Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models

Authors: Pei, Jimin, Andreeva, Antonina, Chuguransky, Sara, Lázaro Pinto, Beatriz, Paysan-Lafosse, Typhaine, Dustin Schaeffer, R., Bateman, Alex, Cong, Qian, Grishin, Nick V.

Source: In Journal of Molecular Biology 15 November 2024 436(22)

Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)

Authors: Espeland, Marianne, Nakahara, Shinichi, Zacca, Thamara, Barbosa, Eduardo P., Huertas, Blanca, Marín, Mario A., Lamas, Gerardo, Benmesbah, Mohamed, Brévignon, Christian, Casagrande, Mirna M., Fåhraeus, Christer, Grishin, Nick, Kawahara, Akito Y., Mielke, Olaf H. H., Miller, Jacqueline Y., Nakamura, Ichiro, Navas, Vanessa, Patrusky, Brooke, Pyrcz, Tomasz W., Richards, Lindsay, Tan, Denise, Tyler, Stephanie, Viloria, Ángel, Warren, Andrew D., Xiao, Lei, Freitas, André V. L., Willmott, Keith R.

Source: Systematic entomology. 48(4):498-570

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100192056924.0x000001&indx=1&recIds=ETOCvdc_100192056924.0x000001

ZNF692 organizes a hub specialized in 40S ribosomal subunit maturation enhancing translation in rapidly proliferating cells

Authors: Lafita-Navarro, M. Carmen, Hao, Yi-Heng, Jiang, Chunhui, Jang, Seoyeon, Chang, Tsung-Cheng, Brown, Isabella N., Venkateswaran, Niranjan, Maurais, Elizabeth, Stachera, Weronika, Zhang, Yanfeng, Mundy, Dorothy, Han, Jungsoo, Tran, Vanna M., Mettlen, Marcel, Xu, Lin, Woodruff, Jeffrey B., Grishin, Nick V., Kinch, Lisa, Mendell, Joshua T., Buszczak, Michael, Conacci-Sorrell, Maralice

Source: In Cell Reports 31 October 2023 42(10)

Erythrina stem borer moth in California – New taxonomic status and implications for control of this emerging pest

Authors: Sourakov, Andrei, Zhang, Jing, Cong, Qian, Song, Leina, Grishin, Nick V.

Source: Journal of applied entomology. 146(10):1225-1229

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100168390274.0x000001&indx=1&recIds=ETOCvdc_100168390274.0x000001

DisEnrich: database of enriched regions in human dark proteome

Authors: Medvedev, Kirill E, Pei, Jimin, Grishin, Nick V

Source: Bioinformatics. 38(7):1870-1876

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164935601.0x000001&indx=1&recIds=ETOCvdc_100164935601.0x000001

Genomics‐based higher classification of the species‐rich hairstreaks (Lepidoptera: Lycaenidae: Eumaeini)

Authors: Robbins, Robert K., Cong, Qian, Zhang, Jing, Shen, Jinhui, Busby, Robert C., Faynel, Christophe, Duarte, Marcelo, Martins, Ananda R. P., Prieto, Carlos, Lamas, Gerardo, Grishin, Nick V.

Source: Systematic entomology. 47(3):445-469

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100154052975.0x000001&indx=1&recIds=ETOCvdc_100154052975.0x000001

The Pfam protein families database: embracing AI/ML.

Authors: Paysan-Lafosse, Typhaine, Andreeva, Antonina, Blum, Matthias, Chuguransky, Sara Rocio, Grego, Tiago, Pinto, Beatriz Lazaro, Salazar, Gustavo A, Bileschi, Maxwell L, Llinares-López, Felipe, Meng-Papaxanthos, Laetitia, Colwell, Lucy J, Grishin, Nick V, Schaeffer, R Dustin, Clementel, Damiano, Tosatto, Silvio C E, Sonnhammer, Erik, Wood, Valerie, Bateman, Alex

Source: Nucleic Acids Research; 1/6/2025, Vol. 53 Issue D1, pD523-D534, 12p

ECOD: integrating classifications of protein domains from experimental and predicted structures.

Authors: Schaeffer, R Dustin, Medvedev, Kirill E, Andreeva, Antonina, Chuguransky, Sara Rocio, Pinto, Beatriz Lazaro, Zhang, Jing, Cong, Qian, Bateman, Alex, Grishin, Nick V

Source: Nucleic Acids Research; 1/6/2025, Vol. 53 Issue D1, pD411-D418, 8p

Gauging ages of tiger swallowtail butterflies using alternate SNP analyses

Authors: Vernygora, Oksana V., Campbell, Erin O., Grishin, Nick V., Sperling, Felix A.H., Dupuis, Julian R.

