Algoritmisk dynamik - avkoda och omprogrammera livet – Narsis Kianis team

Publikationer

Alla gruppmedlemmars publikationer

• Journal article: INFORMATION SCIENCES. 2025;720:122520

  Minimal algorithmic information loss methods for dimension reduction, feature selection and network sparsification

  Zenil H; Kiani NA; Adams A; Abrahao FS; Rueda-Toicen A; Zea AA; Ozelim L; Tegner J
• Preprint: ARXIV. 2025

  Assembly Theory Reduced to Shannon Entropy and Rendered Redundant by Naive Statistical Algorithms

  Ozelim L; Uthamacumaran A; Abrahão FS; Hernández-Orozco S; Kiani NA; Tegnér J; Zenil H
• Journal article: ESMO REAL WORLD DATA AND DIGITAL ONCOLOGY. 2025;9:100176

  Benchmarking cancer outcomes in Europe: a scoping review of methodologies and case-mix adjustments

  Thurell J; Doppelbauer L; Verheul EM; Petrov I; Karsten MM; Koppert LB; Bergh J; Fredriksson I; Lindgren P; Kiani N; Hedayati E
• Journal article: JOURNAL OF HEPATOLOGY. 2025;82:s54-s55

  OS-077 Single-cell RNA sequencing of peripheral blood mononuclear cells in patients with acutely decompensated cirrhosis reveals a specific monocyte subset associated with an increased risk of progression to ACLF

  Wirtz TH; Palomino S; Pollmanns MR; Huergo E; Schreibing F; Reißing J; Sanchez C; López-Vicario C; Aransay AM; Baldassarre M; Zaccherini G; Pompili E; Schulz M; Uschner FE; Klein S; Gu W; Schierwagen R; Valainathan S; Verbeeck A; Campion D; Giovo I; Koch A; Kramann R; Bruns T; Kiani N; Caraceni P; Alessandria C; Moreau R; Trebicka J; Clària J; Planell N; Rautou P-E; Trautwein C; Gómez-Cabrero D
• Journal article: ESMO OPEN. 2025;10:105009

  437P Benchmarking breast cancer survival: A case-mix model for fair hospital comparisons of 5 and 10-year breast cancer-specific mortality

  Thurell J; Petrov I; Lindgren P; Bergh J; Fredriksson I; Kiani N; Hedayati E
• Conference publication: JOURNAL OF HEPATOLOGY. 2025;82

  Single-cell RNA sequencing of peripheral blood mononuclear cells in patients with acutely decompensated cirrhosis reveals a specific monocyte subset associated with an increased risk of progression to ACLF

  Wirtz TH; Palomino S; Pollmanns MR; Huergo E; Schreibing F; Reissing J; Sanchez C; Lopez-Vicario C; Aransay AM; Baldassarre M; Zaccherini G; Pompili E; Schulz M; Uschner FE; Klein S; Gu W; Schierwagen R; Valainathan S; Verbeeck A; Campion D; Giovo I; Koch A; Kramann R; Bruns T; Kiani N; Caraceni P; Alessandria C; Moreau R; Trebicka J; Claria J; Planell N; Rautou P-E; Trautwein C; Gomez-Cabrero D
• Preprint: MEDRXIV. 2025

  Single-cell profiling reveals monocyte mitochondrial dysfunction in patients with cirrhosis progressing to acute-on-chronic liver failure

  Wirtz TH; Palomino-Echeverria S; Pollmanns MR; Huergo E; Schreibing F; Reißing J; Sánchez-Garrido C; López-Vicario C; Aransay AM; Baldassare M; Zaccherini G; Pompili E; Schulz M; Uschner FE; Klein S; Gu W; Schierwagen R; Valainathan S; Verbeeck A; Campion D; Giovo I; Schneider KM; Koch A; Kramann R; Bruns T; Kiani N; Stiles L; Caraceni P; Alessandria C; Moreau R; Trebicka J; Clària J; Planell N; Rautou P-E; Trautwein C; Gomez-Cabrero D
• Article: CARDIO-ONCOLOGY. 2025;11(1):5

  Cardiovascular health in breast cancer patients: insight on BRCA1/2 mutations impact

  Mallios P; Manshadi MD; Hubbert L; Aydin T; Maes C; Rantala J; Liljegren A; Kiani NA; Hedayati E
• Article: PLOS COMPUTATIONAL BIOLOGY. 2024;20(12):e1012656

  ClustAll: An R package for patient stratification in complex diseases

  Ortega-Legarreta A; Palomino-Echeverria S; Huergo E; Lagani V; Kiani NA; Rautou P-E; Picola NP; Tegner J; Gomez-Cabrero D
• Article: ISCIENCE. 2024;27(11):111122

  A comparative analysis of blastoid models through single-cell transcriptomics

  Balubaid A; Alsolami S; Kiani NA; Gomez-Cabrero D; Li M; Tegner J
• Journal article: PLOS COMPLEX SYSTEMS. 2024;1(1):e0000014

  Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution

  Abrahão FS; Hernández-Orozco S; Kiani NA; Tegnér J; Zenil H
• Review: NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 2024;10(1):82

