Identifiability of Directed-Cycle and Catenary Linear Compartmental Models.

Anne Shiu https://orcid.org/0000-0002-5358-3049

Saber Ahmed Natasha Crepeau Paul r. Dessauer Alexis Edozie Odalys Garcia-Lopez Tanisha Grimsley Jordy Lopez Garcia Viridiana Neri Anne Shiu Identifiability of Directed-Cycle and Catenary Linear Compartmental Models. 2026 304-350 25 SIAM J. Appl. Dyn. Syst. 1 https://doi.org/10.1137/25m1728636 db/journals/siamads/siamads25.html#AhmedCDEGGGNS26 streams/journals/siamads

Luis David García-Puente Elizabeth Gross Heather A. Harrington Matthew D. Johnston Nicolette Meshkat Mercedes Pérez Millán Anne Shiu Absolute concentration robustness: Algebra and geometry. 102398 2025 128 J. Symb. Comput. https://doi.org/10.1016/j.jsc.2024.102398 db/journals/jsc/jsc128.html#GarciaPuenteGHJMMS25 streams/journals/jsc

Allison McClure Anne Shiu On the connectedness of multistationarity regions of small reaction networks. 102323 2024 125 J. Symb. Comput. https://doi.org/10.1016/j.jsc.2024.102323 db/journals/jsc/jsc125.html#McClureS24

Cashous Bortner Elizabeth Gross Nicolette Meshkat Anne Shiu Seth Sullivant Identifiability of linear compartmental tree models and a general formula for input-output equations. 102490 2023 146 Adv. Appl. Math. https://doi.org/10.1016/j.aam.2023.102490 db/journals/aam/aam146.html#BortnerGMSS23

Alexander Ruys de Perez Laura Felicia Matusevich Anne Shiu Wheels: A new criterion for non-convexity of neural codes. 102567 2023 September 150 Adv. Appl. Math. https://doi.org/10.1016/j.aam.2023.102567 db/journals/aam/aam150.html#PerezMS23

Badal Joshi Nidhi Kaihnsa Tung D. Nguyen Anne Shiu Prevalence of Multistationarity and Absolute Concentration Robustness in Reaction Networks. 2260-2283 2023 December 83 SIAM J. Appl. Math. 6 https://doi.org/10.1137/23m1549316 db/journals/siamam/siamam83.html#JoshiKNS23

Patrick Chan Katherine Johnston Joseph Lent Alexander Ruys de Perez Anne Shiu Nondegenerate Neural Codes and Obstructions to Closed-Convexity. 114-145 2023 March 37 SIAM J. Discret. Math. 1 https://doi.org/10.1137/21m1452147 db/journals/siamdm/siamdm37.html#ChanJLPS23

Elizabeth Gross Nicolette Meshkat Anne Shiu Identifiability of linear compartmental models: The singular locus. 102268 2022 133 Adv. Appl. Math. https://doi.org/10.1016/j.aam.2021.102268 db/journals/aam/aam133.html#GrossMS22

Alexander Ruys de Perez Laura Felicia Matusevich Anne Shiu Neural codes and the factor complex. 2020 114 Adv. Appl. Math. https://doi.org/10.1016/j.aam.2019.101977 https://www.wikidata.org/entity/Q126567712 db/journals/aam/aam114.html#PerezMS20

Aaron Chen Florian Frick Anne Shiu Neural Codes, Decidability, and a New Local Obstruction to Convexity. 44-66 2019 3 SIAM J. Appl. Algebra Geom. 1 https://doi.org/10.1137/18M1186563 https://www.wikidata.org/entity/Q128350295 db/journals/siaga/siaga3.html#ChenFS19

Elizabeth Gross Heather A. Harrington Nicolette Meshkat Anne Shiu Linear Compartmental Models: Input-Output Equations and Operations That Preserve Identifiability. 1423-1447 2019 79 SIAM J. Appl. Math. 4 https://doi.org/10.1137/18M1204826 db/journals/siamam/siamam79.html#GrossHMS19

