UniRef: comprehensive and non-redundant UniProt reference clusters

Cited by (1,003)

Items 201–300 of 1,003

1. A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica
   Neeraja M. Krishnan, Swetansu Pattnaik, Prachi Jain, Prakhar Gaur, Rakshit Choudhary, Srividya Vaidyanathan, Sa Deepak, Arun K Hariharan, P. B. Krishna, Jayalakshmi Nair et al. · 2012 · BMC Genomics
2. Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona
   Zhemin Zhou, Angela McCann, Eva Litrup, Ronan A. Murphy, Martin Cormican, Séamus Fanning, Derek Brown, David S. Guttman, Sylvain Brisse, Mark Achtman · 2013 · PLoS Genetics
3. Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation
   Chuming Chen, Darren A. Natale, Robert D. Finn, Hongzhan Huang, Jian Zhang, Cathy H. Wu, Raja Mazumder · 2011 · PLoS ONE
4. Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants
   Robert Heyer, Kay Schallert, Corina Siewert, Fabian Kohrs, J. Greve, Irena Maus, Johanna Klang, Michael Klocke, Monika Heiermann, Marcus Hoffmann et al. · 2019 · Microbiome
5. Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches
   Foo Cheung, Joe Win, Jillian M. Lang, John P. Hamilton, Hue Vuong, Jan E. Leach, Sophien Kamoun, C. André Lévesque, Ned A. Tisserat, C. Robin Buell · 2008 · BMC Genomics
6. Discovery of bioactive microbial gene products in inflammatory bowel disease
   Yancong Zhang, Amrisha Bhosle, Sena Bae, Lauren J. McIver, Gleb Pishchany, Emma K. Accorsi, Kelsey N. Thompson, Cesar Arze, Ya Wang, Ayshwarya Subramanian et al. · 2022 · Nature
7. LncRNA-ID: Long non-coding RNA IDentification using balanced random forests
   Rujira Achawanantakun, Jiao Chen, Yanni Sun, Yuan Zhang · 2015 · Bioinformatics
8. kClust: fast and sensitive clustering of large protein sequence databases
   Maria Hauser, C. Mayer, Johannes Söding · 2013 · BMC Bioinformatics
9. Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications
   Himabindu Kudapa, Sarwar Azam, Andrew G. Sharpe, Bunyamin Tar’an, Rong Li, Benjamin Deonovic, Connor T. Cameron, Andrew D Farmer, Steven B. Cannon, Rajeev Kumar Varshney · 2014 · PLoS ONE
10. Sequencing-based analysis of microbiomes
    Yishay Pinto, Ami Siddharth Bhatt · 2024 · Nature Reviews Genetics
11. Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite
    Mark McMullan, Anastasia Gardiner, Kate Bailey, Eric M. Kemen, Ben J. Ward, Volkan Çevik, Alexandre Robert‐Seilaniantz, Torsten Schultz‐Larsen, Alexi L. Balmuth, Eric B. Holub et al. · 2015 · eLife
12. Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone
    Trigg, Jason, Gutwin, Karl, Keating, Amy E., Berger, Bonnie · 2011 · PLoS One
13. Genomic language model predicts protein co-regulation and function
    Hwang, Yunha, Cornman, Andre L., Kellogg, Elizabeth H., Ovchinnikov, Sergey, Girguis, Peter R. · 2024 · Nature Communications
14. Fruit load induces changes in global gene expression and in abscisic acid (ABA) and indole acetic acid (IAA) homeostasis in citrus buds
    Liron Shalom, Sivan Samuels, Naftali Zur, Lyudmila Shlizerman, Adi Doron‐Faigenboim, Eduardo Blumwald, Avi Sadka · 2014 · Journal of Experimental Botany
15. Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion
    Qianmu Yuan, Junjie Xie, Jiancong Xie, Huiying Zhao, Yuedong Yang · 2023 · Briefings in Bioinformatics
16. MonarchBase: the monarch butterfly genome database
    Shuai Zhan, Steven M. Reppert · 2012 · Nucleic Acids Research
17. Protein function prediction by massive integration of evolutionary analyses and multiple data sources
    Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones · 2013 · BMC Bioinformatics
18. Metaproteomic data analysis at a glance: advances in computational microbial community proteomics
    Thilo Muth, Bernhard Y. Renard, Lennart Martens · 2016 · Expert Review of Proteomics
