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2026

Comparative Genomics - 22nd RECOMB International Workshop, RECOMB-CG 2025, Seoul, South Korea, April 24-25, 2025, ProceedingsGiltae Song, editor, Volume 15666 of Lecture Notes in Computer Science, Springer, 2026. [doi]

2025

Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification TasksSarwan Ali, Taslim Murad, Prakash Chourasia, Haris Mansoor, Imdad Ullah Khan, Pin-Yu Chen, Murray Patterson. recombcg 2026: 202-215 [doi]

Evolutionary Reconstruction of Hormone-bHLH Regulatory Networks in Solanaceae: Phylogenomics Insights from PSTVd-Tomato InteractionsKatia Aviña-Padilla, Octavio Zambada-Moreno, Manuel A. Barrios-Izás, Michelle Bustamante-Castillo, Maribel Hernández-Rosales. recombcg 2026: 284-291 [doi]

Adapting the Cov2clusters Tool for Clustering MPOXV Whole Genome SequencesEric CH Chen, Tara Newman, John R. Tyson, Anthea Lam, Michael Chan, Agatha Jassem, Natalie Prystajecky, Shannon Russell, James Zlosnik. recombcg 2026: 231-243 [doi]

Residual Immunity and Seasonality of an EpidemicSiyu Chen, David Sankoff. recombcg 2026: 219-230 [doi]

A Simple Way to Find Related Sequences with Position-Specific ProbabilitiesMartin C. Frith. recombcg 2026: 197-201 [doi]

Detecting and Mapping Local Model Violations During Biomolecular Sequence Analysis: a REsampling and Visual EvALuation ApproachMeijun Gao, Kevin J. Liu. recombcg 2026: 181-196 [doi]

QT-WEAVER: Correcting Quartet Distribution Improves Phylogenomic Analyses Despite Gene Tree Estimation ErrorNavid Bin Hasan, Sohaib, Md. Shamsuzzoha Bayzid. recombcg 2026: 150-156 [doi]

Tree Decomposition for Reconstructing Ancestral RNA Sequences of Multiple FamiliesSongdi Hu, Vladimir Reinharz, Olivier Tremblay Savard. recombcg 2026: 27-50 [doi]

Probability-Based Sequence Comparison Finds the Oldest Ever Nuclear Mitochondrial DNA Segments in Mammalian GenomesMuyao Huang, Martin C. Frith. recombcg 2026: 247-250 [doi]

Whole-Genome Duplication Detection with Phylogenomics Reconciliation: A Scalable ApproachReza Kalhor, Manuel Lafond, Céline Scornavacca. recombcg 2026: 51-68 [doi]

Fast Calculation of Cherry Distance on Level-1 Orchard Networks: Optimization, Heuristic and ImplementationKaari Landry, Olivier Tremblay Savard. recombcg 2026: 157-177 [doi]

Inferring Phylogenetic Trees of Cancer Evolution from Longitudinal Single-Cell Copy Number ProfilesYushu Liu, Luay Nakhleh. recombcg 2026: 9-23 [doi]

Novel Driver Mutations in GCB Lymphoma Patients that Affect Transcription Factors BindingOfek Shami-Schnitzer, Tamir Tuller. recombcg 2026: 3-8 [doi]

Unraveling Insect Immunity: A Cross-Order Comparative Genomic Analysis of Key Immune ProteinsTriveni Shelke, Vanika Gupta, Ishaan Gupta. recombcg 2026: 251-267 [doi]

A Sankoff-Rousseau-Like Algorithm for Minimizing Lateral Gene Transfers and Losses on Single Origin CharactersAlitzel López Sánchez, Guillaume E. Scholz, Peter F. Stadler, Manuel Lafond. recombcg 2026: 69-86 [doi]

Phylogenetic Network Diversity Parameterized by Reticulation Number and BeyondLeo van Iersel, Mark Jones 0001, Jannik Schestag, Céline Scornavacca, Mathias Weller. recombcg 2026: 107-130 [doi]

tMHG-Finder: Tree-Guided Maximal Homologous Group Finder for Bacterial GenomesYongze Yin, Bryce Kille, Huw A. Ogilvie, Todd J. Treangen, Luay Nakhleh. recombcg 2026: 87-104 [doi]

Exact Counts of Binary Phylogenetic Networks with Two and Three Reticulation Events (Extended Abstract)Hao Yu, Louxin Zhang. recombcg 2026: 137-140 [doi]

On the Robustness to Gene Tree Rooting (or Lack Thereof) of Triplet-Based Species Tree Estimation MethodsTanjeem Azwad Zaman, Rabib Jahin Ibn Momin, Md. Shamsuzzoha Bayzid. recombcg 2026: 131-136 [doi]

Analyzing Sequence Similarity Distributions in Salmonidae: A Branching Process ApproachYue Zhang. recombcg 2026: 268-283 [doi]

Ancestral Pangenomes and Their Phylogenetic ReconstructionXintong Zhou, David Sankoff. recombcg 2026: 141-149 [doi]

