Automata and one-dimensional TQFTs with defects, (with Paul Gustafson, Mee Seong Im, Remy Kaldawy and Zachary Lihn), arXiv:2301.00700.
 One-dimensional theories with defects: the linear case, (with Mee Seong Im), arXiv:2210.00371.
 Odd two-variable Soergel bimodules and Rouquier complexes, (with Krzysztof Putyra and Pedro Vaz), arXiv:2205.12794.
 Topological theories and automata, (with Mee Seong Im), arXiv:2202.13398.
 Categorical lifting of the Jones polynomial: a survey, (with Robert Lipshitz), arXiv:2202.02473.
 Monoidal categories, representation gap and cryptography, (with Maithreya Sitaraman and Daniel Tubbenhauer), arXiv:2201.01805.
 Foams, iterated wreath products, field extensions and Sylvester sums (with Mee Seong Im), arXiv:2107.07845.
 Anchored foams and annular homology (with Rostislav Akhmechet), arXiv:2105.00921.
 Planar diagrammatics of self-adjoint functors and recognizable tree series (with Robert Laugwitz), arXiv:2104.01417.
 Two-dimensional topological theories, rational functions and their tensor envelopes (with Victor Ostrik and Yakov Kononov), arXiv:2011.14758.
 Conical SL(3) foams (with Louis-Hadrien Robert), arXiv:2011.11077.
 Decorated one-dimensional cobordisms and tensor envelopes of noncommutative recognizable power series, arXiv:2010.05730.
 Evaluating thin flat surfaces (with You Qi and Lev Rozansky), Communications in Mathematical Physics 385 (2021), 1835–1870, arXiv:2009.01384.
 Bilinear pairings on two-dimensional cobordisms and generalizations of the Deligne category (with Radmila Sazdanovic), arXiv:2007.11640.
 Universal construction of topological theories in two dimensions, arXiv:2007.03361.
 Link homology and Frobenius extensions II, (with Louis-Hadrien Robert), to appear in Fundamenta Mathematicae, arXiv:2005.08048.
 A deformation of Robert-Wagner foam evaluation and link homology (with Nitu Kitchloo), arXiv:2004.14197.
 Diagrammatic categorification of the Chebyshev
polynomials of the second kind
(with Radmila Sazdanovic),
Journal of Pure and Applied Algebra 225, is.6, June 2021, 106592, arXiv:2003.11664.
A faithful braid group action
on the stable category of tricomplexes
(with You Qi),
SIGMA (Symm. Integr. Geom. Methods Appl.) 16 (2020), 019, 32 pages, arXiv:1911.02503.
 Foam evaluation and Kronheimer--Mrowka theories (with Louis-Hadrien Robert), Advances in Mathematics 376 (2021), 107433, arXiv:1808.09662.
 Braid group actions from categorical
symmetric Howe duality on deformed Webster algebras,
(with Aaron D. Lauda, Joshua Sussan, and Yasuyoshi Yonezawa), to appear in Transformation groups, arXiv:1802.05358.
 Towards functor exponentiation, (with Yin Tian), Journal of Algebra 505 (2017), arXiv:1712.02208.
 p-DG cyclotomic nilHecke algebras (with You Qi and Joshua Sussan), arXiv:1711.07159.
 How to categorify the ring of integers localized at two, (with Yin Tian), Quantum Topology 10, is.4 (2019), 723–775, arXiv:1702.07466.
 The Soergel category and the redotted Webster algebra (with Joshua Sussan), Journal of Pure and Applied Algebra 222, is.8, August 2018, 1957-2000, arXiv:1605.02678.
 Linearization and categorification, arXiv:1603.08223.
 A categorification of the positive half of quantum gl(m|1) (with Joshua Sussan), Transactions of the AMS 369 no.3 (2017), 1627-1664, arXiv:1406.1676.
 Positive half of the Witt algebra acts on triply graded link homology (with Lev Rozansky), Quantum Topology 7, no.4 (2016), 737-795, arXiv:1305.1642.
 An approach to categorification of small quantum groups (with You Qi), Quantum Topology 6, no.2 (2015), 185-311, arXiv:1208.0616.