  On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures

  Uthamacumaran A; Abrahao FS; Kiani NA; Zenil H
• Preprint: BIORXIV. 2024

  PrePR-CT: Predicting Perturbation Responses in Unseen Cell Types Using Cell-Type-Specific Graphs

  Alsulami R; Lehmann R; Khan SA; Lagani V; Gómez-Cabrero D; Kiani NA; Tegner J
• Journal article: SCIENTIFIC REPORTS. 2024;14(1):16446

  Systematic analysis of microorganisms' metabolism for selective targeting

  Manshadi MD; Setoodeh P; Zare H
• Preprint: ARXIV. 2024

  T- Hop: A framework for studying the importance path information in molecular graphs for chemical property prediction

  Ibraheem A; Kiani N; Tegner J
• Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2024;22(1):599

  A robust clustering strategy for stratification unveils unique patient subgroups in acutely decompensated cirrhosis

  Palomino-Echeverria S; Huergo E; Ortega-Legarreta A; Raposo EMU; Aguilar F; Pena-Ramirez CDL; Lopez-Vicario C; Alessandria C; Laleman W; Farias AQ; Moreau R; Fernandez J; Arroyo V; Caraceni P; Lagani V; Sanchez-Garrido C; Claria J; Tegner J; Trebicka J; Kiani NA; Planell N; Rautou P-E; Gomez-Cabrero D
• Preprint: BIORXIV. 2024

  SpatialDiffusion: Predicting Spatial Transcriptomics with Denoising Diffusion Probabilistic Models

  Khan SA; Lagani V; Lehmann R; Kiani N; Gomez-Cabrero D; Tegner J
• Journal article: ESMO OPEN. 2024;9:103190

  168P Cardiovascular risks in breast cancer: Insights from BRCA1/2 mutation carriers and sporadic cases

  Mallios P; Hedayati E; Kiani N; Rantala J; Hubbert L; Liljegren A
• Preprint: ARXIV. 2024

  Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution

  Abrahão FS; Hernández-Orozco S; Kiani NA; Tegnér J; Zenil H
• Preprint: BIORXIV. 2023

  Joint Learning of Node Semantics and Graph Topology using a Transformer in the sparse network regime

  Ubingazhibov A; Gomez-Cabrero D; Kiani NA; Tegner J
• Article: NATURE MACHINE INTELLIGENCE. 2023;5(12):1437-1446

  Reusability report: Learning the transcriptional grammar in single-cell RNA-sequencing data using transformers

  Khan SA; Maillo A; Lagani V; Lehmann R; Kiani NA; Gomez-Cabrero D; Tegner J
• Preprint: MEDRXIV. 2023

  ClustALL: A robust clustering strategy for stratification of patients with acutely decompensated cirrhosis

  Palomino-Echeverria S; Huergou E; Ortega-Legarre A; Uson EM; Aguilar F; de la Pena C; Lopez-Vicario C; Alessandria C; Laleman W; Queiroz AF; Moreau R; Fernandez J; Arroyo V; Caraceni P; Lagani V; Sanchez C; Claria J; Tegner J; Trebicka J; Kiani N; Planell N; Rautou P-E; Gomez-Cabrero D
• Meeting abstract: BLOOD. 2023;142:4044

  Uncovering the Cis-Regulatory Program of Early Human B-Cell Commitment and Its Implications in the Pathogenesis of B-Cell Acute Lymphoblastic Leukemia

  Planell N; Martinez-de-Morentin X; Mouzo D; Lara-Astiaso D; Vilas-Zornoza A; San-Martin P; Alignani D; Paiva B; Maillo A; Kurowska A; Urdangarin A; Noori P; Ortega-Legarreta A; Hernaez M; Lagani V; Kiani N; Subero IIM; Ramirez RN; Tegner J; Prosper F; Gomez-Cabrero D
• Preprint: BIORXIV. 2023

  Foundation Models Meet Imbalanced Single-Cell Data When Learning Cell Type Annotations

  Alsabbagh AR; de Infante AMR; Gomez-Cabrero D; Kiani N; Khan SA; Tegnér J
• Preprint: ARXIV. 2023

  Whispering LLaMA: A Cross-Modal Generative Error Correction Framework for Speech Recognition

  Radhakrishnan S; Yang C-HH; Khan SA; Kumar R; Kiani NA; Gomez-Cabrero D; Tegner JN
• Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2023;29:479-480

  Exploring genetic clustering of severity markers to identify groups with reduced heterogeneity in multiple sclerosis

  Stridh P; Shchetynsky K; Harroud A; Moridi T; Moylett S; Pukaj A; Esposito F; Gasperi C; Kiani N; Harbo HF; Saarela J; Giovanni MBF; Alfredsson L; Hillert J; Olsson T; Goris A; Hemmer B; Jagodic M; Cotsapas C; Kockum I
• Journal article: QUANTITATIVE BIOLOGY. 2023;11(3):246-259

  LIBRA: an adaptative integrative tool for paired single-cell multi-omics data

  Martinez-de-Morentin X; Khan SA; Lehmann R; Qu S; Maillo A; Kiani NA; Prosper F; Tegner J; Gomez-Cabrero D
• Conference publication: 2023;:1958-1962

  A Parameter-Efficient Learning Approach to Arabic Dialect Identification with Pre-Trained General-Purpose Speech Model

