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| Other views: | Awards Alphabetical Chronological |
Novels
- Siren Promised (2005) with Alan M. Clark
- Skullcrack City (2015)
- The Loop (2020)
- Angel Dust Apocalypse (2005)
- We Live Inside You (2011)
- Entropy in Bloom (2017)
- Extinction Journals (2006)
- Amniotic Shock in the Last Sacred Place (2003)
- Luminary (2004)
- Working at Home (2004)
- The League of Zeroes (2004)
- The Gravity of Benham Falls (2005)
- Dissociative Skills (2005)
- Saturn's Game (2005)
- Siren Promised (excerpt) (2005) with Alan M. Clark
- Snowfall (2005)
- Last Thoughts Drifting Down (2005)
- Swimming in the House of the Sea (2005)
- The Sharp-Dressed Man at the End of the Line (2006)
- Extinction Journals (2006)
- A Flood of Harriers (2006)
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When Susurrus Stirs (2007)
also appeared as:
- Variant: When Sussurus Stirs (2010)
- Simple Equations (2007)
- Consumerism (2007)
- Faded Into Impalpability (2009) with Bruce Holland Rogers
- Cathedral Mother (2010)
- The Musty Cow's Teat of Death (2010) with Alan M. Clark
- The Oarsman (2010)
- Laws of Virulence (2011)
- Cortical Reorganization (2011)
- Mercy (2011)
- States of Glass (2011)
- The Brilliant Idea (2011)
- The Encore (2011)
- The Witness at Dawn (2011)
- The Sleep of Judges (2017)
- The Protest (2022)
- The Mars Volta's Descent into Bedlam (2007)
- Afterword: What You Need to Know (2009)
- Author's Notes (We Live Inside You) (2011)
- Let's See What Happens: An Introduction (2013)
- Acknowledgments (The Loop) (2020)
- Alan M. Clark & Jeremy Robert Johnson Interview (2005) by James R. Beach (co-interviewed with Alan M. Clark)
- New Voices: Jeremy Robert Johnson (2006) by Steve Vernon
Non-Genre Titles
Short Fiction
- Trigger Variation (2007)
- Persistence Hunting (2011)