Rebecca Garcia Luis David García-Puente Ryan Kruse Jessica Liu Dane Miyata Ethan Petersen Kaitlyn Phillipson Anne Shiu Gröbner bases of neural ideals. 2018 28 Int. J. Algebra Comput. 4 https://doi.org/10.1142/S0218196718500261 db/journals/ijac/ijac28.html#GarciaGKLMPPS18 553-571

Aaron Chen Florian Frick Anne Shiu Neural codes, decidability, and a new local obstruction to convexity. 2018 abs/1803.11516 CoRR http://arxiv.org/abs/1803.11516 db/journals/corr/corr1803.html#abs-1803-11516

Carina Curto Elizabeth Gross Jack Jeffries Katherine Morrison Zvi Rosen Anne Shiu Nora Youngs Algebraic signatures of convex and non-convex codes. 2018 abs/1807.02741 CoRR http://arxiv.org/abs/1807.02741 db/journals/corr/corr1807.html#abs-1807-02741

Caitlin Lienkaemper Anne Shiu Zev Woodstock Obstructions to convexity in neural codes. 31-59 2017 85 Adv. Appl. Math. https://doi.org/10.1016/j.aam.2016.11.006 https://www.wikidata.org/entity/Q57426806 db/journals/aam/aam85.html#LienkaemperSW17

Carina Curto Elizabeth Gross Jack Jeffries Katherine Morrison Mohamed Omar Zvi Rosen Anne Shiu Nora Youngs What Makes a Neural Code Convex? 222-238 2017 1 SIAM J. Appl. Algebra Geom. 1 https://doi.org/10.1137/16M1073170 db/journals/siaga/siaga1.html#CurtoGJMORSY17

Badal Joshi Anne Shiu Which Small Reaction Networks Are Multistationary? 802-833 2017 16 SIAM J. Appl. Dyn. Syst. 2 https://doi.org/10.1137/16M1069705 db/journals/siamads/siamads16.html#JoshiS17

Bryan Félix Anne Shiu Zev Woodstock Analyzing multistationarity in chemical reaction networks using the determinant optimization method. 60-73 2016 287-288 Appl. Math. Comput. https://doi.org/10.1016/j.amc.2016.04.030 db/journals/amc/amc287.html#FelixSW16

Stefan Müller 0009 Elisenda Feliu Georg Regensburger Carsten Conradi Anne Shiu Alicia Dickenstein Sign Conditions for Injectivity of Generalized Polynomial Maps with Applications to Chemical Reaction Networks and Real Algebraic Geometry. 69-97 2016 16 Found. Comput. Math. 1 https://doi.org/10.1007/s10208-014-9239-3 https://www.wikidata.org/entity/Q122417795 db/journals/focm/focm16.html#0009FRCSD16

Manoj Gopalkrishnan Ezra Miller Anne Shiu A Geometric Approach to the Global Attractor Conjecture. 758-797 2014 13 SIAM J. Appl. Dyn. Syst. 2 https://doi.org/10.1137/130928170 https://www.wikidata.org/entity/Q123113078 db/journals/siamads/siamads13.html#GopalkrishnanMS14

Badal Joshi Anne Shiu Simplifying the Jacobian Criterion for Precluding Multistationarity in Chemical Reaction Networks. 857-876 2012 72 SIAM J. Appl. Math. 3 https://doi.org/10.1137/110837206 db/journals/siamam/siamam72.html#JoshiS12

Manoj Gopalkrishnan Ezra Miller Anne Shiu A projection argument for differential inclusions, with applications to persistence of mass-action kinetics http://arxiv.org/abs/1208.0874 2012 CoRR abs/1208.0874 db/journals/corr/corr1208.html#abs-1208-0874