  Radhakrishnan S; Yang C-HH; Khan SA; Kiani NA; Gomez-Cabrero D; Tegner JN
• Article: BREAST. 2023;70:18-24

  Risk-adjusted benchmarking of long-term overall survival in patients with HER2-positive early-stage Breast cancer: A Swedish retrospective cohort study

  Thurell J; Manouchehri N; Fredriksson I; Wilking U; Bergh J; Ryden L; Koppert LB; Karsten MM; Kiani NA; Hedayati E
• Preprint: BIORXIV. 2023

  Uncovering the regulatory landscape of early human B-cell lymphopoiesis and its implications in the pathogenesis of B-cell acute lymphoblastic leukemia

  Planell N; Martínez-de-Morentin X; Mouzo D; Lara-Astiaso D; Vilas-Zornoza A; San Martín-Uriz P; Alignani D; Paiva B; Maillo A; Kurowska A; Berastegui N; Garcia-Olloqui P; Urdangarin A; Noori P; Ortega-Legarreta A; Hernaez M; Lagani V; Kiani N; Merkenschlager M; Ezponda T; Martín-Subero JI; Ramírez RN; Tegner J; Prosper F; Gomez-Cabrero D
• Journal article: JOURNAL OF HEPATOLOGY. 2023;78:s290

  SAT-337 Robust identification of patient subgroups in acute decompensated cirrhosis

  Palomino S; Huergo E; Uson E; Sanchez C; Lagani V; Kiani N; Planell N; Gurbindo U; Trebicka J; Farias AQ; Caraceni P; Rautou P-E; Gomez-Cabrero D
• Book: 2023

  Algorithmic Information Dynamics

  Zenil H; Kiani NA; Tegnér J
• Preprint: ARXIV. 2023

  A Parameter-Efficient Learning Approach to Arabic Dialect Identification with Pre-Trained General-Purpose Speech Model

  Radhakrishnan S; Yang C-HH; Khan SA; Kiani NA; Gomez-Cabrero D; Tegner JN
• Article: CANCER MEDICINE. 2023;12(9):10840-10850

  Planning for return to work during the first year after breast cancer metastasis: A Swedish cohort study

  Johnsson A; Kiani NA; Gernaat SAM; Wilking U; Shabo I; Hedayati E
• Preprint: ARXIV. 2023

  IHCV: Discovery of Hidden Time-Dependent Control Variables in Non-Linear Dynamical Systems

  Munoz J; Balsamy S; Bernal-Tamayo JP; Balubaid A; de Infante AMR; Lagani V; Gomez-Cabrero D; Kiani NA; Tegner J
• Preprint: BIORXIV. 2023

  LEP-AD: Language Embedding of Proteins and Attention to Drugs predicts drug target interactions

  Daga A; Khan SA; Cabrero DG; Hoehndorf R; Kiani N; Tegner J
• Article: PLOS ONE. 2023;18(2):e0281315

  scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences

  Khan SA; Lehmann R; Martinez-de-Morentin X; Maillo A; Lagani V; Kiani NA; Gomez-Cabrero D; Tegner J
• Article: PLOS COMPUTATIONAL BIOLOGY. 2023;19(2):e1010811

  LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics

  Ruffini G; Damiani G; Lozano-Soldevilla D; Deco N; Rosas FEE; Kiani NAA; Ponce-Alvarez A; Kringelbach MLL; Carhart-Harris R; Deco G
• Conference publication: 2023;:10007-10016

  Whispering LLaMA: A Cross-Modal Generative Error Correction Framework for Speech Recognition

  Radhakrishnan S; Yang C-H; Khan S; Kumar R; Kiani N; Gomez-Cabrero D; Tegnér J
• Conference publication: MULTIPLE SCLEROSIS JOURNAL. 2022;28(3_SUPPL):172-173

  A susceptibility network analysis of disease pathways leading to multiple sclerosis

  Manouchehrinia A; Ebrahimi A; Wiil UK; Kiani NA; Lio P; Olsson T; Kockum I
• Preprint: ARXIV. 2022

  On the Salient Limitations of the Methods of Assembly Theory and their Classification of Molecular Biosignatures

  Uthamacumaran A; Abrahão FS; Kiani NA; Zenil H
• Article: EUROPEAN JOURNAL OF CANCER CARE. 2022;31(5):e13626

  Use of sickness benefits by patients with metastatic breast cancer-A Swedish cohort study

  Altena R; Gernaat SAM; Wilking U; Kiani NA; Johnsson A; Hedayati E
• Preprint: BIORXIV. 2022

  LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics

  Ruffini G; Damiani G; Lozano-Soldevilla D; Deco N; Rosas F; Kiani N; Ponce-Alvarez A; Kringelbach M; Carhart-Harris R; Deco G
• Journal article: SCIENTIFIC REPORTS. 2022;12(1):14022

  Rapid-SL identifies synthetic lethal sets with an arbitrary cardinality

  Manshadi MD; Setoodeh P; Zare H
• Preprint: BIORXIV. 2022

  scAEGAN: Unification of Single-Cell Genomics Data by Adversarial Learning of Latent Space Correspondences

