As leader
- Tongue in Groove (JMT, 1992)
- RAIsedpleasuredot (New World, 1993)
- Crackshot (Avant, 1995)
- Down Home (Intuition, 1997)
- We'll Soon Find Out (Intuition, 1999)
- Beyond (Auditorium, 2001)
- Venice, dal vivo (D'Autres Cordes, 2010)
As sideman
With John Abercrombie
With the Toshiko Akiyoshi
With Laurie Anderson
With Tim Berne
With David Bowie
With Uri Caine
With Anthony Coleman
With Dave Douglas
With Mark Feldman
With Bill Frisell
With Fred Frith
With Richard Galliano
With Jim Hall
- These Rooms (Columbia, 1988)
- Hemispheres (ArtistShare, 2008) with Bill Frisell
- Conversations (ArtistShare, 2009)
With Fred Hersch
- Sarabande (SunnySide, 1987)
With Mark Johnson
With Haino Keiji
- An Unclear Trial: More Than This (Avant, 1998)
With Steve Kuhn
With Joe Lovano
With Pat Martino
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With Carmen McRae
With Enrico Pieranunzi
- New Lands (Timeless, 1984)
- Deep Down (Soul Note, 1986)
- Play Morricone (CamJazz, 2001)
- Current Conditions (CamJazz, 2003)
- Play Morricone 2 (CamJazz, 2003)
- Ballads (CamJazz, 2006)
- Live in Japan (CamJazz, 2007)
- As Never Before (CamJazz, 2008)
With Hank Roberts
With Herb Robertson
With John Scofield
With John Taylor
With Toots Thielemans
- Only Trust Your Heart (Concord, 1988)
- Do Not Leave Me (Stash, 1989)
With Roseanna Vitro
With John Zorn
- The Big Gundown (Icon, 1985)
- Spy vs Spy (Elektra/Musician, 1989)
- Naked City (Elektra Nonesuch, 1989) with Naked City
- Torture Garden (Shimmy Disc, 1990) with Naked City
- Grand Guignol (Avant, 1992) with Naked City
- Heretic (Avant, 1992) with Naked City
- Leng Tch'e (Toy's Factory, 1992) with Naked City
- Radio (Avant, 1993) with Naked City
- Absinthe (Avant, 1993) with Naked City
- Masada: Alef (DIW, 1994) with Masada
- Masada: Beit (DIW, 1994) with Masada
- Masada: Gimel (DIW, 1994) with Masada
- Masada: Dalet (DIW, 1995) with Masada
- Masada: Hei (DIW, 1995) with Masada
- Masada: Vav (DIW, 1995) with Masada
- Filmworks III: 1990–1995 (Toys Factory, 1996)
- Masada: Zayin (DIW, 1996) with Masada
- Masada: Het (DIW, 1997) with Masada
- Masada: Tet (DIW, 1997) with Masada
- Masada: Yod (DIW, 1997) with Masada
- Filmworks IV: S&M + More (Tzadik, 1997)
- New Traditions in East Asian Bar Bands (Tzadik, 1997)
- The Circle Maker (Tzadik, 1997)
- Black Box (Tzadik, 1997) with Naked City
- Taboo & Exile (Tzadik, 1999)
- Live in Jerusalem 1994 (Tzadik, 1999) with Masada
- Live in Taipei 1995 (Tzadik, 1999) with Masada
- Live in Middelheim 1999 (Tzadik, 1999) with Masada
- Live in Sevilla 2000 (Tzadik, 2000)
- The Gift (Tzadik, 2001)
- Live at Tonic 2001 (Tzadik, 2001) with Masada
- Naked City Live, Vol. 1: The Knitting Factory 1989 (Tzadik, 2002) with Naked City
- First Live 1993 (Tzadik, 2002) with Masada
- 50th Birthday Celebration Volume 4 (Tzadik, 2004) with Electric Masada
- 50th Birthday Celebration Volume 7 (Tzadik, 2004) with Masada
- Naked City: The Complete Studio Recordings (Tzadik, 2005) with Naked City
- Electric Masada: At the Mountains of Madness (Tzadik, 2005) with Electric Masada
- 50th Birthday Celebration Volume 11 (Tzadik, 2005) with Bar Kokhba Sextet
- Sanhedrin 1994–1997 (Tzadik, 2005) with Masada
- Moonchild: Songs Without Words (Tzadik, 2005) with Moonchild Trio
- Astronome (Tzadik, 2006) with Moonchild Trio
- Six Litanies for Heliogabalus (Tzadik, 2007) with Moonchild Trio
- The Crucible (Tzadik, 2008) with Moonchild Trio
- Lucifer: Book of Angels Volume 10 (Tzadik, 2008) with Bar Kokhba Sextet
- The Dreamers (Tzadik, 2008) with The Dreamers
- Stolas: Book of Angels Volume 12 (Tzadik, 2009) with Masada Quintet
- O'o (Tzadik, 2009) with The Dreamers
- Ipsissimus (Tzadik, 2010) with Moonchild
- Ipos: Book of Angels Volume 14 (Tzadik, 2010) with The Dreamers
- Nova Express (Tzadik, 2011) with the Nova Quartet
- At the Gates of Paradise (Tzadik, 2011)
- A Dreamers Christmas (Tzadik, 2011) with The Dreamers
- Templars: In Sacred Blood (Tzadik, 2012) with Moonchild
- A Vision in Blakelight (Tzadik, 2012)
- The Concealed (Tzadik, 2012)
- Dreamachines (Tzadik, 2013) with the Nova Quartet
- On Leaves of Grass (Tzadik, 2014) with the Nova Quartet
- Pellucidar: A Dreamers Fantabula (Tzadik, 2015) with The Dreamers
With Marc Johnson
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