 The odd nilHecke algebra and its diagrammatics (with Alexander Ellis and Aaron Lauda), Int. Math. Research Notices v.2014, no.4 (2014), 991-1062, arXiv:1111.1320.
 The Hopf algebra of odd symmetric functions (with Alexander Ellis), Advances in Math. 231, no.2 (2012), 965-999, arXiv:1107.5610.
 Categorification of the polynomial ring (with Radmila Sazdanovic), Fundamenta Mathematicae 230, no.3 (2015), 251-280, arXiv:1101.0293.
 Heisenberg algebra and a graphical calculus, Fundamenta Mathematicae 225, (2014), 169-210, arXiv:1009.3295.
 Categorifications from planar diagrammatics, Japanese J. of Mathematics 5, 153--181 (2010), arXiv:1008.5084.
 A categorification of the Casimir of quantum sl(2) (with Anna Beliakova and Aaron Lauda), Advances in Math. 230, is.3 (2012), 1442-1501, arXiv:1008.0370.
 How to categorify one-half of quantum gl(1|2), Banach Center Publications 103, Pt.3: Khots in Poland III (2014), 211-232, arXiv:1007.3517.
 Extended graphical calculus for categorified quantum sl(2) (with Aaron Lauda, Marco Mackaay, and Marko Stosic), Memoirs of the AMS 219, no.1029 (2012), arXiv:1006.2866.
 Diagrammatics for Soergel cattegories (with Ben Elias), Int. J. Math. Math. Sci. (2010) Article 978635, arXiv:0902.4700.
 A diagrammatic approach to categorification of quantum groups III (with Aaron Lauda), Quantum Topology 1, is.1 (2010), 1-92, arXiv:0807.3250.
 A diagrammatic approach to categorification of quantum groups II (with Aaron Lauda), Trans. Amer. Math. Soc. 363 (2011), 2685-2700, arXiv:0804.2080.
 Notes on link homology (with Marta Asaeda), in Low-Dimensional Topology, ed. T.Mrowka and P.Ozsvath, IAS/Park City Mathematics Series, 139-196, 2009, arXiv:0804.1279.
 A diagrammatic approach to categorification of quantum groups I (with Aaron Lauda), Representation Theory 13 (2009), 309-347, arXiv:0803.4121.
 A brief review of abelian categorifications (with Volodymyr Mazorchuk and Catharina Stroppel), Theory and Applications of Categories 22, n.19 (2009), 479-508, arXiv:math.RT/0702746.
 Virtual crossings, convolutions and a categorification of the SO(2N) Kauffman polynomial (with Lev Rozansky), Journal of G�kova Geometry Topology 1 (2007), 116-214, arXiv:math.QA/0701333.
 An invariant of tangle cobordisms via subquotients of arc rings (with Yanfeng Chen), arXiv:math.QA/0610054.
 Braid cobordisms, triangulated categories, and flag varieties (with Richard Thomas), Homology, Homotopy and Applications 9 (2007), 19--94, arXiv:math.QA/0609335.
 A categorification of integral Specht modules (with Volodymyr Mazorchuk and Catharina Stroppel), Proceedings of the AMS, vol.136, no.4 (2008), 1163-1169, arXiv:math.RT/0607630.
 Link homology and categorification, Proceedings of the ICM-2006, Madrid, vol.2 989--999, arXiv:math.QA/0605339.
 A categorification of finite-dimensional irreducible representations of quantum sl(2) and their tensor products (with Igor Frenkel and Catharina Stroppel), Selecta Mathematica, vol.12, n.3-4 (2006), 379-431, arXiv:math.QA/0511467.
 Triply-graded link homology and Hochschild homology of Soergel bimodules, International Journal of Math., vol.18, no.8 (2007), 869-885, arXiv:math.GT/0510265.
 Hopfological algebra and categorification at a root of unity: the first steps, to appear in Communications in Contemporary Math., arXiv:math.QA/0509083.
 Matrix factorizations and link homology II (with Lev Rozansky), Geometry and Topology, vol.12 (2008), 1387-1425, arXiv:math.QA/0505056.