  Khan SA; Lehmann R; Martinez-de-Morentin X; Ruiz AM; Lagani V; Kiani N; Gomez-Cabrero D; Tegner J
• Book chapter: AUTOMATA AND COMPLEXITY: EMERGENCE, COMPLEXITY AND COMPUTATION. 2022;p. 433-453

  Model Discovery and Discrete Inverse Problems with Cellular Automata and Boolean Networks

  Zenil H; Zhang Y; Kiani NA
• Book chapter: WSPC BOOK SERIES IN UNCONVENTIONAL COMPUTING. 2021;p. 171-219

  Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying

  Hernández-Espinosa A; Zenil H; Kiani NA; Tegnér J
• Preprint: RESEARCH SQUARE. 2021

  Use of Sickness Benefits by Patients With Metastatic Breast Cancer – A Swedish Cohort Study

  Altena R; Gernaat SAM; Wilking U; Kiani N; Johnsson A; Hedayati E
• Review: CARDIO-ONCOLOGY. 2021;7(1):20

  Evidence-based prediction and prevention of cardiovascular morbidity in adults treated for cancer

  Altena R; Hubbert L; Kiani NA; Wengstrom Y; Bergh J; Hedayati E
• Preprint: BIORXIV. 2021

  Adaptative Machine Translation between paired Single-Cell Multi-Omics Data

  Martinez-de-Morentin X; Khan S; Lehmann R; Qu S; Maillo A; Kiani N; Prosper F; Tegner J; Gomez-Cabrero D
• Preprint: BIORXIV. 2020

  scMomentum: Inference of Cell-Type-Specific Regulatory Networks and Energy Landscapes

  Soto L; Bernal-Tamayo J; Lehmann R; Balsamy S; Martinez-de-Morentin X; Vilas-Zornoza A; San-Martin P; Prosper F; Gomez-Cabrero D; Kiani N; Tegner J
• Article: NUCLEIC ACIDS RESEARCH. 2020;48(19):10867-10876

  MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells

  Sumida N; Sifakis EG; Kiani NA; Ronnegren AL; Scholz BA; Vestlund J; Gomez-Cabrero D; Tegner J; Gondor A; Ohlsson R
• Journal article: DIAMOND AND RELATED MATERIALS. 2020;108:107987

  Kinetic study on the copper electroless coating on carbon nanotubes

  Shakibhamedan S; Kiani N; Sheibani S
• Conference publication: 2020 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC). 2020;:1-10

  Evolving Neural Networks through a Reverse Encoding Tree

  Zhang H; Yang C-HH; Zenil H; Kiani NA; Shen Y; Tegner JN
• Other: RECHARGEABLE BATTERIES. 2020;:441-464

  Aqueous Na‐Air Batteries

  Manshadi MD; Rahimpour MR
• Article: PLASMONICS. 2020;15(2):417-426

  Polarization Controlling of Multi Resonant Graphene-Based Microstrip Antenna

  Jafari Chashmi M; Rezaei P; Kiani N
• Article: FRONTIERS IN ONCOLOGY. 2020;10:51

  Immunometabolic Network Interactions of the Kynurenine Pathway in Cutaneous Malignant Melanoma

  Rad Pour S; Morikawa H; Kiani NA; Gomez-Cabrero D; Hayes A; Zheng X; Pernemalm M; Lehtio J; Mole DJ; Hansson J; Eriksson H; Tegner J
• Preprint: ARXIV. 2020

  Evolving Neural Networks through a Reverse Encoding Tree

  Zhang H; Yang C-HH; Zenil H; Kiani NA; Shen Y; Tegner JN
• Article: FRONTIERS IN ARTIFICIAL INTELLIGENCE. 2020;3:567356

  Algorithmic Probability-Guided Machine Learning on Non-Differentiable Spaces

  Hernandez-Orozco S; Zenil H; Riedel J; Uccello A; Kiani NA; Tegner J
• Article: OPTIK. 2020;200:163321

  Y-shaped graphene-based antenna with switchable circular polarization

  Chashmi MJ; Rezaei P; Kiani N
• Journal article: SCHOLARPEDIA. 2020;15(7):53143

  Algorithmic Information Dynamics

  Zenil H; Kiani N; Abrahão F; Tegnér J
• Book chapter: ADVANCES IN CARBON CAPTURE. 2020;p. 455-477

  CO2 removal from biogas and syngas

  Samipour S; Manshadi MD; Setoodeh P
• Book chapter: ADVANCES IN CARBON CAPTURE. 2020;p. 431-451

  Challenges in industrialization of biological CO2 capture

  Samipour S; Ahmadi A; Manshadi MD; Setoodeh P
• Preprint: ARXIV. 2019

  Algorithmic Probability-guided Supervised Machine Learning on Non-differentiable Spaces

  Hernández-Orozco S; Zenil H; Riedel J; Uccello A; Kiani NA; Tegnér J
• Article: ISCIENCE. 2019;19:1160-1172

  An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

  Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegner J
• Article: SCIENTIFIC REPORTS. 2019;9(1):12150

  Exhaustion of CD4+T-cells mediated by the Kynurenine Pathway in Melanoma

  Pour SR; Morikawa H; Kiani N; Yang M; Azimi A; Shafi G; Shang M; Baumgartner R; Ketelhuth DFJ; Kamleh MA; Wheelock CE; Lundqvist A; Hansson J; Tegner J
• Article: JOURNAL OF LEUKOCYTE BIOLOGY. 2019;106(2):413-430

  Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg-mediated suppression of cytokine expression

  Joshi RN; Fernandes SJ; Shang M-M; Kiani NA; Gomez-Cabrero D; Tegner J; Schmidt A
• Article: NATURE COMMUNICATIONS. 2019;10(1):2674

  Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

  Menden MP; Wang D; Mason MJ; Szalai B; Bulusu KC; Guan Y; Yu T; Kang J; Jeon M; Wolfinger R; Nguyen T; Zaslavskiy M; Jang IS; Ghazoui Z; Ahsen ME; Vogel R; Neto EC; Norman T; Tang EKY; Garnett MJ; Di Veroli GY; Fawell S; Stolovitzky G; Guinney J; Dry JR; Saez-Rodriguez J; Abante J; Abecassis BS; Aben N; Aghamirzaie D; Aittokallio T; Akhtari FS; Al-lazikani B; Alam T; Allam A; Allen C; de Almeida MP; Altarawy D; Alves V; Amadoz A; Anchang B; Antolin AA; Ash JR; Romeo Aznar V; Ba-alawi W; Bagheri M; Bajic V; Ball G; Ballester PJ; Baptista D; Bare C; Bateson M; Bender A; Bertrand D; Wijayawardena B; Boroevich KA; Bosdriesz E; Bougouffa S; Bounova G; Brouwer T; Bryant B; Calaza M; Calderone A; Calza S; Capuzzi S; Carbonell-Caballero J; Carlin D; Carter H; Castagnoli L; Celebi R; Cesareni G; Chang H; Chen G; Chen H; Chen H; Cheng L; Chernomoretz A; Chicco D; Cho K-H; Cho S; Choi D; Choi J; Choi K; Choi M; De Cock M; Coker E; Cortes-Ciriano I; Cserzo M; Cubuk C; Curtis C; Van Daele D; Dang CC; Dijkstra T; Dopazo J; Draghici S; Drosou A; Dumontier M; Ehrhart F; Eid F-E; ElHefnawi M; Elmarakeby H; van Engelen B; Engin HB; de Esch I; Evelo C; Falcao AO; Farag S; Fernandez-Lozano C; Fisch K; Flobak A; Fornari C; Foroushani ABK; Fotso DC; Fourches D; Friend S; Frigessi A; Gao F; Gao X; Gerold JM; Gestraud P; Ghosh S; Gillberg J; Godoy-Lorite A; Godynyuk L; Godzik A; Goldenberg A; Gomez-Cabrero D; Gonen M; de Graaf C; Gray H; Grechkin M; Guimera R; Guney E; Haibe-Kains B; Han Y; Hase T; He D; He L; Heath LS; Hellton KH; Helmer-Citterich M; Hidalgo MR; Hidru D; Hill SM; Hochreiter S; Hong S; Hovig E; Hsueh Y-C; Hu Z; Huang JK; Huang RS; Hunyady L; Hwang J; Hwang TH; Hwang W; Hwang Y; Isayev O; Walk OBD; Jack J; Jahandideh S; Ji J; Jo Y; Kamola PJ; Kanev GK; Karacosta L; Karimi M; Kaski S; Kazanov M; Khamis AM; Khan SA; Kiani NA; Kim A; Kim J; Kim J; Kim K; Kim K; Kim S; Kim Y; Kim Y; Kirk PDW; Kitano H; Klambauer G; Knowles D; Ko M; Kohn-Luque A; Kooistra AJ; Kuenemann MA; Kuiper M; Kurz C; Kwon M; van Laarhoven T; Laegreid A; Lederer S; Lee H; Lee J; Lee YW; Leppaho E; Lewis R; Li J; Li L; Liley J; Lim WK; Lin C; Liu Y; Lopez Y; Low J; Lysenko A; Machado D; Madhukar N; De Maeyer D; Malpartida AB; Mamitsuka H; Marabita F; Marchal K; Marttinen P; Mason D; Mazaheri A; Mehmood A; Mehreen A; Michaut M; Miller RA; Mitsopoulos C; Modos D; Van Moerbeke M; Moo K; Motsinger-Reif A; Movva R; Muraru S; Muratov E; Mushthofa M; Nagarajan N; Nakken S; Nath A; Neuvial P; Newton R; Ning Z; De Niz C; Oliva B; Olsen C; Palmeri A; Panesar B; Papadopoulos S; Park J; Park S; Park S; Pawitan Y; Peluso D; Pendyala S; Peng J; Perfetto L; Pirro S; Plevritis S; Politi R; Poon H; Porta E; Prellner I; Preuer K; Angel Pujana M; Ramnarine R; Reid JE; Reyal F; Richardson S; Ricketts C; Rieswijk L; Rocha M; Rodriguez-Gonzalvez C; Roell K; Rotroff D; de Ruiter JR; Rukawa P; Sadacca B; Safikhani Z; Safitri F; Sales-Pardo M; Sauer S; Schlichting M; Seoane JA; Serra J; Shang M-M; Sharma A; Sharma H; Shen Y; Shiga M; Shin M; Shkedy Z; Shopsowitz K; Sinai S; Skola D; Smirnov P; Soerensen IF; Soerensen P; Song J-H; Song SO; Soufan O; Spitzmueller A; Steipe B; Suphavilai C; Tamayo SP; Tamborero D; Tang J; Tanoli Z-U; Tarres-Deulofeu M; Tegner J; Thommesen L; Tonekaboni SAM; Tran H; De Troyer E; Truong A; Tsunoda T; Turu G; Tzeng G-Y; Verbeke L; Videla S; Vis D; Voronkov A; Votis K; Wang A; Wang H-QH; Wang P-W; Wang S; Wang W; Wang X; Wang X; Wennerberg K; Wernisch L; Wessels L; van Westen GJP; Westerman BA; White SR; Willighagen E; Wurdinger T; Xie L; Xie S; Xu H; Yadav B; Yau C; Yeerna H; Yin JW; Yu M; Yu M; Yun SJ; Zakharov A; Zamichos A; Zanin M; Zeng L; Zenil H; Zhang F; Zhang P; Zhang W; Zhao H; Zhao L; Zheng W; Zoufir A; Zucknick M
• Article: ENTROPY. 2019;21(6):E560-560

