James F. Brinkley

79 papers A* 1B 3Misc 43Journal 26Unranked 6
YearRankTypeTitle / Venue / Authors
2017 Misc conf
AMIA
José L. V. Mejino Jr., Landon T. Detwiler, Timothy C. Cox, James F. Brinkley
2016 J jnl
Artif. Intell. Medicine
Landon T. Detwiler, José L. V. Mejino Jr., James F. Brinkley
2016 conf
ICBO/BioCreative
José Leonardo Villaraza Mejino Jr., James F. Brinkley, Timothy C. Cox, Landon Detwiler
2015 Misc conf
AMIA
Landon T. Detwiler, José L. V. Mejino Jr., James F. Brinkley
2014 J jnl
J. Biomed. Semant.
B. Nolan Nichols, José L. V. Mejino Jr., Landon Detwiler, Trond T. Nilsen, Maryann E. Martone, Jessica A. Turner, Daniel L. Rubin, James F. Brinkley
2013 conf
ICBO
José L. V. Mejino Jr., Ravensara S. Travillian, Timothy C. Cox, Linda G. Shapiro, James F. Brinkley
2012 B conf
SSDBM
Marianne Shaw, Landon Detwiler, James F. Brinkley, Dan Suciu
2012 J jnl
J. Biomed. Informatics
James F. Brinkley, Landon Detwiler
2012 J jnl
J. Biomed. Informatics
Shane Steinert-Threlkeld, Siamak Ardekani, José L. V. Mejino Jr., Landon Detwiler, James F. Brinkley, Michael Halle, Ron Kikinis, Raimond L. Winslow, Michael I. Miller, J. Tilak Ratnanather
2012 Misc conf
AMIA
Ida Sim, Simona Carini, Samson W. Tu, Landon Detwiler, James F. Brinkley, Shamin Mollah, Karl Burke, Harold P. Lehmann, Swati Chakraborty, Knut M. Wittkowski, Brad Pollock, Thomas Johnson, Vojtech Huser
2011 J jnl
J. Biomed. Informatics
Joshua D. Franklin, Alicia F. Guidry, James F. Brinkley
2011 conf
ICSC
Shane Steinert-Threlkeld, Siamak Ardekani, José L. V. Mejino Jr., Landon Detwiler, James F. Brinkley, Michael Halle, Ron Kikinis, Raimond L. Winslow, Michael I. Miller, J. Tilak Ratnanather
2011 conf
ICBO
B. Nolan Nichols, José L. V. Mejino Jr., James F. Brinkley
2011 J jnl
J. Biomed. Informatics
Marianne Shaw, Landon Fridman Detwiler, Natalya Fridman Noy, James F. Brinkley, Dan Suciu
2010 J jnl
Frontiers Neuroinformatics
Jessica A. Turner, José L. V. Mejino Jr., James F. Brinkley, Landon T. Detwiler, Hyo Jong Lee, Maryann E. Martone, Daniel L. Rubin
2009 B conf
Image Processing
Rosalia F. Tungaraza, J. Guan, S. M. Rolfe, Indriyati Atmosukarto, Andrew V. Poliakov, Natalia M. Kleinhans, Elizabeth H. Aylward, Jeffrey G. Ojemann, James F. Brinkley, Linda G. Shapiro
2009 B conf
Image Processing
S. M. Rolfe, L. Finney, Rosalia F. Tungaraza, J. Guan, Linda G. Shapiro, James F. Brinkley, Andrew V. Poliakov, Natalia M. Kleinhans, E. Alyward
2009 J jnl
J. Biomed. Informatics
Ira J. Kalet, José L. V. Mejino Jr., Vania Wang, Mark Whipple, James F. Brinkley
2009 J jnl
Frontiers Neuroinformatics
Landon T. Detwiler, Dan Suciu, Joshua D. Franklin, Eider B. Moore, Andrew V. Poliakov, Eunjung Lee, David P. Corina, George A. Ojemann, James F. Brinkley
2008 Misc conf
AMIA
José L. V. Mejino Jr., Daniel L. Rubin, James F. Brinkley
2008 Misc conf
AMIA
Marianne Shaw, Landon Detwiler, James F. Brinkley, Dan Suciu
2008 Misc conf
AMIA
Landon Detwiler, Dan Suciu, James F. Brinkley
2007 Misc conf
AMIA
Gary Yngve, James F. Brinkley, Daniel L. Cook, Linda G. Shapiro
2007 J jnl
BMC Bioinform.
