Y. Murakami

Education

Projects

IDEE: Transition from VWO to WO

An interdisciplinary TU Delft project on the transition from secondary to higher education, focusing on study progress, well-being, and competency development.

Supervision

Current supervision

Postdoc

Alaa Abdalla

Co-supervised with Hylkje Geertsema

2025–present

PhD students

Louisa Henze

2026–present

BSc thesis

Diederik Ten Bosch

Catastrophe Theory in Optical Optimization Landscapes

Double bachelor · Co-supervised with Florian Bociort

2026–present

Completed supervision

Completed theses link to the TU Delft Repository; the honours project links to its resulting preprint.

Visiting PhD students

WhenStudentVisit
June 2025Takatora SuzukiOne-month research visitResulting preprint: How many cherry-picking sequences are needed to reduce all subtrees of a phylogenetic tree?

MSc projects & theses (7)

YearStudentProject / thesis
2026Lars van EeuwijkGrafen, Routes & BrandenMSc BTOI project · Bètatechnische OnderwijsinnovatieCo-supervised with Rutger Ockhorst and Jeroen Spandaw
2026Stephan DemmendalOptimization of Pick Order Assignment to Reduce Aisle Congestion in Manual Order-Picking WarehousesCo-supervised with Teun Janssen
2026Max ReindersDegree-Constrained Graph Burning: Extremal Bounds, Regular Constructions, and α-Angular TreesCo-supervised with Nikolaas Verhulst
2025Britt JanssenFault-tolerant optimization and reconfiguration of actuator allocation in multi-stage rockets
2025Tim LevertTriplet Encoding of Stemmata
2025Merel SusannaGraph burning and cooling: An interactive, probabilistic and optimization approachCo-supervised with Nikolaas Verhulst
2023Christopher ReichlingClasses of Semi-binary Phylogenetic Networks encoded by μ-representationsCo-supervised with Leo van Iersel

BSc projects & theses (10)

YearStudentProject / thesis
2024–2026Bálint KollmannBSc Honours ProjectResulting preprint: How many cherry-picking sequences are needed to reduce all subtrees of a phylogenetic tree?
2026Annabel GrootendorstGraph Burning: Bounds on the burning number of higher-dimensional grid and king’s graphsCo-supervised with Nikolaas Verhulst
2025Nynke BaarsSpectra of binary rooted phylogenetic trees: Exploring the link between tree topology and eigenvalue patterns
2025Abel KooijmansGraph Burning: On necklace graphs and cycle-forestsCo-supervised with Nikolaas Verhulst
2024Marissa van der TolThe burning number conjecture: On cat-constructs and trees with a single degree-2 vertex
2024Marit DeeCounting cherry-picking sequences in phylogenetic trees
2023Lars van EeuwijkComputing the Rooted Triplet Distance for Phylogenetic Trees and Caterpillars
2022Merel SusannaMaking phylogenetic networks orchard: Algorithms to determine if a phylogenetic network is orchard and to transform non-orchard to orchard networksCo-supervised with Leo van Iersel
2020Riche MolReconstruction of Phylogenetic Networks: An algorithm for deconstructing and reconstructing Level-2 Binary Networks based on their distancesCo-supervised with Leo van Iersel
2019Robbert HuijsmanTree-child Network ContainmentCo-supervised with Leo van Iersel and Remie Janssen

Lectures

TermCourse · TU Delft
Fall 2026Spatial Decision Support Systems (BK7955) — BSc Architecture, Urbanism and Building Sciences
Fall 2024–2026Optimization (AM2020: 2024; TW2-13: 2025–2026) — BSc Applied Mathematics
Fall 2024–2026Modelling and Problem Solving (CS4530) — MSc Computer Science Engineering
Fall 2026Calculus (CSE12A) — BSc Computer Science Engineering
Spring 2025, 2026Probability and Statistics (CSE1210) — BSc Computer Science Engineering
Fall 2025Bewijstechnieken (Proofs and Problem Solving) (TW1-11) — BSc Applied Mathematics
Fall 2023, 2024Calculus (Kaleidoscope AM1020: 2023; TW1-12: 2024) — BSc Applied Mathematics
Spring 2024Linear Algebra (CSE1205) — BSc Computer Science Engineering
Fall 2023Advanced Algorithms (IN4344) — MSc Computer Science Engineering
Spring 2022, 2023Calculus II — BSc Aerospace Engineering
Spring 2022Linear Algebra — BSc Aerospace Engineering
Fall 2021Calculus 1 (WI1421LR) — BSc (Online chat moderation)
Fall 2021Linear Algebra (AESB121) — BSc Applied Earth Sciences (Online chat moderation)

Exercise Classes

TermCourse · TU Delft
Fall 2023Optimization (AM2020) — BSc Applied Mathematics
Fall 2022Advanced Algorithms (IN4344) — MSc Computer Science Engineering (Exam grading)
Fall 2020Multivariable Analysis and Linear Algebra (TB132B) — BSc Technology Policy and Management
Fall 2020Differential Equations and Linear Algebra (TB131B) — BSc Technology Policy and Management
Spring 2019–2021, 2023Algebra I (TW1061 and AM1060) — BSc Applied Mathematics
Fall 2018, 2019Analysis and Differential Equations (TB131A) — BSc Technology Policy and Management

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