19. Protein model quality assessment using 3D oriented convolutional neural networks
    Guillaume Pagès, Benoit Charmettant, Sergei Grudinin · 2019 · Bioinformatics
20. A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria
    Lina Yao, Gabriel D. D’Agostino, Jinseok Park, Saiyu Hang, Arijit A. Adhikari, Yancong Zhang, Wei Li, Julián Ávila-Pacheco, Sena Bae, Clary B. Clish et al. · 2022 · Nature Microbiology
21. Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
    Chi Nam Ignatius Pang, Elisabeth Gasteiger, Marc Ronald Wilkins · 2010 · BMC Genomics
22. Complete Genome Sequence of the Photosynthetic Purple Nonsulfur Bacterium Rhodobacter capsulatus SB 1003
    Hynek Strnad, Alla L Lapidus, Jan Pačes, Pavel Ulbrich, Čestmı́r Vlček, Václav Pačes, Robert Haselkorn · 2010 · Journal of Bacteriology
23. Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface
    Lianna Poghosyan, Hanna Koch, Adi Lavy, J. Frank, M. van Kessel, M. Jetten, J. Banfield, S. Lücker · 2019 · Environmental Microbiology
24. A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle
    Jacoline Gerritsen, Bastian Hornung, Jarmo Ritari, Lars G. Paulin, Ger T. Rijkers, Peter J. Schaap, Willem M. de Vos, Hauke Smidt · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
25. SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
    T. P. Walsh, Caleb Webber, Stephen M. J. Searle, Shane S. Sturrock, Geoffrey J. Barton · 2008 · Nucleic Acids Research
26. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants
    Kymberleigh A. Pagel, Vikas Rao Pejaver, Guan Ning Lin, Hyun-Jun Nam, Matthew E. Mort, D.N. Cooper, Jonathan L. Sebat, Lilia M. Iakoucheva, Sean David Mooney, Predrag Radivojac A · 2017 · Bioinformatics
27. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
    Christian Rinke, Serene Low, Ben J. Woodcroft, Jean‐Baptiste Raina, Adam Skarshewski, Xuyen H. Le, Margaret K. Butler, Roman Stocker, Justin Robert Seymour, Gene W. Tyson et al. · 2016 · PeerJ
28. Rules and mechanisms governing G protein coupling selectivity of GPCRs
    Ikuo Masuho, Ryoji Kise, Pablo Gaínza, Ee Von Moo, Xiaona Li, Ryosuke Tany, Hideko Wakasugi-Masuho, Bruno E. Correia, Kirill A. Martemyanov · 2023 · Cell Reports
29. The Large Language Models on Biomedical Data Analysis: A Survey
    Wei Lan, Zhentao Tang, Mingyang Liu, Qingfeng Chen, Wei Peng, Yi‐Ping Phoebe Chen, Yi Feng Pan · 2025 · IEEE Journal of Biomedical and Health Informatics
30. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
    Rick E. Masonbrink, Tom R. Maier, Usha K. Muppirala, Arun Somwarpet Seetharam, Étienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nathan T. Johnson, Dmitry Korkin, Melissa Goellner Mitchum et al. · 2019 · BMC Genomics
31. Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis
    John P. Hamilton, Sung‐Chur Sim, Kevin M. Stoffel, Allen Van Deynze, C. Robin Buell, David Merrill Francis · 2012 · The Plant Genome
32. The s2D Method: Simultaneous Sequence-Based Prediction of the Statistical Populations of Ordered and Disordered Regions in Proteins
    Pietro Sormanni, Carlo Camilloni, Piero Fariselli, Michele Vendruscolo · 2014 · Journal of Molecular Biology
33. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome
    Emily B. Hollister, Numan Oezguen, Bruno Pedro Chumpitazi, Ruth Ann Luna, Erica M. Weidler, Michelle Rubio-Gonzales, Mahmoud Dahdouli, Julia L. Cope, Toni‐Ann Mistretta, Sabeen Raza et al. · 2019 · Journal of Molecular Diagnostics
34. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
    Irene Huang Zhang, Xin Sun, Amal Jayakumar, Samantha G. Fortin, Bess B. Ward, Andrew R. Babbin · 2023 · ISME Communications
35. Enterotypes of the human gut mycobiome