Eider B. Moore, Andrew V. Poliakov, Peter Lincoln, James F. Brinkley
2007 J jnl
J. Am. Medical Informatics Assoc.
Nicholas R. Anderson, E. Sally Lee, J. Scott Brockenbrough, Mark E. Minie, Sherrilynne S. Fuller, James F. Brinkley, Peter Tarczy-Hornoch
2007 J jnl
Neuroinformatics
Andrew V. Poliakov, Xenia Hertzenberg, Eider B. Moore, David P. Corina, George A. Ojemann, James F. Brinkley
2007 Misc conf
AMIA
Xiang Li, John H. Gennari, James F. Brinkley
2006 Misc conf
AMIA
James F. Brinkley, Dan Suciu, Landon Detwiler, John H. Gennari, Cornelius Rosse
2006 Misc conf
AMIA
Landon Detwiler, James F. Brinkley
2006 Misc conf
AMIA
Christine Fong, James F. Brinkley
2006 Misc conf
AMIA
Wayne Warren, Augusto V. Agoncillo, Joshua D. Franklin, James F. Brinkley
2006 Misc conf
AMIA
Hao Li, John H. Gennari, James F. Brinkley
2005 conf
XSym
Nathan Bales, James F. Brinkley, E. Sally Lee, Shobhit Mathur, Christopher Ré, Dan Suciu
2005 Misc conf
AMIA
Sophia Jeng, Kelan Wang, Janos Barbero, James F. Brinkley, Peter Tarczy-Hornoch
2005 J jnl
J. Am. Medical Informatics Assoc.
Linda G. Shapiro, Emily Chung, Landon Detwiler, José L. V. Mejino Jr., Augusto V. Agoncillo, James F. Brinkley, Cornelius Rosse
2005 J jnl
J. Am. Medical Informatics Assoc.
Andrew V. Poliakov, Evan Albright, Kevin P. Hinshaw, David P. Corina, George A. Ojemann, Richard F. Martin, James F. Brinkley
2005 Misc conf
AMIA
E. Sally Lee, Dan Suciu, James F. Brinkley
2005 Misc conf
AMIA
Kelan Wang, Peter Tarczy-Hornoch, Ron Shaker, Peter Mork, James F. Brinkley
2005 Misc conf
AMIA
Wayne Warren, James F. Brinkley
2004 conf
MedInfo
Landon T. Detwiler, Emily Chung, Ann Li, José L. V. Mejino Jr., Augusto V. Agoncillo, James F. Brinkley, Cornelius Rosse, Linda G. Shapiro
2003 Misc conf
AMIA
Gregory Distelhorst, Vishrut Srivastava, Cornelius Rosse, James F. Brinkley
2003 Misc conf
AMIA
Zhengming Tang, Yana Kadiyska, Hao Li, Dan Suciu, James F. Brinkley
2003 Misc conf
AMIA
Landon T. Detwiler, José L. V. Mejino Jr., Cornelius Rosse, James F. Brinkley
2003 J jnl
J. Biomed. Informatics
Peter Mork, James F. Brinkley, Cornelius Rosse
2003 Misc conf
AMIA
Richard F. Martin, Kurt L. Rickard, José L. V. Mejino Jr., Augusto V. Agoncillo, James F. Brinkley, Cornelius Rosse
2003 J jnl
Neuroinformatics
Daniel Gardner, Arthur W. Toga, Giorgio A. Ascoli, Jackson T. Beatty, James F. Brinkley, Anders M. Dale, Peter T. Fox, Esther P. Gardner, John S. George, Nigel H. Goddard, Kristen M. Harris, Edward Herskovits, Michael L. Hines, Gwen A. Jacobs, Russell E. Jacobs, Edward G. Jones, David N. Kennedy, Daniel Y. Kimberg, John C. Mazziotta, Perry L. Miller, Susumu Mori, David C. Mountain, Allan L. Reiss, Glenn D. Rosen, David A. Rottenberg, Gordon M. Shepherd, Neil R. Smalheiser, Kenneth P. Smith, Tom Strachan, David C. Van Essen, Robert W. Williams, Stephen T. C. Wong
