On the Inference of Parsimonious Indel Evolutionary Scenarios. - Leonid Chindelevitch; Zhentao Li; Eric Blais; Mathieu Blanchette (J. Bioinform. Comput. Biol., 2006)

Inverting the Viterbi algorithm: an abstract framework for structure design. - Michael Schnall-Levin; Leonid Chindelevitch; Bonnie Berger (ICML, 2008)

Local Optimization for Global Alignment of Protein Interaction Networks. - Leonid Chindelevitch; Chung-Shou Liao; Bonnie Berger (Pacific Symposium on Biocomputing, 2010)

Metabolic Network Analysis Demystified. - Leonid Chindelevitch; Aviv Regev; Bonnie Berger (RECOMB, 2011)

Causal Reasoning on Biological Networks: Interpreting Transcriptional Changes - (Extended Abstract). - Leonid Chindelevitch; Daniel Ziemek; Ahmed Enayetallah; Ranjit Randhawa; Ben Sidders; Christoph Brockel; Enoch S. Huang (RECOMB, 2011)

Causal reasoning on biological networks: interpreting transcriptional changes. - Leonid Chindelevitch; Daniel Ziemek; Ahmed Enayetallah; Ranjit Randhawa; Ben Sidders; Christoph Brockel; Enoch S. Huang (Bioinform., 2012)

Assessing statistical significance in causal graphs. - Leonid Chindelevitch; Po-Ru Loh; Ahmed Enayetallah; Bonnie Berger; Daniel Ziemek (BMC Bioinform., 2012)

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. - Chia-Ling Huang; John Lamb; Leonid Chindelevitch; Jarek Kostrowicki; Justin Guinney; Charles DeLisi; Daniel Ziemek (BMC Bioinform., 2012)

Optimizing a global alignment of protein interaction networks. - Leonid Chindelevitch; Cheng-Yu Ma; Chung-Shou Liao; Bonnie Berger (Bioinform., 2013)

ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. - Leonid Chindelevitch; Caroline Colijn; Prashini Moodley; Douglas Wilson; Ted Cohen (PLoS Comput. Biol., 2016)

On the Rank-Distance Median of 3 Permutations. - Leonid Chindelevitch; João Meidanis (RECOMB-CG, 2017)

A Cubic Algorithm for the Generalized Rank Median of Three Genomes. - Leonid Chindelevitch; Joao Meidanis (RECOMB-CG, 2018)

PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats. - Mehrdad Mansouri; Julian Booth; Margaryta Vityaz; Cédric Chauve; Leonid Chindelevitch (WABI, 2018)

A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. - Hooman Zabeti; Tamon Stephen; Bonnie Berger; Leonid Chindelevitch (WABI, 2018)

Speeding up Dualization in the Fredman-Khachiyan Algorithm B. - Nafiseh Sedaghat; Tamon Stephen; Leonid Chindelevitch (SEA, 2018)

On the rank-distance median of 3 permutations. - Leonid Chindelevitch; João Paulo Pereira Zanetti; João Meidanis (BMC Bioinform., 2018)

Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance. - João Paulo Pereira Zanetti; Leonid Chindelevitch; João Meidanis (AlCoB, 2019)

Generalizations of the Genomic Rank Distance to Indels. - João Paulo Pereira Zanetti; Leonid Chindelevitch; João Meidanis (AlCoB, 2019)

A cubic algorithm for the generalized rank median of three genomes. - Leonid Chindelevitch; Sean La; Joao Meidanis (Algorithms Mol. Biol., 2019)

Collaborative intra-tumor heterogeneity detection. - Sahand Khakabimamaghani; Salem Malikic; Jeffrey Tang; Dujian Ding; Ryan D. Morin; Leonid Chindelevitch; Martin Ester (Bioinform., 2019)

MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks. - Reza Miraskarshahi; Hooman Zabeti; Tamon Stephen; Leonid Chindelevitch (Bioinform., 2019)