  The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

  Zenil H; Kiani NA; Tegner J
• Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019;116(19):9671-9676

  MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis

  Kotelnikova E; Kiani NA; Messinis D; Pertsovskaya I; Pliaka V; Bernardo-Faura M; Rinas M; Vila G; Zubizarreta I; Pulido-Valdeolivas I; Sakellaropoulos T; Faigle W; Silberberg G; Masso M; Stridh P; Behrens J; Olsson T; Martin R; Paul F; Alexopoulos LG; Saez-Rodriguez J; Tegner J; Villoslada P
• Article: OPTIK. 2019;184:421-427

  Reconfigurable graphene-based V-shaped dipole antenna: From quasi-isotropic to directional radiation pattern

  Chashmi MJ; Rezaei P; Kiani N
• Preprint: ARXIV. 2019

  Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying

  Hernández-Espinosa A; Zenil H; Kiani NA; Tegnér J
• Book chapter: FROM PARALLEL TO EMERGENT COMPUTING. 2019;p. 367-384

  Algorithmic Information Dynamics of Emergent, Persistent, and Colliding Particles in the Game of Life *

  Zenil H; Kiani NA; Tegnér J
• Article: NATURE MACHINE INTELLIGENCE. 2019;1(1):58-66

  Causal deconvolution by algorithmic generative models

  Zenil H; Kiani NA; Zea AA; Tegner J
• Preprint: ARXIV. 2018

  Controllability, Multiplexing, and Transfer Learning in Networks using Evolutionary Learning

  Ooi R; Yang C-HH; Chen P-Y; Eguìluz V; Kiani N; Zenil H; Gomez-Cabrero D; Tegnèr J
• Article: ENTROPY. 2018;20(8):E605-605

  A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

  Zenil H; Hernandez-Orozco S; Kiani NA; Soler-Toscano F; Rueda-Toicen A; Tegner J
• Article: ROYAL SOCIETY OPEN SCIENCE. 2018;5(8):180399

  Algorithmically probable mutations reproduce aspects of evolution, such as convergence rate, genetic memory and modularity

  Hernandez-Orozco S; Kiani NA; Zenil H
• Review: ENTROPY. 2018;20(8):E551-551

  A Review of Graph and Network Complexity from an Algorithmic Information Perspective

  Zenil H; Kiani NA; Tegner J
• Article: ENTROPY. 2018;20(7):E534-534

  Symmetry and Correspondence of Algorithmic Complexity over Geometric, Spatial and Topological Representations

  Zenil H; Kiani NA; Tegner J
• Preprint: ARXIV. 2018

  The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

  Zenil H; Kiani NA; Tegnér J
• Article: BMC BIOLOGY. 2018;16(1):47

  Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

  Schmidt A; Marabita F; Kiani NA; Gross CC; Johansson HJ; Elias S; Rautio S; Eriksson M; Fernandes SJ; Silberberg G; Ullah U; Bhatia U; Lahdesmaki H; Lehtio J; Gomez-Cabrero D; Wiendl H; Lahesmaa R; Tegner J
• Preprint: BIORXIV. 2018

  The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulatingMYCin 3D: Implications for the fitness of cancer cells

  Sumida N; Sifakis E; Scholz B; Fernandez-Woodbridge A; Kiani N; Gomez-Cabrero D; Svensson P; Tegner J; Göndör A; Ohlsson R
• Journal article: PARALLEL PROCESSING LETTERS. 2018;28(1):1850005

  Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

  Zenil H; Kiani NA; Shang M-M; Tegner J
• Preprint: ARXIV. 2018

  Symmetry and Algorithmic Complexity of Polyominoes and Polyhedral Graphs

  Zenil H; Kiani NA; Tegnér J
• Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2018;16(1):34

  Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients

  Tenyi A; Cano I; Marabita F; Kiani N; Kalko SG; Barreiro E; de Atauri P; Cascante M; Gomez-Cabrero D; Roca J
• Preprint: ARXIV. 2018

  Algorithmic Causal Deconvolution of Intertwined Programs and Networks by Generative Mechanism

