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)

Tangle analysis of DNA unlinking by the Xer/FtsK system
Koya Shimokawa, Kai Ishihara, and Mariel Vazquez,
Bussei Kenkyu 92 no.1 89-92 (2009)
Proceedings of the International Conference "Knots and soft-matter physics: topology of polymers and related topics in physics, mathematics and biology",

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)

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"

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)

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.