Article
Agronomy
Laszlo Sandor Koncz, Marietta Petroczy, Bela Penzes, Marta Ladanyi, Laszlo Palkovics, Piroska Gyocsi, Geza Nagy, Janos agoston, Jozsef Fail
Summary: The pathogen 'Candidatus Phytoplasma prunorum' was identified as the cause of apricot tree decline in European countries. It was found in both plant tissues and insects, with a 29.6% incidence rate in apricot trees. The plum psyllid, Cacopsylla pruni, was confirmed as the main insect vector, with several infected adults observed. The related species, Cacopsylla crataegi, was also abundant and infected with the pathogen.
Article
Biochemical Research Methods
Martin Pirkl, Niko Beerenwinkel
Summary: A novel mathematical method has been developed to analyze cancer driver genes and patient-specific perturbation profiles by combining genetic aberrations with gene expression data in a causal network derived across patients to infer unobserved perturbations. The method has been shown to predict perturbations in simulations, CRISPR perturbation screens, and breast cancer samples from The Cancer Genome Atlas.
Article
Mycology
Bagdevi Mishra, Sebastian Ploch, Claus Weiland, Marco Thines
Summary: Phylogenetic inference is often used as a tool in biological studies to interpret laboratory experiments, but it is often performed at low standards, leading to potential misinterpretations. The TrEase web service was developed to provide a user-friendly and comprehensive pipeline for phylogenetic analysis, enabling beginners and researchers in biodiversity studies to easily access current phylogenetic methods.
MYCOLOGICAL PROGRESS
(2023)
Article
Biochemical Research Methods
Bennett J. Kapili, Anne E. Dekas
Summary: This study introduces an R package called PPIT that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. By placing query sequences on a reference nifH gene tree, PPIT searches the phylogenetic neighborhood of each query sequence and attempts to draw microbial taxonomy inferences. The results show that PPIT returns a higher proportion of correct taxonomic inferences compared to BLAST-based approaches.
Article
Biotechnology & Applied Microbiology
Mohammad Shahrokh Esfahani, Emily G. Hamilton, Mahya Mehrmohamadi, Barzin Y. Nabet, Stefan K. Alig, Daniel A. King, Chloe B. Steen, Charles W. Macaulay, Andre Schultz, Monica C. Nesselbush, Joanne Soo, Joseph G. Schroers-Martin, Binbin Chen, Michael S. Binkley, Henning Stehr, Jacob J. Chabon, Brian J. Sworder, Angela B-Y Hui, Matthew J. Frank, Everett J. Moding, Chih Long Liu, Aaron M. Newman, James M. Isbell, Charles M. Rudin, Bob T. Li, David M. Kurtz, Maximilian Diehn, Ash A. Alizadeh
Summary: EPIC-seq is a method that predicts gene expression levels at individual genes from cfDNA. We demonstrate the potential of EPIC-seq in cancer subtype classification and prediction of clinical response.
NATURE BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, Nozomu Yachie
Summary: This study proposes a deep distributed computing framework, FRACTAL, for inferring large-scale cell lineages. The framework constructs lineages from a large number of input sequences through recursive iteration, significantly enhancing scalability, and demonstrates its utility in different experiments.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Juho Timonen, Henrik Mannerstrom, Aki Vehtari, Harri Lahdesmaki
Summary: Longitudinal study designs are crucial for studying disease progression, but interpreting covariate effects from such data is challenging. The proposed method lgpr outperforms previous approaches in identifying relevant covariates and incorporates features to handle covariate heterogeneity and temporal uncertainty in biomedical data analysis. The tool is implemented as a comprehensive and user-friendly R-package.
Article
Biodiversity Conservation
Daijiang Li
Summary: Despite the availability of phylogenetic hypotheses for many taxonomic groups, most do not include all species. In phylogenetic ecology, there is a demand for phylogenies that encompass all species in a study. Existing software tools for grafting species to megatrees are limited to specific taxonomic groups. The new R package 'rtrees' aims to provide an easy, flexible, and reliable way to assemble phylogenies from megatrees, facilitating progress in phylogenetic ecology.
