Preprints :

Rational tangle surgery and Xer recombination on catenanes
Isabel K. Darcy, Kai Ishihara, Ram Medikonduri and Koya Shimokawa,
preprint (2009).

Published research papers :

Bounds for the minimum step number of knots in the simple cubic lattice
R. Scharein, K. Ishihara, J. Arsuaga, Y. Diao, K. Shimokawa, and M. Vazquez,
J. Phys. A: Math. Theor. 42 (2009) 475006 (24pp)
doi: 10.1088/1751-8113/42/47/475006

Finite surgeries on three-tangle pretzel knots
David Futer, Masaharu Ishikawa, Yuichi Kabaya, Thomas W. Mattman, and Koya Shimokawa ,
Algebr. Geom. Topol. 9 issue 2, 743-771 (2009)
(arXive 0809.4278)

Exceptional surgery and boundary slopes
Masaharu Ishikawa and Thomas W. Mattman, and Koya Shimokawa,
Osaka J. Math. 43 No.4, 807-821 (2006)
(math.GT/0211147)

Essential laminations and branched surfaces in the exteriors of links
Mark Brittenham, Chuichiro Hayashi, Mikami Hirasawa, Tsuyoshi Kobayashi, and Koya Shimokawa
Japan. J. Math. 31 No.1, 25-96 (2005)

Tangle sum and constructible spheres
Masahiro Hachimori and Koya Shimokawa,
J. Knot Theory Ramifications 13, 373-383 (2004)

On non-simple reflexive links
Hiroshi Matsuda, Makoto Ozawa, and Koya Shimokawa,
J. Knot Theory Ramifications 11 787-791 (2002)

Heegaard splittings of the pair of the solid torus and the core loop
Chuichiro Hayashi and Koya Shimokawa,
Rev. Mat. Complut. 14 No.2, 479-501 (2001)

Heegaard splittings of trivial arcs in compression bodies
Chuichiro Hayashi and Koya Shimokawa,
J. Knot Theory Ramifications 10, 71-87 (2001)

Thin position of a pair (3-manifold, 1-submanifold)
Chuichiro Hayashi and Koya Shimokawa,
Pacific J. Math. 197, 301-324 (2001)

Dehn surgeries on strongly invertible knots which yield lens spaces
Mikami Hirasawa and Koya Shimokawa,
Proc. Amer. Math. Soc. 128 number 11, 3445-3451 (2000)
Citation

Hyperbolicity and boudary-irreducibility of alternating tangles
Koya Shimokawa,
Topology Appl. 96 issue 3, 217-239 (1999)

Heegaard splittings of the trivial knot
Chuichiro Hayashi and Koya Shimokawa,
J. Knot Theory Ramifications 7, 1073-1085 (1998)

On tunnel number one alternating knots and links
Koya Shimokawa,
J. Math. Sci. Univ. Tokyo 5, 547-560 (1998)

Parallelism of two strings in alternating tangles
Koya Shimokawa,
J. Knot Theory Ramifications 7, 489-502 (1998)
more information

Symmetric knots satisfy the cabling conjecture
Chuichiro Hayashi and Koya Shimokawa,
Math. Proc. Camb. Phil. Soc. 123, 501-529 (1998)

Incompressibility of closed surfaces in toroidally alternating link complements
Koya Shimokawa,
Osaka J. Math. 35, 191-234 (1998)

Proceedings :

Tangle analysis of DNA unlinking by the Xer/FtsK system
Koya Shimokawa, Kai Ishihara, and Mariel Vazquez,
to appear in Bussei Kenkyu (2009).
Proceedings of the International Conference "Knots and soft-matter physics: topology of polymers and related topics in physics, mathematics and biology",

A condition for a graph in the disc to contain the half hemisphere of the dodecahedron
-- Application to Dehn surgery theory --
Chuichiro Hayashi and Koya Shimokawa
Interdiscip. Inform. Sci. 7, 5-16 (2001)
Proceedings of the Workshop "Graph Theory and Related Topics"

Tangles with alternating diagrams
--Alternating tanlge decompositions of knots and laminar surgery--
Koya Shimokawa
Proceedings of the 5-th Korea-Japan School of Knots and Links,
267--272 (1997), Center for Applied Mathematics, KAIST, Korea.