2024

Maximum Alternating Balanced Cycle Decomposition and Applications in Sorting by Intergenic Operations ProblemsKlairton Lima Brito, Alexsandro Oliveira Alexandrino, Gabriel Siqueira, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias. recombcg 2024: 153-172 [doi]

Sampling Gene Adjacencies and Geodesic Points of Random GenomesPoly H. da Silva, Arash Jamshidpey, David Sankoff. recombcg 2024: 189-210 [doi]

Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to HumansAlma Davidson, Marina Parr, Franziska Totzeck, Alexander Churkin, Danny Barash, Dmitrij Frishman, Tamir Tuller. recombcg 2024: 248-270 [doi]

Gene-Adjacency-Based Phylogenetics Under a Stochastic Gain-Loss ModelYoav Dvir, Shelly Brezner, Sagi Snir. recombcg 2024: 69-85 [doi]

Revisiting the Effects of MDR1 Variants Using Computational ApproachesTal Gutman, Tamir Tuller. recombcg 2024: 226-247 [doi]

Transcription Factors Across the Escherichia coli Pangenome: A 3D PerspectiveGabriel Moreno-Hagelsieb. recombcg 2024: 213-225 [doi]

Inferring Transcript Phylogenies from Transcript Ortholog ClustersWend Yam Donald Davy Ouedraogo, Aïda Ouangraoua. recombcg 2024: 47-68 [doi]

REvolutionH-tl: Reconstruction of Evolutionary Histories toolJosé Antonio Ramírez-Rafael, Annachiara Korchmaros, Katia Aviña-Padilla, Alitzel López Sánchez, Andrea Arlette España-Tinajero, Marc Hellmuth, Peter F. Stadler, Maribel Hernández-Rosales. recombcg 2024: 89-109 [doi]

Gene Tree Parsimony in the Presence of Gene Duplication, Loss, and Incomplete Lineage SortingProttoy Saha, Md Shamiul Islam, Tasnim Rahman, Adiba Shaira, Kazi Noshin, Rezwana Reaz, Md. Shamsuzzoha Bayzid. recombcg 2024: 110-128 [doi]

Comparative Genomics - 21st International Conference, RECOMB-CG 2024, Boston, MA, USA, April 27-28, 2024, ProceedingsCéline Scornavacca, Maribel Hernández-Rosales, editors, Volume 14616 of Lecture Notes in Computer Science, Springer, 2024. [doi]

On the Distribution of Synteny Blocks Under a Neutral Model of Genome DynamicsSagi Snir, Yuri I. Wolf, Shelly Brezner, Eugene V. Koonin, Mike Steel. recombcg 2024: 173-188 [doi]

Galled Perfect Transfer NetworksAlitzel López Sánchez, Manuel Lafond. recombcg 2024: 24-43 [doi]

Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP DataTandy J. Warnow, Yasamin Tabatabaee, Steven N. Evans. recombcg 2024: 3-23 [doi]

Assessing the Potential of Gene Tree Parsimony for Microbial PhylogenomicsSamson Weiner, Yutian Feng, J. Peter Gogarten, Mukul S. Bansal. recombcg 2024: 129-149 [doi]

2023

The Floor Is Lava - Halving Genomes with Viaducts, Piers and PontoonsLeonard Bohnenkämper. recombcg 2023: 51-67 [doi]

On the Class of Double Distance ProblemsMarília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye. recombcg 2023: 35-50 [doi]

MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural NetworksMohammad Amin Edrisi, Huw A. Ogilvie, Meng Li 0002, Luay Nakhleh. recombcg 2023: 232-247 [doi]

Comparative Genomics - 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14-15, 2023, ProceedingsKatharina Jahn, Tomás Vinar, editors, Volume 13883 of Lecture Notes in Computer Science, Springer, 2023. [doi]

Classifying the Post-duplication Fate of Paralogous GenesReza Kalhor, Guillaume Beslon, Manuel Lafond, Céline Scornavacca. recombcg 2023: 1-18 [doi]

The K-Robinson Foulds Measures for Labeled TreesElahe Khayatian, Gabriel Valiente, Louxin Zhang. recombcg 2023: 146-161 [doi]

Two Strikes Against the Phage Recombination ProblemManuel Lafond, Anne Bergeron, Krister M. Swenson. recombcg 2023: 68-83 [doi]

Finding Agreement Cherry-Reduced Subnetworks in Level-1 NetworksKaari Landry, Olivier Tremblay Savard, Manuel Lafond. recombcg 2023: 179-195 [doi]

Inferring Clusters of Orthologous and Paralogous TranscriptsWend Yam Donald Davy Ouedraogo, Aida Ouangraoua. recombcg 2023: 19-34 [doi]

Prior Density Learning in Variational Bayesian Phylogenetic Parameters InferenceAmine M. Remita, Golrokh Vitae, Abdoulaye Baniré Diallo. recombcg 2023: 112-130 [doi]