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework. - Guo Liang Gan; Elijah Willie; Cédric Chauve; Leonid Chindelevitch (BMC Bioinform., 2019)

PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals. - Mohsen Katebi; Pedro Feijão; Julius Booth; Mehrdad Mansouri; Sean La; Alex Sweeten; Reza Miraskarshahi; Matthew Nguyen; Johnathan Wong; William Hsiao; Cédric Chauve; Leonid Chindelevitch (AlCoB, 2020)

How Robust are the Estimated Effects of Nonpharmaceutical Interventions against COVID-19? - Mrinank Sharma; Sören Mindermann; Jan Markus Brauner; Gavin Leech; Anna B. Stephenson; Tomas Gavenciak; Jan Kulveit; Yee Whye Teh; Leonid Chindelevitch; Yarin Gal (NeurIPS, 2020)

An Interpretable Classification Method for Predicting Drug Resistance in M. Tuberculosis. - Hooman Zabeti; Nick C. Dexter; Amir Hosein Safari; Nafiseh Sedaghat; Maxwell W. Libbrecht; Leonid Chindelevitch (WABI, 2020)

Computing the distribution of the Robinson-Foulds distance. - Maryam Hayati; Leonid Chindelevitch (Comput. Biol. Chem., 2020)

On the robustness of effectiveness estimation of nonpharmaceutical interventions against COVID-19 transmission. - Mrinank Sharma; Sören Mindermann; Jan Markus Brauner; Gavin Leech; Anna B. Stephenson; Tomas Gavenciak; Jan Kulveit; Yee Whye Teh; Leonid Chindelevitch; Yarin Gal (CoRR, 2020)

Predicting drug resistance in M. tuberculosis using a long-term recurrent convolutional network. - Amir Hosein Safari; Nafiseh Sedaghat; Hooman Zabeti; Alpha Forna; Leonid Chindelevitch; Maxwell W. Libbrecht (BCB, 2021)

INGOT-DR: an interpretable classifier for predicting drug resistance in M. tuberculosis. - Hooman Zabeti; Nick C. Dexter; Amir Hosein Safari; Nafiseh Sedaghat; Maxwell W. Libbrecht; Leonid Chindelevitch (Algorithms Mol. Biol., 2021)

Aristotle: stratified causal discovery for omics data. - Mehrdad Mansouri; Sahand Khakabimamaghani; Leonid Chindelevitch; Martin Ester (BMC Bioinform., 2022)

Applying data technologies to combat AMR: current status, challenges, and opportunities on the way forward. - Leonid Chindelevitch; Elita Jauneikaite; Nicole E. Wheeler; Kasim Allel; Bede Yaw Ansiri-Asafoakaa; Wireko A. Awuah; Denis C. Bauer; Stephan Beisken; Kara Fan; Gary Grant; Michael Graz; Yara Khalaf; et al. (CoRR, 2022)

Ten simple rules for the sharing of bacterial genotype - Phenotype data on antimicrobial resistance. - Leonid Chindelevitch; Maarten van Dongen; Heather Graz; Antonio Pedrotta; Anita Suresh; Swapna Uplekar; Elita Jauneikaite; Nicole E. Wheeler (PLoS Comput. Biol., 2023)

Generalizations of the genomic rank distance to indels. - João Paulo Pereira Zanetti; Lucas Peres Oliveira; Leonid Chindelevitch; João Meidanis (Bioinform., 2023)

Speeding Up the Structural Analysis of Metabolic Network Models Using the Fredman-Khachiyan Algorithm B. - Nafiseh Sedaghat; Tamon Stephen; Leonid Chindelevitch (J. Comput. Biol., 2023)

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing. - Romain Derelle; John Lees; Jody Phelan; Ajit Lalvani; Nimalan Arinaminpathy; Leonid Chindelevitch (Bioinform., 2023)

Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance. - João Paulo Pereira Zanetti; Lucas Peres Oliveira; João Meidanis; Leonid Chindelevitch (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)