Article
Biochemical Research Methods
Ben Bettisworth, Alexandros Stamatakis
Summary: RootDigger is a software that uses a non-reversible Markov model to compute the most likely root location and infer confidence values for each possible root placement on a tree. It is successful at finding roots and occasionally outperforms similar tools like IQ-TREE and MAD. The exhaustive mode of RootDigger helps in quantifying and explaining uncertainty in rooting positions.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu
Summary: The reconstruction of phylogenetic networks is a challenging task due to the vastness of the network space. One approach is to solve the minimum phylogenetic network problem by inferring phylogenetic trees first and then computing the smallest network that displays all the trees. A new method, named ALTS, was developed to infer the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees, overcoming the limitations of existing programs. ALTS is fast enough to handle large-scale networks with reticulations for a set of up to 50 phylogenetic trees with 50 taxa in about 15 minutes on average.
Article
Biochemical Research Methods
Nadia Tahiri, Bernard Fichet, Vladimir Makarenkov
Summary: Every gene has its own evolutionary history which can differ from that of other genes. We present a new efficient method for inferring multiple alternative consensus trees and supertrees to represent the important evolutionary patterns of gene phylogenies.
Article
Biochemical Research Methods
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova
Summary: Recent studies have identified limitations in current computational methods for inferring tumor phylogenies. The new SASC approach, based on simulated annealing and using the Dollo-k model, demonstrates high accuracy in inferring cancer progressions.
Article
Immunology
Molly J. Stout, Anoop K. Brar, Brandi N. Herter, Ananda Rankin, Kristine M. Wylie
Summary: Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Our study found that Black race was associated with higher viral richness in maternal blood samples during pregnancy.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pierre Barbera, Lucas Czech, Sarah Lutteropp, Alexandros Stamatakis
Summary: Microbial ecology research benefits from the decreasing cost of DNA sequencing and improved accuracy of data analysis methods. The tool scrapp, utilizing a molecular species delimitation algorithm, quantifies diversity distribution over a reference phylogeny based on phylogenetic placements of samples. Employing placement space clustering for dimensionality reduction, scrapp performs well on simulated and empirical data sets for classifying samples based on diversity features.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Education, Scientific Disciplines
Marise Ph Born, Karen M. Stegers-Jager, Chantal E. E. van Andel
Summary: This paper discusses how to infer students' overall competency profile from convenience samples using insights from psychology. It adapts Smith's theory of predictor validity to clinical competency assessment, emphasizing the importance of considering whether traits are universals, occupationals, or relationals when generalizing from assessed clinical competencies to generic competencies. Smith's distinction offers a promising way forward for medical education in terms of assessment, student selection, and career choice.
Article
Biotechnology & Applied Microbiology
Simone Zaccaria, Benjamin J. Raphael
Summary: Single-cell barcoding technologies enable simultaneous genome sequencing of thousands of individual cells, but with low sequencing coverage per cell. A method called CHISEL was introduced to infer allele- and haplotype-specific copy numbers in single cells and subpopulations by aggregating sparse signal across hundreds or thousands of individual cells. Application of CHISEL to single-cell sequencing datasets from breast cancer patients identified extensive allele-specific copy-number aberrations affecting genomic regions containing well-known breast cancer genes.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rebecca Elyanow, Ron Zeira, Max Land, Benjamin J. Raphael
Summary: Tumors are highly heterogeneous with different cell populations, creating a distinct microenvironment. Spatial transcriptomics technology can measure spatial patterns of gene expression. Gene expression patterns represent the combined contribution of regulatory mechanisms and genetic diversity. The new method STARCH can infer CNAs from spatial transcriptomics data.