François Boulier Anne Shiu Thomas Sturm 0001 Andreas Weber 0004 Symbolic Methods for Chemical Reaction Networks (Dagstuhl Seminar 12462). 66-86 2012 2 Dagstuhl Reports 11 https://doi.org/10.4230/DagRep.2.11.66 db/journals/dagstuhl-reports/dagstuhl-reports2.html#BoulierSS012

Anne Shiu Algebraic methods for biochemical reaction network theory. 2010 University of California, Berkeley, USA http://www.escholarship.org/uc/item/0n79k458 http://n2t.net/ark:/13030/m5zc872p https://www.base-search.net/Record/a5234a9f6bde1879fa943bd4d75a498d664c49740d8bde6cb92c05272717f11b base-search.net (ftcdlib:qt0n79k458)

David F. Anderson Anne Shiu The Dynamics of Weakly Reversible Population Processes near Facets. 1840-1858 2010 70 SIAM J. Appl. Math. 6 https://doi.org/10.1137/090764098 db/journals/siamam/siamam70.html#AndersonS10

Gheorghe Craciun Alicia Dickenstein Anne Shiu Bernd Sturmfels Toric dynamical systems. 1551-1565 2009 44 J. Symb. Comput. 11 https://doi.org/10.1016/j.jsc.2008.08.006 db/journals/jsc/jsc44.html#CraciunDSS09

Jason Morton Lior Pachter Anne Shiu Bernd Sturmfels Oliver Wienand Convex Rank Tests and Semigraphoids. 1117-1134 2009 23 SIAM J. Discret. Math. 3 https://doi.org/10.1137/080715822 db/journals/siamdm/siamdm23.html#MortonPSSW09

Raymond Hemmecke Jason Morton Anne Shiu Bernd Sturmfels Oliver Wienand Three Counter-Examples on Semi-Graphoids. 239-257 2008 17 Comb. Probab. Comput. 2 https://doi.org/10.1017/S0963548307008838 db/journals/cpc/cpc17.html#HemmeckeMSSW08

Anne Shiu The Smallest Multistationary Mass-Preserving Chemical Reaction Network. 172-184 2008 AB https://doi.org/10.1007/978-3-540-85101-1_13 conf/ab/2008 db/conf/ab/ab2008.html#Shiu08 Jason Morton Lior Pachter Anne Shiu Bernd Sturmfels Oliver Wienand Geometry of rank tests. 207-214 2006 Probabilistic Graphical Models http://www.utia.cas.cz/files/mtr/pgm06/7_paper.pdf conf/pgm/2006 db/conf/pgm/pgm2006.html#MortonPSSW06 Saber Ahmed David F. Anderson Cashous Bortner François Boulier Patrick Chan Aaron Chen Carsten Conradi Gheorghe Craciun Natasha Crepeau Carina Curto Paul r. Dessauer Alicia Dickenstein Alexis Edozie Elisenda Feliu Bryan Félix Florian Frick Jordy Lopez Garcia Rebecca Garcia Odalys Garcia-Lopez Luis David García-Puente Manoj Gopalkrishnan Tanisha Grimsley Elizabeth Gross Heather A. Harrington Raymond Hemmecke Jack Jeffries Katherine Johnston Matthew D. Johnston Badal Joshi Nidhi Kaihnsa Ryan Kruse Joseph Lent Caitlin Lienkaemper Jessica Liu Laura Felicia Matusevich Allison McClure Nicolette Meshkat Mercedes Pérez Millán Ezra Miller Dane Miyata Katherine Morrison Jason Morton Stefan Müller 0009 Viridiana Neri Tung D. Nguyen Mohamed Omar Lior Pachter Alexander Ruys de Perez Ethan Petersen Kaitlyn Phillipson Georg Regensburger Zvi Rosen Thomas Sturm 0001 Bernd Sturmfels Seth Sullivant Andreas Weber 0004 Oliver Wienand Zev Woodstock Nora Youngs