    Senying Lai, Yan Yan, Yanni Pu, Shuchun Lin, Jian‐Ge Qiu, Bing‐Hua Jiang, Marisa Isabell Keller, Mingyu Wang, Peer Bork, Wei‐Hua Chen et al. · 2023 · Microbiome
36. Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis
    Shivraj Braich, Rebecca C. Baillie, Larry S. Jewell, GERMAN C. SPANGENBERG, Noel O. I. Cogan · 2019 · Scientific Reports
37. Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network
    Keith Bouma‐Gregson, Matthew R. Olm, Alexander J. Probst, Karthik Anantharaman, Mary E. Power, Jillian F. Banfield · 2019 · The ISME Journal
38. Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense
    Qian Cong, Dominika Borek, Zbyszek Otwinowski, Nick V. Grishin · 2015 · Cell Reports
39. Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit
    Ebenezer A. Ogundiwin, Cristina Martí, Javier Forment, Clara Pons, Antonio Granell, Thomas M. Gradziel, Cameron Peace, Carlos H. Crisosto · 2008 · Plant Molecular Biology
40. Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
    Paula B. Matheus Carnevali, Frederik Schulz, Cindy J. Castelle, Rose S. Kantor, Patrick M. Shih, Itai Sharon, Joanne M. Santini, Matthew R. Olm, Yuki Amano, Brian C. Thomas et al. · 2019 · Nature Communications
41. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite
    Sun-Yang Park, Chitong Rao, Katharine Z. Coyte, Gavin A. Kuziel, Yancong Zhang, Wentao Huang, Eric A. Franzosa, Jing‐Ke Weng, Curtis Huttenhower, Seth Rakoff-Nahoum · 2022 · Cell
42. Establishing an In Vivo Assay System to Identify Components Involved in Environmental RNA Interference in the Western Corn Rootworm
    Keita Miyata, Parthasarathy Ramaseshadri, Yuanji Zhang, Gerrit C. Segers, Renata Bolognesi, Yoshinori Tomoyasu · 2014 · PLoS ONE
43. Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae
    Andy O Leu, Simon Jon McIlroy, Jun Ye, Donovan H. Parks, Victoria J. Orphan, Gene W. Tyson · 2020 · mBio
44. Improving protein succinylation sites prediction using embeddings from protein language model
    Suresh Pokharel, Pawel Pratyush, Michael Heinzinger, Robert Howard Newman, Dukka B. KC · 2022 · Scientific Reports
45. Enhancing efficiency of protein language models with minimal wet-lab data through few-shot learning
    Ziyi Zhou, Liang Zhang, Yuanxi Yu, Banghao Wu, Mingchen Li, Liang Hong, Pan Tan · 2024 · Nature Communications
46. Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures
    Yidong Song, Qianmu Yuan, Sheng Chen, Yuansong Zeng, Huiying Zhao, Yuedong Yang · 2024 · Nature Communications
47. GoFDR: A sequence alignment based method for predicting protein functions
    Qingtian Gong, Wei Ning, Weidong Tian · 2015 · Methods
48. Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies
    Megan A. Supple, Heather M. Hines, Kanchon K. Dasmahapatra, James J. Lewis, Dahlia M. Nielsen, Christine A. Lavoie, David A. Ray, Camilo A. Salazar, W. Owen McMillan, Brian A. Counterman · 2013 · Genome Research
49. Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma
    Wind, Thijs T., Gacesa, Ranko, Vich Vila, Arnau, de Haan, Jacco J., Jalving, Mathilde, Weersma, Rinse K., Hospers, Geke A.P. · 2020 · Melanoma Research
50. A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
    Alexa M. Nicolas, Ella Tali Sieradzki, Jennifer Pett‐Ridge, Jillian F. Banfield, Michiko E. Taga, Mary K. Firestone, Steven J. Blazewicz · 2023 · Nature Communications
51. Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei
    Fernando E. Vega, Stuart M. Brown, Hao Chen, Eric Shen, Mridul B. Nair, Javier A. Ceja-Navarro, Eoin Brodie, Francisco Infante, Patrick F. Dowd, Arnab Pain · 2015 · Scientific Reports
52. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence
    Elsa Góngora‐Castillo, C. Robin Buell · 2013 · Natural Product Reports
53. Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L.
