Books for reference

Algorithms

• Introduction to algorithms - Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, Clifford Stein
• Algorithms - Christos Papadimitriou, Sanjoy Dasgupta, Umesh Vazirani
• Algorithm design - Jon Kleinberg, Eva Tardos
• Foundations of Computer Science: C Edition - Alfred V. Aho, Jeffrey D. Ullman
• The Design and Analysis of Computer Algorithms - Alfred V. Aho, John E. Hopcroft, Jeffrey D. Ullman
• Algorithms in C, Parts 1-4: Fundamentals, Data Structures, Sorting Searching - Robert Sedgewick
• Compared to what?: An introduction to the analysis of algorithms - Gregory J. E. Rawlins

• Programming pearls - Jon Bentley
• Data Structures with C - Seymour Lipschutz (Schaum's outlines)
• Fundamentals of Computer Algorithms - Ellis Horowitz, Sartaj Sahni

Mathematics

• Discrete mathematics and its applications - Kenneth H. Rosen
• Discrete mathematics - Norman L. Biggs
• p-adic Numbers, p-adic Analysis, and Zeta-Functions - Neal Koblitz

• A book of abstract algebra (2e) - Charles C. Pinter

• Calculus for scientists and engineers: An analytical approach - K. D. Joshi

• Thomas' Calculus (12e) - George B. Thomas Jr., Maruice D. Weir, Joel R. Hass

• Applied abstract algebra (2e) - Rudolf Lidl, Günter Pilz

• An introduction to the theory of numbers - G. H. Hardy, E. M. Wright

• Analysis - I (3e) - Terrence Tao

• Mathematical Analysis - Tom Apostol

• Understanding Analysis - Stephen Abbott

• Geometric algebra - Emil Artin

Article/essay:

• How to write mathematics - Paul R. Halmos

Formal methods

• Principles of abstract interpretations - Patrick Cousot
• Principles of Cyber-Physical Systems - Rajeev Alur
• Handbook of satisfiability - Armin Biere, Marijn Heule, Hans van Maaren, Toby Walsh
• SAT SMT by example - pdf

Types and programming languages

• Types and Programming Languages - Benjamin C. Pierce
• Advanced topics in types and programming languages - Benjamin C. Pierce
• Practical foundations for programming languages - Robert Harper
• Theories of programming languages - John C. Reynolds
• The formal semantics of programming languages: An introduction - Glynn Winskel
• Call by push-value: A functional/imperative synthesis - P.B. Levy
• Purely functional data structures - Chris Okasaki
• How to design programs (HtDP) - Matthias Felleisen, Robert Bruce Findler, Matthew Flatt, and Shriram Krishnamurthi (online)
• Type theory and formal proofs - Rob Nederpelt, Herman Geuvers
• The algebra of programming - Richard Bird, Oege de Moor

• Programming Languages: Application and Interpretation (2e) - Shriram Krishnamurthi

• Semantics with applications - Hanne Riis Nielson, Flemming Nielson

• Structure and Interpretation of Computer Programs - Harold Abelson, Gerald Sussman

• Concepts of programming languages, 10th edition - Robert Sebesta

• Control structures in programming languages: from goto to algebraic effects - Xavier Leroy link)

• Proofs and Types - Jean-Yves Girard along with Paul Taylor, Yves Lafont

• Lectures on the Curry-Howard isomorphism - Morten Heine Sorensen, Pawel Urzyczyn (advanced)
• Type Theory and Functional Programming - Simon Thompson
• Basic simple type theory - Hindley (advanced)
• Term Rewriting and All That - Franz Baader, Tobias Nipkow
• The little typer - Daniel P. Friedman, David Thrane Christiansen
• Formal Reasoning About Programs - Adam Chlipala ᵖᵈᶠ
• Compiling with continuations - Andrew Appel
• Semantics with applications: A Formal Introduction - Hanne Riis Nielson, Flemming Nielson
• Introduction to Neural Network Verification - Aws Albarghouthi

• Handbook of automated reasoning - Alan Robinson, Andrei Voronkov

• Unifying theories of programming - C. A. R. Hoare, He Jifeng

• Homotopy type theory - Univalent foundations of mathematics (tex source)
• Introduction to homotopy type theory - Egbert Rijke

Isabelle:

• Functional data structures and algorithms: A proof assistant approach - Tobias Nipkow (ᵖᵈᶠ)
• Concrete semantics with Isabelle/HOL - Tobias Nipkow, Gewin Klein (ᵖᵈᶠ)

Lean:

• The hitchhiker's guide to logical verification (ᵖᵈᶠ)

Logic

• Logic in computer science modelling and reasoning about systems - Michael Huth, Mark Ryan
• A Computational Logic - Robert S. Moore, J Strother Moore
• Handbook of practical logic and automated reasoning - John Harrison
• Handbook of logic in computer science
• Handbook of the history of logic

Theory of computation

• Introduction to the theory of computation - Micheal Sipser
• An introduction formal languages and automata - Peter Linz
  • An introduction formal languages and automata (7e) - Peter Linz, Susan H. Rodger
• Intro to Automata Theory, Languages and Computation - Motwani, Ullman and Hopcroft
• Introduction to languages and the theory of computation - John C. Martin
• Automata and Computability - Dexter C. Kozen
• Theory of computation - Dexter C. Kozen

Compilers and related

• Compilers: Principles, techniques and tools, 1st edition (The green dragon book) - Alfred V. Aho, Ravi Sethi, Jeffrey D. Ullman
• Compilers: Principles, techniques and tools, 2nd edition (The purple dragon book) - Alfred V. Aho, Monica S. Lam, Ravi Sethi, Jeffrey D. Ullman
• Enginnering a compiler - Keith D. Cooper, Linda Torczon
• Advanced Compiler Design and Implementation - Steven S. Muchnick
• Modern compiler implementation in ML - Andrew W. Appel

• Writing a C compiler - Nora Sandler

• Compiler design in C - Allen Holub link)

• Compiling lambda calculus - Nils M. Holm

• Write your own compiler - Nils M. Holm

• Lisp from nothing - Nils M. Holm

• System software: An introduction to systems programming - Leland L. Beck

• The theory of parsing, translation, and compiling - Alfred V. Aho, Jeffrey D. Ullman

• Recursive Programming Techniques - William H. Burge

• Garbage collection - Richard Jones
• The garbage collection handbook: The art of automatic memory management (2e) - Richard Jones, Anthony Hosking, Eliot Moss ˡ

Graph theory

• Graph theory - Reinhard Diestel ²³
• The Petersen graph - Derek Holton, John Sheehan

Statistics and probability

• The cartoon guide to statistics - Larry Gonick, Woollcott Smith
• How not to be wrong - Jordan Ellenberg
• Statistics and truth: Putting chance to work - C. R. Rao
• Art of statistics - David Spiegelhalter

• How to lie with statistics - Darrell Huff

• The truthful art: Data, charts, and maps for communication - Alberto Cairo (about data visualization)

• High-dimensional statistics: A non-asymptotic viewpoint - Martin J. Wainwright
• High-dimensional probability: An introduction with applications in data science - Roman Vershynin (pdf)

• A practical guide to quantitative finance interviews - Xinfeng Zhou

Computer architecture

• Computer ogranization - Carl Hamacher, Zvonko Vranesic, Safwat Zaky
• Computer organization and design (RISC-V edition) - David A. Patterson, John L. Hennessy
• Computer organization: A quantitative approach - David A. Patterson, John L. Hennessy

Switching theory and logic design

• Digital logic and computer design - Morris Mano
• Switching and finite automata theory - Zvi Kohavi, Niraj K. Jha
• Synthesis and optimization of digital circuits - Giovanni De Micheli

• The elements of computing systems: Building a modern computer from first principles - Noam Nisan, Shimon Schocken (Nand to Tetris)
• Getting started with FPGAs - Russell Merrick

Electrical and electronics

• Practical electronics for inventors 4e - Paul Scherz, Simon Mon

Operating systems

• Operating system concepts, 9th edition - Greg Gagne, Peter Baer Galvin, Avi Silberschatz
• Modern operating systems - Andrew S. Tanenbaum
• Real-time systems - Jane W. S. Liu

Computer networks

• Computer Networks: A systems approach - Bruce S. Davie, Larry L. Peterson
• Computer Networks - Andrew S. Tanenbaum

DBMS

• Fundamentals of database system - Elmasri, Navathe
• Database system concepts - Henry F Korth, Abraham Silberschatz