  Zenil H; Kiani NA; Zea AA; Tegnér J
• Preprint: ARXIV. 2018

  Algorithmic Information Dynamics of Persistent Patterns and Colliding Particles in the Game of Life

  Zenil H; Kiani NA; Tegnér J
• Preprint: ARXIV. 2018

  Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

  Zenil H; Kiani NA; Shang M-M; Tegnér J
• Preprint: ARXIV. 2018

  Minimal Algorithmic Information Loss Methods for Dimension Reduction, Feature Selection and Network Sparsification

  Zenil H; Kiani NA; Adams A; Abrahão FS; Rueda-Toicen A; Zea AA; Ozelim L; Tegnér J
• Preprint: ARXIV. 2018

  Predictive Systems Toxicology

  Kiani NA; Shang M-M; Zenil H; Tegnér J
• Preprint: SSRN ELECTRONIC JOURNAL. 2018

  An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

  Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegnér J
• Review: METHODS IN MOLECULAR BIOLOGY. 2018;1800:535-557

  Predictive Systems Toxicology.

  Kiani NA; Shang M-M; Zenil H; Tegner J
• Article: BIOINFORMATICS. 2017;33(24):3964-3972

  HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation

  Deng Y; Zenil H; Tegner J; Kiani NA
• Article: PLOS COMPUTATIONAL BIOLOGY. 2017;13(10):e1005757

  Dynamics and heterogeneity of brain damage in multiple sclerosis

  Kotelnikova E; Kiani NA; Abad E; Martinez-Lapiscina EH; Andorra M; Zubizarreta I; Pulido-Valdeolivas I; Pertsovskaya I; Alexopoulos LG; Olsson T; Martin R; Paul F; Tegner J; Garcia-Ojalvo J; Villoslada P
• Preprint: ARXIV. 2017

  An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

  Zenil H; Kiani NA; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegnér J
• Preprint: BIORXIV. 2017

  An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

  Zenil H; Kiani N; Marabita F; Deng Y; Elias S; Schmidt A; Ball G; Tegnér J
• Preprint: ARXIV. 2017

  Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, and modularity

  Hernández-Orozco S; Kiani NA; Zenil H
• Article: PHYSICAL REVIEW E. 2017;96(1):012308

  Low-algorithmic-complexity entropy-deceiving graphs

  Zenil H; Kiani NA; Tegner J
• Article: MATHEMATICAL BIOSCIENCES. 2017;289:1-8

  A minimal unified model of disease trajectories captures hallmarks of multiple sclerosis

  Kannan V; Kiani NA; Piehl F; Tegner J
• Preprint: ARXIV. 2017

  HiDi: An efficient reverse engineering schema for large scale dynamic regulatory network reconstruction using adaptive differentiation

  Deng Y; Zenil H; Tégner J; Kiani NA
• Corrigendum: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;60:168

  Methods of information theory and algorithmic complexity for network biology (vol 51, pg 32, 2016)

  Zenil H; Kiani NA; Tegner J
• Review: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES. 2016;374(2080):20160144

  A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

  Tegner J; Zenil H; Kiani NA; Ball G; Gomez-Cabrero D
• Preprint: ARXIV. 2016

  A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

  Zenil H; Hernández-Orozco S; Kiani NA; Soler-Toscano F; Rueda-Toicen A
• Journal article: JOURNAL OF COMPLEX NETWORKS. 2016;4(3):342-362

  Quantifying loss of information in network-based dimensionality reduction techniques

  Zenil H; Kiani NA; Tegner J
• Preprint: ARXIV. 2016

  Low Algorithmic Complexity Entropy-deceiving Graphs

  Zenil H; Kiani N; Tegnér J
• Article: SCIENTIFIC REPORTS. 2016;6:26170

  Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction

  Kannan V; Swartz F; Kiani NA; Silberberg G; Tsipras G; Gomez-Cabrero D; Alexanderson K; Tegner J
• Review: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;51:32-43

  Methods of information theory and algorithmic complexity for network biology

  Zenil H; Kiani NA; Tegner J
• Review: SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY. 2016;51:44-52

  Evaluating network inference methods in terms of their ability to preserve the topology and complexity of genetic networks

  Kiani NA; Zenil H; Olczak J; Tegner J
• Review: CURRENT PHARMACEUTICAL DESIGN. 2016;22(46):6911-6917

  Systems Toxicology: Systematic Approach to Predict Toxicity

  Kiani NA; Shang M-M; Tegner J
• Preprint: ARXIV. 2015

  Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks

  Kiani NA; Zenil H; Olczak J; Tegnér J
• Conference publication: 2015 11TH INTERNATIONAL CONFERENCE ON SIGNAL-IMAGE TECHNOLOGY & INTERNET-BASED SYSTEMS (SITIS). 2015;:468-473

  Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks

  Olczak J; Kiani NA; Zenil H; Tegner J
• Preprint: ARXIV. 2015

  Quantifying Loss of Information in Network-based Dimensionality Reduction Techniques

  Zenil H; Kiani NA; Tegnér J
• Article: MULTIPLE SCLEROSIS JOURNAL. 2015;21(2):138-146

  Signaling networks in MS: A systems-based approach to developing new pharmacological therapies