    Anna Schallau, Francesco Arzenton, Amal J. Johnston, Urs Hähnel, Dávid Kőszegi, Frank R. Blattner, Lothar Altschmied, Georg Haberer, Gianni Barcaccia, Helmut Bäumlein · 2010 · The Plant Journal
54. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers
    João M. P. Alves, Cecília C. Klein, Flávia da Silva, André G. Costa-Martins, Myrna G. Serrano, Gregory A. Buck, Ana Tereza Ribeiro de Vasconcelos, Marie‐France Sagot, Marta M. G. Teixeira, María Cristina M. Motta et al. · 2013 · BMC Evolutionary Biology
55. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome
    Kymberleigh A. Pagel, Danny Antaki, Aojie Lian, Matthew E. Mort, D.N. Cooper, Jonathan L. Sebat, Lilia M. Iakoucheva, Sean David Mooney, Predrag Radivojac A · 2019 · PLoS Computational Biology
56. Codon language embeddings provide strong signals for use in protein engineering
    Carlos Outeiral, Charlotte Mary Deane · 2024 · Nature Machine Intelligence
57. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota
    Paul O. Sheridan, Sébastien Raguideau, Christopher Quince, Jennifer M. Holden, Lihong Zhang, William H. Gaze, Jennifer M. Holden, Andrew Mead, Sébastien Raguideau, Christopher Quince et al. · 2020 · Nature Communications
58. Prediction of hemolytic peptides and their hemolytic concentration
    Anand Singh Rathore, Nishant Kumar, Shubham Choudhury, Naman Kumar Mehta, Gajendra P. S. Raghava · 2025 · Communications Biology
59. Model quality assessment for membrane proteins
    Arjun Ray, Erik R. Lindahl, Björn Wallner · 2010 · Bioinformatics
60. A statistical view of protein chemical synthesis using NCL and extended methodologies
    Vangelis Agouridas, Ouafâa El Mahdi, Marine Cargoët, Oleg Melnyk · 2017 · Bioorganic & Medicinal Chemistry
61. Probiotic bacteria and bile acid profile are modulated by prebiotic diet and associate with facilitated diurnal clock/sleep realignment after chronic disruption of rhythms
    Robert S. Thompson, Michelle Gaffney, Shelby Hopkins, Tel Kelley, Antonio González, Samuel J. Bowers, Martha Hotz Vitaterna, Fred William Turek, Christine L. Foxx, Christopher A. Lowry et al. · 2021 · Brain Behavior and Immunity
62. A Root-Expressed l -Phenylalanine:4-Hydroxyphenylpyruvate Aminotransferase Is Required for Tropane Alkaloid Biosynthesis in Atropa belladonna
    Matthew A. Bedewitz, Elsa Góngora‐Castillo, Joseph B. Uebler, Eliana Gonzales‐Vigil, Krystle E. Wiegert-Rininger, Kevin L. Childs, John P. Hamilton, Brieanne Vaillancourt, Yunsoo Yeo, Joseph Chappell et al. · 2014 · The Plant Cell
63. Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods
    Andrew D. Huang, Chengwei Luo, Ángela Peña, Michael R. Weigand, Cheryl L. Tarr, Konstantinos T. Konstantinidis · 2016 · Applied and Environmental Microbiology
64. Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean
    Kyle R. Frischkorn, Mónica Rouco, Benjamin A. S. Van Mooy, Sonya T. Dyhrman · 2017 · The ISME Journal
65. Expression of Lignin Biosynthetic Genes in Wheat during Development and upon Infection by Fungal Pathogens
    Caili Bi, Fang Chen, Lisa Jackson, Bikram Singh Gill, Wanlong Li · 2010 · Plant Molecular Biology Reporter
66. Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis
    Bishwo N. Adhikari, Elizabeth A. Savory, Brieanne Vaillancourt, Kevin L. Childs, John P. Hamilton, Brad Day, C. Robin Buell · 2012 · PLoS ONE
67. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