Article
Cell Biology
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A. A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J. C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
Summary: Alterations in the RTK/RAS/RAF pathway are a characteristic feature of lung adenocarcinoma (LUAD). A study using whole-genome sequencing of 85 cases initially identified as RPA(-) revealed that around 33% of cases were actually RPA(+). The remaining cases showed genetic mutations associated with tumor suppressor deletions and genome instability.
Article
Biochemistry & Molecular Biology
Stefan C. Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester, Ignacio Vazquez-Garcia, Kortine Kleinheinz, Dimitri G. Livitz, Salem Malikic, Nilgun Donmez, Subhajit Sengupta, Pavana Anur, Clemency Jolly, Marek Cmero, Daniel Rosebrock, Steven E. Schumacher, Yu Fan, Matthew Fittall, Ruben M. Drews, Xiaotong Yao, Thomas B. K. Watkins, Juhee Lee, Matthias Schlesner, Hongtu Zhu, David J. Adams, Nicholas McGranahan, Charles Swanton, Gad Getz, Paul C. Boutros, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Inigo Martincorena, Florian Markowetz, Ville Mustonen, Ke Yuan, Moritz Gerstung, Paul T. Spellman, Wenyi Wang, Quaid D. Morris, David C. Wedge, Peter Van Loo
Summary: By extensively characterizing intra-tumor heterogeneity (ITH) across 2,658 cancer samples spanning 38 cancer types, this study found evidence of distinct subclonal expansions in nearly all informative samples, with frequent branching relationships between subclones. Positive selection of subclonal driver mutations was observed across most cancer types, indicating the importance of ITH and its drivers in tumor evolution.
Article
Multidisciplinary Sciences
Kuan-lin Huang, Adam D. Scott, Daniel Cui Zhou, Liang-Bo Wang, Amila Weerasinghe, Abdulkadir Elmas, Ruiyang Liu, Yige Wu, Michael C. Wendl, Matthew A. Wyczalkowski, Jessika Baral, Sohini Sengupta, Chin-Wen Lai, Kelly Ruggles, Samuel H. Payne, Benjamin Raphael, David Fenyo, Ken Chen, Gordon Mills, Li Ding
Summary: Advances in mass-spectrometry have led to the generation of large-scale proteomics datasets containing tens of thousands of phosphorylation sites. Using a bioinformatics tool called HotPho, researchers identified 474 hybrid clusters of phosphosites and cancer mutations on protein structures, highlighting nearly 3,000 likely functional mutations and over 1,000 cancer phosphosites for potential clinical relevance.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Gryte Satas, Simone Zaccaria, Mohammed El-Kebir, Benjamin J. Raphael
Summary: DeCiFer is a new algorithm that improves the estimation of cancer cell fraction (CCF) by utilizing the descendant cell fraction (DCF), providing more accurate quantification of tumor heterogeneity and evolution.
Article
Biochemical Research Methods
Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J. Raphael
Summary: PASTE is a method for aligning and integrating spatial transcriptomics data from adjacent tissue slices, which utilizes transcriptomic similarity and spatial coordinates to increase downstream analysis power. PASTE accurately aligns spots, constructs 3D alignments or integrates into a consensus slice, and improves the identification of cell types and differentially expressed genes.
Article
Neurosciences
Sasi Arunachalam, Karol Szlachta, Samuel W. Brady, Xiaotu Ma, Bensheng Ju, Bridget Shaner, Heather L. Mulder, John Easton, Benjamin J. Raphael, Matthew Myers, Christopher Tinkle, Sariah J. Allen, Brent A. Orr, Cynthia J. Wetmore, Suzanne J. Baker, Jinghui Zhang
Summary: This study investigates the tumor invasion patterns in diffuse midline gliomas with H3 K27 alteration. The findings reveal the existence of multiple waves of invasion and the association between somatic mutations and convergent evolution. The results provide insights for the design of future clinical trials.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Editorial Material
Oncology
Shree Bose, Margarida Barroso, Milan G. Chheda, Hans Clevers, Elena Elez, Salma Kaochar, Scott E. Kopetz, Xiao-Nan Li, Funda Meric-Bernstam, Clifford A. Meyer, Haiwei Mou, Kristen M. Naegle, Martin F. Pera, Zinaida Perova, Katerina A. Politi, Benjamin J. Raphael, Paul Robson, Rosalie C. Sears, Josep Tabernero, David A. Tuveson, Alana L. Welm, Bryan E. Welm, Christopher D. Willey, Konstantin Salnikow, Jeffrey H. Chuang, Xiling Shen
Summary: 3D patient tumor avatars hold great promise for precision medicine, but their clinical benefits need to be established through standardization and prospective trials. Innovative trial designs and integrated platforms combining diagnostics and therapeutics can accelerate the development of new treatments for refractory diseases.