Computer graphics

• Computer Graphics (C version) - Donald Hearn & Pauline Baker

Cryptography

• Cryptography and network security - principles and practices - William Stallings

AI/ML

• Artificial Intelligence: A modern approach - Stuart Russell, Peter Norvig
• Artificial Intelligence - Elaine A. Rich and Kevin Knight
• Pattern recognition and Machine learning - Christopher Bishop
• Deep learning - Aaron Courville, Ian Goodfellow, Yoshua Bengio (link)
• Machine learning: A probabilistic perspective - Kevin P. Murphy
• Introduction to statistical learning (with applications in Python) - Gareth James, Daniela Witten, Trevor Hastie, Robert Tibshirani, Jonathan Taylor
• Introduction to machine learning - Ethem Alpaydin

Electronics and electrical

• Microchip Fabrication: A Practical Guide to Semiconductor Processing (6e) - by Peter Van Zant

• Microelectronics Circuits: Theory and applications - Adel S. Sedra, Kenneth C. Smith (analog electronics)

• Design of Analog CMOS Integrated Circuits - Behzad Razavi (analog electronics)

• Fundamentals of semiconductor manufacturing and process control - Gary S. May, Costas J. Spanos

• Formal verification: An essential toolkit for modern VLSI design - Erik Seligman, Tom Schubert, M V Achutha Kiran Kumar

• A Practical Introduction to PSL - Cindy Eisner, Dana Fisman

• Introduction to VLSI systems - Carver Mead, Lynn Conway

Information theory

• Fundamentals of error-correcting codes - W. Cary Huffman, Vera Pless
• Error control coding: fundamentals and applications - Daniel J. Costello, Shu Lin

Linear algebra

• Introduction to linear algebra - Gilbert Strang
• Thirty-three miniatures: Mathematical and algorithmic applications of linear algebra ᵈʳᵃᶠᵗ - Jiří Matoušek
• Linear algebra done right - Sheldon Axler ᵖᵈᶠ

• Introduction to linear algebra - Gilbert Strang
• Linear algebra - Jim Hefferon (free with TeX source: link)
• Introduction to quantum algorithms via linear algebra - Richard J Lipton
• Interactive linear algebra - Dan Margalit, Joseph Rabinoff, Ben Williams, Ulrik Buchholtz (ˡⁱⁿᵏ)

Quantum computing

• An introduction to quantum computing - Phillip Kaye, Raymond Laflamme, Michele Mosca
• Quantum computation and quantum information - Michael Nielsen, Isaac Chuang

Game theory

• Introduction to game theory - Martin J. Osborne
• Handbook of Game Theory with Economic Applications (4 volumes)

Writing

• Style: Toward Clarity and Grace - Gregory G. Colomb, Joseph M. Williams
• The elements of style - Strunk and White
• The Sense of Style: The Thinking Person’s Guide to Writing in the 21st Century - Steven Pinker
• The elements of eloquence - Mark Forsyth
• BUGS in writing: A Guide to Debugging Your Prose - Lyn Dupré
• How to write a lot: A practical guide to academic writing - Paul J. Silvia

General

• The Universal Computer: The Road from Leibniz to Turing - Martin Davis

• Computability and unsolvability - Martin Davis

• Gödel's proof - Ernest Nagel, James R. Newman

• Computability: Turing, Gödel, Church, and Beyond - Edited by B. Jack Copeland, Carl J. Posy, and Oron Shagrir

• Infinity and the Mind - Rudy Rucker

• One Two Three… Infinity - George Gamow

• Gödel, Escher, Bach - Douglas Hofstadter

• The First Six Books Of The Elements Of Euclid - Euclid, Oliver Byrne (a modern rendition here)

• How to solve it - G. Pólya
• How to solve it by computer - R. G. Dromey
• God created the integers - Stephen Hawking
• Beyond infinity: An expedition to the outer limits of mathematics - Eugenia Cheng
• The colossal book of Mathematics - Martin Gardner

• The music of the primes - Marcus du Sautoy
• How to cut a cake: And other mathematical conundrums - Ian Stewart

• Love and Math - Edward Frenkel

• The undecidable - Martin Davis (editor)

• Calendrical Calculations: The Millennium Edition - Edward M. Reingold, Nachum Dershowitz ³⁶

• The cartoon guide to calculus - Larry Gonick

• Birth of a theorem: A mathematical adventure - Cedric Villani

Not-so-familiar topics

• Foundations of probabilistic programming - Edited by Gilles Barthe, Joost-Pieter Katoen, Alexandra Silva

Miscellaneous

• Design patterns: Elements of reusable object-oriented software - Erich Gamma, Richard Helm, Ralph Johnson, John Vlissides

• Hacker's Delight - Henry S. Warren Jr.