CONSULT-II: Taxonomic Identification Using Locality Sensitive HashingAli Osman Berk Sapci, Eleonora Rachtman, Siavash Mirarab. recombcg 2023: 196-214 [doi]

Physical Mapping of Two Nested Fixed Inversions in the X Chromosome of the Malaria Mosquito Anopheles messeaeEvgenia S. Soboleva, Kirill M. Kirilenko, Valentina S. Fedorova, Alina A. Kokhanenko, Gleb N. Artemov, Igor V. Sharakhov. recombcg 2023: 84-99 [doi]

The Asymmetric Cluster Affinity CostSanket Wagle, Alexey Markin, Pawel Górecki 0001, Tavis K. Anderson, Oliver Eulenstein. recombcg 2023: 131-145 [doi]

MAGE: Strain Level Profiling of Metagenome SamplesVidushi Walia, VG Saipradeep, Rajgopal Srinivasan, Naveen Sivadasan. recombcg 2023: 215-231 [doi]

Bounding the Number of Reticulations in a Tree-Child Network that Displays a Set of TreesYufeng Wu, Louxin Zhang. recombcg 2023: 162-178 [doi]

Gene Order Phylogeny via Ancestral Genome Reconstruction Under DolloQiaoji Xu, David Sankoff. recombcg 2023: 100-111 [doi]

2022

Reconciliation with Segmental Duplication, Transfer, Loss and GainYoann Anselmetti, Mattéo Delabre, Nadia El-Mabrouk. recombcg 2022: 124-145 [doi]

Deciphering the Tissue-Specific Regulatory Role of Intronless Genes Across CancersKatia Aviña-Padilla, José Antonio Ramírez-Rafael, Octavio Zambada-Moreno, Gabriel Emilio Herrera-Oropeza, Guillermo Romero, Ishaan Gupta, Maribel Hernández-Rosales. recombcg 2022: 311-339 [doi]

On the Comparison of Bacteriophage PopulationsAnne Bergeron, Marie-Jean Meurs, Romy Valiquette-Labonté, Krister M. Swenson. recombcg 2022: 3-20 [doi]

A New Approach for the Reversal Distance with Indels and Moves in Intergenic RegionsKlairton Lima Brito, Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Ulisses Dias, Zanoni Dias. recombcg 2022: 205-220 [doi]

Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic PlacementsNavid Bin Hasan, Avijit Biswas, Metin Balaban, Siavash Mirarab, Md. Shamsuzzoha Bayzid. recombcg 2022: 33-51 [doi]

Phylogenetic Placement Problem: A Hyperbolic Embedding ApproachYueyu Jiang, Puoya Tabaghi, Siavash Mirarab. recombcg 2022: 68-85 [doi]

Comparative Genomics - 19th International Conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20-21, 2022, ProceedingsLingling Jin, Dannie Durand, editors, Volume 13234 of Lecture Notes in Computer Science, Springer, 2022. [doi]

The Complexity of Finding Common Partitions of Genomes with Predefined Block SizesManuel Lafond, Adiesha Liyanage, Binhai Zhu, Peng Zou. recombcg 2022: 105-123 [doi]

Using Computational Synthetic Biology Tools to Modulate Gene Expression Within a MicrobiomeLiyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron, Tamir Tuller. recombcg 2022: 235-259 [doi]

A Mixed Integer Linear Programming Algorithm for Plasmid BinningAniket C. Mane, Mahsa Faizrahnemoon, Cédric Chauve. recombcg 2022: 279-292 [doi]

Sorting by k-Cuts on Signed PermutationsAndre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Géraldine Jean, Guillaume Fertin, Ulisses Dias, Zanoni Dias. recombcg 2022: 189-204 [doi]

Chromothripsis Rearrangements Are Informed by 3D-Genome OrganizationNatalia Petukhova, Alexey Zabelkin, Vitaly Dravgelis, Sergey Aganezov, Nikita Alexeev. recombcg 2022: 221-231 [doi]

Benchmarking Penalized Regression Methods in Machine Learning for Single Cell RNA Sequencing DataBhavithry Sen Puliparambil, Jabed H. Tomal, Yan Yan. recombcg 2022: 295-310 [doi]

Quantifying Hierarchical Conflicts in Homology StatementsKrister M. Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab, Mathias Weller. recombcg 2022: 146-167 [doi]

Metagenomics Binning of Long Reads Using Read-Overlap GraphsAnuradha Wickramarachchi, Yu Lin 0001. recombcg 2022: 260-278 [doi]

Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into AccountBerk A. Yakici, Huw A. Ogilvie, Luay Nakhleh. recombcg 2022: 86-102 [doi]

Syntenic Dimensions of Genomic EvolutionZhe Yu, David Sankoff. recombcg 2022: 21-30 [doi]

On Partial Gene Transfer and Its Impact on Gene Tree ReconstructionSumaira Zaman, Mukul S. Bansal. recombcg 2022: 168-186 [doi]

The Sackin Index of Simplex NetworksLouxin Zhang. recombcg 2022: 52-67 [doi]

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