Article
Biochemistry & Molecular Biology
Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael
Summary: Spatially resolved transcriptomics technology allows for the measurement of gene expression at known locations in tissue slices, enabling the identification of spatially varying genes or cell types. This study proposes a model and algorithm for SRT data from layered tissues that considers both continuous and discrete spatial variation in gene expression. The algorithm accurately identifies tissue layers and biologically meaningful spatially varying genes in SRT data from the brain and skin.
Article
Multidisciplinary Sciences
Di Zhang, Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartosovic, Mingze Dong, Cong Ma, Sai Ma, Graham Su, Shuozhen Bao, Yang Liu, Yang Xiao, Gorazd B. Rosoklija, Andrew J. Dwork, J. John Mann, Kam W. Leong, Maura Boldrini, Liya Wang, Maximilian Haeussler, Benjamin J. Raphael, Yuval Kluger, Goncalo Castelo-Branco, Rong Fan
Summary: Emerging spatial technologies such as spatial transcriptomics and spatial epigenomics have become powerful tools in profiling cellular states in tissue contexts. However, current methods only capture one layer of omics information at a time, limiting the examination of mechanistic relationships in molecular biology. In this study, two technologies are presented for joint profiling of the epigenome and transcriptome at a genome-wide, spatially resolved, and near-single-cell resolution. These technologies provide new insights into spatial epigenetic priming, differentiation, and gene regulation within tissue architecture.
Article
Oncology
Sanjana Rajan, Simone Zaccaria, Matthew V. Cannon, Maren Cam, Amy C. Gross, Benjamin J. Raphael, Ryan D. Roberts
Summary: Osteosarcoma is a malignancy with high genomic complexity. Through single-cell DNA sequencing, it is found that despite extensive structural complexity, there is a high degree of cell-cell homogeneity in these tumors with little subclonal diversification. Longitudinal analysis also shows that most somatic copy-number aberrations (SCNAs) are acquired early in the oncogenic process and are preserved over tumor evolution. These findings have implications for diagnosis, biomarker assessment, and understanding tumor heterogeneity and evolution.
CANCER RESEARCH COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Palash Sashittal, Haochen Zhang, Christine A. Iacobuzio-Donahue, Benjamin J. Raphael
Summary: This article introduces a new evolutionary model and algorithm, ConDoR, for inferring phylogeny in tumors. The model uses SNVs as phylogenetic markers and constrains losses of SNVs according to clusters of cells. The advantages of ConDoR are demonstrated through simulations and real data.
Article
Biochemical Research Methods
Henri Schmidt, Palash Sashittal, Benjamin J. Raphael
Summary: New low-coverage single-cell DNA sequencing technologies enable the inference of tumor evolutionary history by modeling copy number aberrations. A widely used model is the copy number transformation (CNT) model, but no efficient algorithm has been developed to find the most parsimonious phylogeny. This study introduces the zero-agnostic copy number transformation (ZCNT) model and develops efficient algorithms for inferring phylogenies on copy number profiles.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael
Summary: A standard paradigm in computational biology is to analyze high-throughput biological data using interaction networks as prior knowledge. This study introduces NetMix2, an algorithm that combines the advantages of subnetwork families and network propagation methods to identify altered subnetworks. NetMix2 outperforms other methods in various applications.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