2002 Misc conf
AMIA
Peter Mork, Dan Suciu, James F. Brinkley, Cornelius Rosse
2002 Misc conf
AMIA
James F. Brinkley, Rex M. Jakobovits, Cornelius Rosse
2002 J jnl
J. Am. Medical Informatics Assoc.
Rex M. Jakobovits, Cornelius Rosse, James F. Brinkley
2002 J jnl
NeuroImage
Kevin P. Hinshaw, Andrew V. Poliakov, Eider B. Moore, Richard F. Martin, Linda G. Shapiro, James F. Brinkley
2001 Misc conf
AMIA
Rex M. Jakobovits, James F. Brinkley, Cornelius Rosse, Ed Weinberger
2001 Misc conf
AMIA
Richard F. Martin, José L. V. Mejino Jr., Douglas M. Bowden, James F. Brinkley, Cornelius Rosse
2001 Misc conf
AMIA
José L. V. Mejino Jr., Natalya Fridman Noy, Mark A. Musen, James F. Brinkley, Cornelius Rosse
2001 Misc conf
AMIA
Andrew V. Poliakov, Evan Albright, David P. Corina, George A. Ojemann, Richard F. Martin, James F. Brinkley
2000 Misc conf
AMIA
William B. Lober, James F. Brinkley
2000 Misc conf
AMIA
Rex M. Jakobovits, Stephen Soderland, Ricky K. Taira, James F. Brinkley
1999 Misc conf
AMIA
William B. Lober, James F. Brinkley
1999 Misc conf
AMIA
Ira J. Kalet, Jonn Wu, Matthew Lease, Mary M. Austin-Seymour, James F. Brinkley, Cornelius Rosse
1999 Misc conf
AMIA
Sara Kim, James F. Brinkley, Cornelius Rosse
1999 J jnl
IEEE Computer Graphics and Applications
James F. Brinkley, Benjamin A. Wong, Kevin P. Hinshaw, Cornelius Rosse
1999 Misc conf
AMIA
Andrew V. Poliakov, Kevin P. Hinshaw, Cornelius Rosse, James F. Brinkley
1999 Misc conf
AMIA
Jin S. Hahn, Elizabeth S. Burnside, James F. Brinkley, Cornelius Rosse, Mark A. Musen
1999 Misc conf
AMIA
Benjamin A. Wong, Cornelius Rosse, James F. Brinkley
1998 Misc conf
AMIA
Benjamin A. Wong, James F. Brinkley
1998 Misc conf
AMIA
Kevin P. Hinshaw, James F. Brinkley
1998 Misc conf
AMIA
Rex M. Jakobovits, James F. Brinkley
1998 Misc conf
AMIA
James F. Brinkley, Cornelius Rosse
1998 J jnl
J. Am. Medical Informatics Assoc.
Cornelius Rosse, José L. V. Mejino Jr., Bharath R. Modayur, Rex M. Jakobovits, Kevin P. Hinshaw, James F. Brinkley
1998 Misc conf
AMIA
Cornelius Rosse, Linda G. Shapiro, James F. Brinkley
1997 Misc conf
AMIA
Bharath R. Modayur, Rex M. Jakobovits, Kenneth Maravilla, George A. Ojemann, James F. Brinkley
1997 Misc conf
AMIA
Rex M. Jakobovits, James F. Brinkley
1997 J jnl
Softw. Pract. Exp.
James F. Brinkley, Jeffrey S. Prothero
1997 J jnl
J. Am. Medical Informatics Assoc.
James F. Brinkley, Cornelius Rosse
1997 Misc conf
AMIA
Kevin P. Hinshaw, James F. Brinkley
1996 J jnl
J. Vis. Lang. Comput.
Rex M. Jakobovits, Lara M. Lewis, James P. Ahrens, Linda G. Shapiro, Steven L. Tanimoto, James F. Brinkley
1996 J jnl
IEEE Trans. Syst. Man Cybern. Part A
D. J. Dailey, James F. Brinkley
1988 J jnl
J. Chem. Inf. Comput. Sci.
James F. Brinkley, Russ B. Altman, Bruce S. Duncan, Bruce G. Buchanan, Oleg Jardetzky
1986 A* conf
AAAI
Barbara Hayes-Roth, Bruce G. Buchanan, Olivier Lichtarge, Mike Hewitt, Russ B. Altman, James F. Brinkley, Craig Cornelius, Bruce S. Duncan, Oleg Jardetzky
1985 J jnl
IEEE Trans. Pattern Anal. Mach. Intell.
James F. Brinkley
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;