    Yuji Sekiguchi, Akiko Ohashi, Donovan H. Parks, Toshihiro Yamauchi, Gene W. Tyson, Philip Hugenholtz · 2015 · PeerJ
68. Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome
    Qin Liu, Qi Su, Fen Zhang, Hein M. Tun, Joyce Wing Yan Mak, Grace Chung-Yan Lui, Susanna S. Ng, Jessica Y. L. Ching, Wenqi Lu, Wenqi Lu et al. · 2022 · Nature Communications
69. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment
    Kohei Ino, Alex W Hernsdorf, Uta Konno, Mariko Kouduka, Katsunori Yanagawa, Shingo Kato, Michinari Sunamura, Akinari Hirota, Yoko S. Togo, Kazumasa Ito et al. · 2017 · The ISME Journal
70. De novo transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set
    Sonal Singhal · 2013 · Molecular Ecology Resources
71. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae
    François Fauteux, Martina V. Strömvik · 2009 · BMC Plant Biology
72. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
    Nicholas B. Justice, Anders Norman, Christopher T. Brown, Andrea Singh, Brian C. Thomas, Jillian F. Banfield · 2014 · BMC Genomics
73. A structural model of the copper ATPase ATP7B to facilitate analysis of Wilson disease-causing mutations and studies of the transport mechanism
    Maya Schushan, Ashima Bhattacharjee, Nir Ben‐Tal, Svetlana Lutsenko · 2012 · Metallomics
74. The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome
    Shengzhi Yang, Yu Liu, Nan Yang, Yue Lan, Weiqi Lan, Jinyi Feng, Bisong Yue, Miao He, Liang Zhang, Anyun Zhang et al. · 2022 · Microbiome
75. Survey of the green picoalga Bathycoccus genomes in the global ocean
    Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Éric Pelletier, Jean‐Marc Aury, Colomban de Vargas, Michael E. Sieracki, Daniele Iudicone, Daniel Vaulot et al. · 2016 · Scientific Reports
76. Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model
    Zeng, Yuansong, Wei, Zhuoyi, Yuan, Qianmu, Chen, Sheng, Yu, Weijiang, Lu, Yutong, Gao, Jianzhao, Yang, Yuedong · 2023 · Bioinformatics
77. Comparative Genomic Characterization of Actinobacillus pleuropneumoniae
    Zhuofei Xu, Xiabing Chen, Lu Li, Tingting Li, Shengyue Wang, Huanchun Chen, Rui Zhou · 2010 · Journal of Bacteriology
78. Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses
    Eric G. Sakowski, Erik V. Munsell, Mara Hyatt, William Kress, Shannon J. Williamson, Daniel J. Nasko, Shawn W. Polson, K. Eric Wommack · 2014 · Proceedings of the National Academy of Sciences
79. SCLpred: protein subcellular localization prediction by N-to-1 neural networks
    Catherine Mooney, Yonghong Wang, Gianluca Pollastri · 2011 · Bioinformatics
80. Fine-tuning of BERT Model to Accurately Predict Drug–Target Interactions
    Hyeunseok Kang, Sungwoo Goo, Hyunjung Lee, Jung‐woo Chae, Hwi‐yeol Yun, Sangkeun Jung · 2022 · Pharmaceutics
81. The role and application of bioinformatics techniques and tools in drug discovery
    Shujun Zhang, Kaijie Liu, Yafeng Liu, Xinjun Hu, Xinyu Gu · 2025 · Frontiers in Pharmacology
82. Bioinformatics for personal genome interpretation
    Emidio Capriotti, Nathan L Nehrt, Maricel G. Kann, Yana Bromberg · 2012 · Briefings in Bioinformatics
83. Coordinated gene expression betweenTrichodesmiumand its microbiome over day–night cycles in the North Pacific Subtropical Gyre
    Kyle R. Frischkorn, Sheean T. Haley, Sonya T. Dyhrman · 2018 · The ISME Journal
84. Metaproteomics of fecal samples of Crohn's disease and Ulcerative Colitis
