME COLUMN content_normalized TO text_normalized;

-- 9. Add revealed_by_deobf flag to redb_js_suspicious_apis. The strings/APIs
--    extractors now scan both the raw source and the deobfuscated text so APIs
--    hidden behind one obfuscation layer (Vjw0rm-style array.join + eval,
--    Dean-Edwards packers, ...) surface in the table. The flag is 1 only when
--    the API was *not* found in the raw source — querying for it isolates
--    "deobf-only" findings without joining redb_js_deobfuscation.
--
--    Run once against an existing deployment. The CREATE TABLE above
--    already reflects the post-migration shape, so fresh installs skip this.
ALTER TABLE redb_js_suspicious_apis
    ADD COLUMN IF NOT EXISTS revealed_by_deobf UInt8 AFTER context_snippet;