• The Structure of Scientific Revolutionsʷ - Thomas S. Kuhn

• 24 deadly sins of software security: Programming flaws and how to fix them - David Le Blanc, John Viega, Michael Howard

• Crafting interpreters - Robert Nystrom

• Game programming patterns - Robert Nystrom

• Competitive programmer's handbook - Antti Laaksonen

• The visual display of quantitative information - Edward Tufte

Specific programming languages and environments

OCaml:

• OCaml from the very beginning - John Whitington pdf
• More OCaml: Algorithms, methods & diversions - John Whitington
• Real world OCaml (2e) - Yaron Minsky, Anil Madhavapeddy

Rust:

• Rust atomics and locks: Low-level concurrency in practice - Mara Bos ᵖᵈᶠ

C:

• The C programming language, 2nd edition - Brian Kernighan, Dennis Ritchie
• C traps and pitfalls - Andrew Koenig
• Numerical Recipes in C: The Art of Scientific Computing (2e) - William H. Press, Saul A. Teukolsky, William T. Vetterling, Brian P. Flannery

C++:

• Effective C++ - Scott Meyers
• More effective C++ - Scott Meyers
• Effective STL - Scott Meyers
• Object-oriented programming in C++, 4th edition - Robert Lafore
• Functional Programming in C++ - Ivan Čukić (Manning publications)

Haskell:

• Practical Haskell: A real world guide to programming (2e) - Alejandro Serrano Mena
• Real world haskell - Bryan O'Sullivan, Don Stewart, John Goerzen ³⁰
• Thinking functionally with Haskell - Richard Bird
• Programming in Haskell (2e) Second Edition - Graham Hutton
• Haskell in depth - Vitaly Bragilevsky
• Retrocomputing with Clash: Haskell for FPGA Hardware Design (a Haskell extension) - Gergő Érdi
• Optics by example: Functional lenses in Haskell - Chris Penner

• The Haskell school of music: From signals to symphonies - Paul Hudak, Donya Quick

• Thinking with Types: Type-Level Programming in Haskell - Sandy Maguire

Unix:

• The UNIX programming environment - Brian Kernighan, Rob Pike
• The Design of the UNIX Operating System - Maurice J. Bach
• Lion's commentary on UNIX (Lion's book) - John Lions
• The AWK programming language - Alfred Aho, Brian Kernighan, Peter J. Weinberger

sml:

• Commentary on Standard ML - Robert Harper, Mads Tofte
• ML for the Working Programmer - Lawrence C. Paulson
• Elements of ML programming - Jeffrey Ullman

Java:

• Functional Programming in Java (2e) - Venkat Subramaniam
• Functional Programming in Java - Pierre-Yves Saumont

prolog:

• The art of Prolog - Leon Sterling, Ehud Shapiro
• Programming in Prolog (5e) - W. F. Clocksin, C. S. Mellish
• Clause and effect - W. F. Clocksin

ACL2:

• Computer-aided reasoning: An approach - Matt Kaufmann, Panagiotis Manolios, and J Strother Moore ³⁷

lean prover:

• The Hitchhiker’s Guide to Logical Verification

R:

• R Graphics Cookbook (2e) - Winston Chang
  • https://r-graphics.org/

Other resources

• Advice to a young Mathematician - M. F. Atiyah
• Using LaTeX to write a PhD thesis - Nicola L. C. Talbot
• The TeXbook Book - Donald Knuth
• More math into LaTeX - George Grätzer
• LaTeX: A Document Preparation System - Leslie Lamport
• Xv6: A kernel written in ANSI C, modeled on V6 UNIX.

Research life

• How to Get a PhD: A Handbook for Students and their Supervisor - Estelle M. Phillips, Derek S. Pugh
• The Good Supervisor: Supervising Postgraduate and Undergraduate Research for Doctoral Theses and Dissertations - Gina Wisker
• Tuesdays with Morrie - Mitch Albom
• Grading for growth - David Clark, Robert Talbert