Source: In Molecular Phylogenetics and Evolution June 2022 171

A switch to feeding on cycads generates parallel accelerated evolution of toxin tolerance in two clades of Eumaeus caterpillars (Lepidoptera: Lycaenidae)

Authors: Robbins, Robert K., Cong, Qian, Zhang, Jing, Shen, Jinhui, Riera, Julia Quer, Murray, Debra, Busby, Robert C., Faynel, Christophe, Hallwachs, Winnie, Janzen, Daniel H., Grishin, Nick V.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Feb . 118(7), 1-6.

Access URL: https://www.jstor.org/stable/27027329

The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers
Mathematical and computational oncology (2nd international symposium) held online

Authors: Medvedev, Kirill E., Savelyeva, Anna V., Bagrodia, Aditya, Grishin, Nick V.

Source: Lecture notes in computer science. 12508:79-86

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN606529087&indx=1&recIds=ETOCCN606529087

Structural Differences between Proteins with Similar Sequences

Authors: Cong, Qian, Kim, Bong-Hyun, Kinch, Lisa N., Grishin, Nick V.

Source: 2010 IEEE International Conference on BioInformatics and BioEngineering BioInformatics and BioEngineering (BIBE), 2010 IEEE International Conference on. :250-256 May, 2010

Relation: 2010 International Conference on BioInformatics and BioEngineering (BIBE)

The DBSAV Database: Predicting Deleteriousness of Single Amino Acid Variations in the Human Proteome

Authors: Pei, Jimin, Grishin, Nick V.

Source: In Journal of Molecular Biology 28 May 2021 433(11)

A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy

Authors: Ni, Min, Afroze, Bushra, Xing, Chao, Pan, Chunxiao, Shao, Yanqiu, Cai, Ling, Cantarel, Brandi L., Pei, Jimin, Grishin, Nick V., Hewson, Stacy, Knight, Devon, Mahida, Sonal, Michel, Donnice, Tarnopolsky, Mark, Poduri, Annapurna, Rotenberg, Alexander, Sondheimer, Neal, DeBerardinis, Ralph J.

Source: In Genetics in Medicine May 2021 23(5):900-908

A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit

Authors: Medvedev, Kirill E., Kinch, Lisa N., Dustin Schaeffer, R., Pei, Jimin, Grishin, Nick V.

Source: In Journal of Molecular Biology 19 February 2021 433(4)

Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14)

Authors: Kinch, Lisa N., Schaeffer, R. Dustin, Kryshtafovych, Andriy, Grishin, Nick V.

Source: Proteins. 89(12):1618-1632

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100134836054.0x000001&indx=1&recIds=ETOCvdc_100134836054.0x000001

Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14)

Authors: Schaeffer, R. Dustin, Kinch, Lisa, Kryshtafovych, Andriy, Grishin, Nick V.

Source: Proteins. 89(12):1700-1710

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100134836085.0x000001&indx=1&recIds=ETOCvdc_100134836085.0x000001

Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14)

Authors: Kinch, Lisa N., Pei, Jimin, Kryshtafovych, Andriy, Schaeffer, R. Dustin, Grishin, Nick V.

Source: Proteins. 89(12):1673-1686

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100134836022.0x000001&indx=1&recIds=ETOCvdc_100134836022.0x000001

Influence of the large‐Z effect during contact between butterfly sister species

Authors: Nelson, Erik D., Cong, Qian, Grishin, Nick V.

Source: Ecology and evolution. 11(17):11615-11626

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132550778.0x000001&indx=1&recIds=ETOCvdc_100132550778.0x000001

Metabolic impact of pathogenic variants in the mitochondrial glutamyl‐tRNA synthetase EARS2

Authors: Ni, Min, Black, Lauren F., Pan, Chunxiao, Vu, Hieu, Pei, Jimin, Ko, Bookyung, Cai, Ling, Solmonson, Ashley, Yang, Chendong, Nugent, Kimberly M., Grishin, Nick V., Xing, Chao, Roeder, Elizabeth, DeBerardinis, Ralph J.

Source: Journal of inherited metabolic disease. 44(4):949-960

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127368410.0x000001&indx=1&recIds=ETOCvdc_100127368410.0x000001