 Link homology and Frobenius extensions, Fundamenta Mathematicae, 190 (2006), 179-190, arXiv:math.QA/0411447.
 Topological Landau-Ginzburg models on a world-sheet foam (with Lev Rozansky), Adv. Theor. Math. Phys., vol.11, no.2 (2007), 233-259, arXiv:hep-th/0404189.
 Matrix factorizations and link homology (with Lev Rozansky), Fundamenta Mathematicae, vol.199 (2008), 1-91, arXiv:math.QA/0401268.
 Homological realization of Nakajima varieties and Weyl group actions (with Igor Frenkel and Olivier Schiffmann), Compositio Mathematica 141, n. 6 (2005) 1504-1530, arXiv:math.QA/0311485.
 sl(3) link homology I, Algebr. Geom. Topol. 4 (2004) 1045--1081 (electronic), arXiv:math.QA/0304375.
 Categorifications of the colored Jones polynomial, J. Knot theory and its Ramifications 14 (2005) no.1, 111--130, arXiv:math.QA/0302060.
 An invariant of tangle cobordisms, Trans. Amer. Math. Soc. 358 (2006), 315-327, arXiv:math.QA/0207264.
 Categorification of some level two representations of sl(n) (with Stella Huerfano), J. Knot theory and its Ramifications 15 (2006) no.6, 695-713, arXiv:math.QA/0204333.
 Crossingless matchings and the cohomology of (n,n) Springer varieties, Communications in Contemporary Math. 6 (2004) no.2, 561--577, arXiv:math.QA/0202110.
 Patterns in knot cohomology I, Experimental mathematics 12 (2003) no.3, 365--374, arXiv:math.QA/0201306.
 A functor-valued invariant of tangles, Algebr. Geom. Topol. 2 (2002), 665--741 (electronic), arXiv:math.QA/0103190.
 Quivers, Floer cohomology, and braid group actions (with Paul Seidel), J. Amer. Math. Soc. 15 (2002), no. 1, 203--271 (electronic), arXiv:math.QA/0006056.
A categorification of the Temperley-Lieb algebra and Schur quotients of U(sl(2))
via projective and Zuckerman functors
(with Joseph Bernstein and Igor Frenkel), Selecta Math. (N.S.) 5 (1999), no. 2, 199--241, arXiv:math.QA/0002087.
 A category for the adjoint representation (with Stella Huerfano), J. Algebra 246 (2001), no. 2, 514--542, arXiv:math.QA/0002060.
 A categorification of the Jones polynomial, Duke Math. J. 101 (2000), no. 3, 359--426, arXiv:math.QA/9908171.
 NilCoxeter algebras categorify the Weyl algebra, Comm. Algebra 29 (2001), no. 11, 5033--5052, arXiv:math.RT/9906166.
 Web bases for sl(3) are not dual canonical (with Greg Kuperberg), Pacific J. Math. 188 (1999), no. 1, 129--153, arXiv:q-alg/9712046.
 Kazhdan-Lusztig polynomials and canonical basis (with Igor Frenkel and Alexander Kirillov Jr), Transform. Groups 3 (1998), no. 4, 321--336, arXiv:q-alg/9709042.
 Graphical calculus, canonical bases and Kazhdan-Lusztig theory, PhD thesis, Yale University, May 1997.
 Canonical bases in tensor products and graphical calculus for Uq(sl2) (with Igor Frenkel), Duke Math. J. 87 (1997) no.3, 409--480.
 Doodle groups, Trans. Amer. Math. Soc. 349 (1997), no. 6, 2297--2315.
 Real K(π,1) arrangements from finite root systems, Math. Res. Lett. 3 (1996), no. 2, 261--274.
 Some remarks on Tabachnikov's invariants of plane curves. J. Knot Theory Ramifications 5 (1996), no. 6, 849--857.
 Representations of tensor categories and Dynkin diagrams (with Pavel Etingof), Internat. Math. Res. Notices (1995) no.5, 235--247. arXiv:hep-th/9408078.
 The set of slice doodles is NP-complete, preprint 1995.
 Surfaces in three-space and braided algebras, preprint 1995.
 New geometrical constructions in low-dimensional topology, preprint 1990.