    Theresa Lehmann, Kay Schallert, Ramiro Vilchez‐Vargas, Dirk Benndorf, Sebastian Püttker, Svenja Sydor, Christian Schulz, Lars P. Bechmann, Ali E. Canbay, Benjamin Heidrich et al. · 2019 · Journal of Proteomics
85. Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities
    Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan, Phillip G. Popovich · 2021 · mSystems
86. Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
    Qianmu Yuan, Sheng Chen, Yu Wang, Huiying Zhao, Yuedong Yang · 2022 · Briefings in Bioinformatics
87. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus
    Eduardo Leal Oliveira Camargo, Leandro Costa do Nascimento, Marçal Soler, Marcela Mendes Salazar, Jorge Lepikson-Neto, Wesley Leoricy Marques, Ana Maria Martins Alves, Paulo José Pereira Lima Teixeira, Piotr A. Mieczkowski, Marcelo Falsarella Carazzolle et al. · 2014 · BMC Plant Biology
88. Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV‑2 Spike Proteins
    Gennady M. Verkhivker · 2020 · Journal of Proteome Research
89. Microbial Dark Matter: From Discovery to Applications
    Yuguo Zha, Hui Chong, Pengshuo Yang, Kang Ning · 2022 · Genomics Proteomics & Bioinformatics
90. Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution
    RLM Guedes, Francisco Prosdocimi, Gabriel da Rocha Fernandes, LK Moura, HAL Ribeiro, José Miguel Ortega · 2011 · BMC Genomics
91. Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance
    Lakshmipuram S. Swapna, Kuchi Srikeerthana, Narayanaswamy Srinivasan · 2012 · PLoS ONE
92. Functional profiling of the gut microbiome in disease-associated inflammation
    Daniela Börnigen, Xochitl C. Morgan, Eric A. Franzosa, Boyu Ren, Ramnik J. Xavier, Wendy S. Garrett, Curtis Huttenhower · 2013 · Genome Medicine
93. Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type
    Robert Heyer, Dirk Benndorf, Fabian Kohrs, Jo De Vrieze, Nico Boon, Marcus Hoffmann, Erdmann Rapp, Andreas Schlüter, Alexander Sczyrba, Udo Reichl · 2016 · Biotechnology for Biofuels
94. Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms
    Valeria Di Dato, Francesco Musacchia, Giuseppe Petrosino, Shrikant Patil, Marina Montresor, Remo Sanges, Maria Immacolata Ferrante · 2015 · Scientific Reports
95. De novo design of symmetric ferredoxins that shuttle electrons in vivo
    Andrew C. Mutter, Alexei M. Tyryshkin, Ian J. Campbell, Saroj Poudel, George N. Bennett, Jonathan J. Silberg, Vikas Nanda, Paul G. Falkowski · 2019 · Proceedings of the National Academy of Sciences
96. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation
    Glenn T. Howe, Jianbin Yu, Brian J. Knaus, Richard Cronn, Scott E. Kolpak, Peter C. Dolan, W. Walter Lorenz, Jeffrey F. D. Dean · 2013 · BMC Genomics
97. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study
    Qingyu Chen, Justin Zobel, Karin M. Verspoor · 2016 · Database
98. Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment
    Califf, Katy J., Schwarzberg-Lipson, Karen, Garg, Neha, Gibbons, Sean M., Caporaso, J. Gregory, Slots, Jørgen, Cohen, Chloe, Dorrestein, Pieter C., Kelley, Scott T. · 2017 · mSystems
99. Protein remote homology detection based on bidirectional long short-term memory
    Shumin Li, Junjie Chen, Bin Liu · 2017 · BMC Bioinformatics
100. Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil
     Evan P. Starr, Shengjing Shi, Steven J. Blazewicz, Benjamin J. Koch, Alexander J. Probst, Bruce A. Hungate, Jennifer Pett‐Ridge, Mary K. Firestone, Jillian F. Banfield · 2021 · mSphere