  Kotelnikova E; Bernardo-Faura M; Silberberg G; Kiani NA; Messinis D; Melas IN; Artigas L; Schwartz E; Mazo I; Masso M; Alexopoulos LG; Manuel Mas J; Olsson T; Tegner J; Martin R; Zamora A; Paul F; Saez-Rodriguez J; Villoslada P
• Preprint: ARXIV. 2015

  Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues

  Zenil H; Kiani NA; Tegnér J
• Book chapter: LECTURE NOTES IN COMPUTER SCIENCE. 2015;p. 395-405

  Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues

  Zenil H; Kiani NA; Tegner J
• Article: SOFT COMPUTING. 2014;18(12):2461-2469

  Laplace transform formula on fuzzy nth-order derivative and its application in fuzzy ordinary differential equations

  Ahmadi MB; Kiani NA; Mikaeilvand N
• Article: JOURNAL OF TRANSLATIONAL MEDICINE. 2014;12(Suppl 2):S4

  Systems Medicine: from molecular features and models to the clinic in COPD

  Gomez-Cabrero D; Menche J; Cano I; Abugessaisa I; Huertas-Miguelanez M; Tenyi A; Marin de Mas I; Kiani NA; Marabita F; Falciani F; Burrowes K; Maier D; Wagner P; Selivanov V; Cascante M; Roca J; Barabasi A-L; Tegner J
• Article: BMC BIOINFORMATICS. 2014;15(1):250

  Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data

  Kiani NA; Kaderali L
• Preprint: ARXIV. 2014

  Methods of Information Theory and Algorithmic Complexity for Network Biology

  Zenil H; Kiani NA; Tegnér J
• Conference publication: 2013 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM). 2013;:74-76

  Algorithmic complexity of motifs clusters superfamilies of networks

  Zenil H; Kiani NA; Tegner J
• Review: WORLD J VIROL. 2013;2(2):18-31

  High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay.

  Amberkar S; Kiani NA; Bartenschlager R; Alvisi G; Kaderali L
• Book chapter: ENCYCLOPEDIA OF SYSTEMS BIOLOGY. 2013;p. 2108-2110

  Systems Virology

  Kiani NA; Kaderali L
• Article: ANNALS OF OPERATIONS RESEARCH. 2012;196(1):459-468

  Resource allocation for performance improvement

  Nasrabadi N; Dehnokhalaji A; Kiani NA; Korhonen PJ; Wallenius J
• Article: BMC BIOINFORMATICS. 2011;12:485

  Normalizing for individual cell population context in the analysis of high-content cellular screens

  Knapp B; Rebhan I; Kumar A; Matula P; Kiani NA; Binder M; Erfle H; Rohr K; Eils R; Bartenschlager R; Kaderali L
• Article: INTERNATIONAL JOURNAL OF UNCERTAINTY FUZZINESS AND KNOWLEDGE-BASED SYSTEMS. 2011;19(6):999-1012

  DEGENERACY IN FUZZY LINEAR PROGRAMMING AND ITS APPLICATION

  Sigarpich LA; Allahviranloo T; Lotfi FH; Kiani NA
• Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2011;286(31):27278-27287

  Molecular Mechanism of Signal Perception and Integration by the Innate Immune Sensor Retinoic Acid-inducible Gene-I (RIG-I)

  Binder M; Eberle F; Seitz S; Muecke N; Hueber CM; Kiani N; Kaderali L; Lohmann V; Dalpke A; Bartenschlager R
• Article: INFORMATION SCIENCES. 2009;179(8):1207-1215

  Toward the existence and uniqueness of solutions of second-order fuzzy differential equations

  Allahviranloo T; Kiani NA; Barkhordari M
• Article: INFORMATION SCIENCES. 2009;179(7):956-966

  Solving fuzzy differential equations by differential transformation method

  Allahviranloo T; Kiani NA; Motamedi N
• Journal article: COMPUTATIONAL MATHEMATICS AND MODELING. 2008;19(3):282-291

  Homomorphic solution of fully fuzzy linear systems

  Allahviranloo T; Kiani NA; Barkhordary M; Mosleh M
• Journal article: APPLICATIONS AND APPLIED MATHEMATICS-AN INTERNATIONAL JOURNAL. 2008;3(1):77-88

  Signed Decomposition of Fully Fuzzy Linear Systems

  Allahviranloo T; Mikaeilvand N; Kiani NA; Shabestari RM
• Journal article: INTERNATIONAL JOURNAL OF CONTEMPORARY MATHEMATICAL SCIENCES. 2007;2:167-181

  Fuzzy integer linear programming problems

  Allahviranloo T; Shamsolkotabi K; Kiani NA; Alizadeh L
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Medarbetare och kontakt

Gruppledare

• 

  Narsis Kiani

  Senior Forskningsspecialist

  E-postadress narsis.kiani@ki.se

Alla medarbetare i gruppen

• 

  Mehdi Dehghan Manshadi

  Postdoktor

  E-postadress mehdi.dehghan.manshadi@ki.se
• Sneha Karthikeyan

  Anknuten till Forskning

  E-postadress sneha.karthikeyan@ki.se
• 

  Narsis Kiani

  Senior Forskningsspecialist

  E-postadress narsis.kiani@ki.se
• Narges Manouchehri

  Postdoktorala Studier

  E-postadress narges.manouchehri@ki.se