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2020 – today
- 2024
[j48]R. Dustin Schaeffer
, Jing Zhang, Kirill E. Medvedev, Lisa N. Kinch, Qian Cong, Nick V. Grishin:
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput. Biol. 20(2) (2024)- 2022
- [j47]Kirill E. Medvedev, Jimin Pei, Nick V. Grishin:
DisEnrich: database of enriched regions in human dark proteome. Bioinform. 38(7): 1870-1876 (2022) - 2020
- [j46]Yoonji Lee, Jordan M. Baumhardt, Jimin Pei, Yuh Min Chook, Nick V. Grishin:
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. Bioinform. 36(3): 961-963 (2020) - [j45]Jimin Pei, Lisa N. Kinch, Zbyszek Otwinowski, Nick V. Grishin:
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PLoS Comput. Biol. 16(5) (2020) - [c2]Kirill E. Medvedev, Anna V. Savelyeva, Aditya Bagrodia, Nick V. Grishin:
The Potential of Single Cell RNA-Sequencing Data for the Prediction of Gastric Cancer Serum Biomarkers. ISMCO 2020: 79-84
2010 – 2019
- 2019
- [j44]Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin:
Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PLoS Comput. Biol. 15(12) (2019) - 2018
- [j43]Yuxing Liao, R. Dustin Schaeffer, Jimin Pei, Nick V. Grishin:
A sequence family database built on ECOD structural domains. Bioinform. 34(17): 2997-3003 (2018) - 2017
- [j42]R. Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin:
ECOD: new developments in the evolutionary classification of domains. Nucleic Acids Res. 45(Database-Issue): D296-D302 (2017) - 2016
- [j41]Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski:
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput. Biol. 12(6) (2016) - 2015
- [j40]Darui Xu, Kara Marquis, Jimin Pei, Szu-Chin Fu, Tolga Cagatay, Nick V. Grishin, Yuh Min Chook:
LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins. Bioinform. 31(9): 1357-1365 (2015) - [j39]Jing Tong, Jimin Pei, Nick V. Grishin:
SFESA: a web server for pairwise alignment refinement by secondary structure shifts. BMC Bioinform. 16: 282:1-282:7 (2015) - 2014
- [j38]Hua Cheng, R. Dustin Schaeffer, Yuxing Liao, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V. Grishin:
ECOD: An Evolutionary Classification of Protein Domains. PLoS Comput. Biol. 10(12) (2014) - 2013
- [j37]Ivan K. Huang, Jimin Pei, Nick V. Grishin:
Defining and predicting structurally conserved regions in protein superfamilies. Bioinform. 29(2): 175-181 (2013) - [j36]Wenlin Li, Lisa N. Kinch, Nick V. Grishin:
Pclust: protein network visualization highlighting experimental data. Bioinform. 29(20): 2647-2648 (2013) - [j35]Renkai Ji, Qian Cong, Wenlin Li, Nick V. Grishin:
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. Bioinform. 29(22): 2953-2954 (2013) - [j34]Wenlin Li, Qian Cong, Lisa N. Kinch, Nick V. Grishin:
Seq2Ref: a web server to facilitate functional interpretation. BMC Bioinform. 14: 30 (2013) - 2012
- [j33]Bong-Hyun Kim, Bhadrachalam Chitturi, Nick V. Grishin:
Self consistency grouping: a stringent clustering method. BMC Bioinform. 13(S-13): S3 (2012) - 2011
- [j32]Qian Cong, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Vyacheslav N. Grishin, Wenlin Li, Nick V. Grishin:
An automatic method for CASP9 free modeling structure prediction assessment. Bioinform. 27(24): 3371-3378 (2011) - [j31]Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley:
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J. Comput. Chem. 32(8): 1680-1686 (2011) - 2010
- [j30]Bong-Hyun Kim, Qian Cong, Nick V. Grishin:
HangOut: generating clean PSI-BLAST profiles for domains with long insertions. Bioinform. 26(12): 1564-1565 (2010) - [c1]Qian Cong, Bong-Hyun Kim, Lisa N. Kinch, Nick V. Grishin:
Structural Differences between Proteins with Similar Sequences. BIBE 2010: 250-256
2000 – 2009
- 2009
- [j29]Shuoyong Shi, Jimin Pei, Ruslan Sadreyev, Lisa N. Kinch, Indraneel Majumdar, Jing Tong, Hua Cheng, Bong-Hyun Kim, Nick V. Grishin:
Analysis of CASP8 targets, predictions and assessment methods. Database J. Biol. Databases Curation 2009 (2009) - [j28]Ruslan Sadreyev, Shuoyong Shi, David Baker, Nick V. Grishin:
Structure similarity measure with penalty for close non-equivalent residues. Bioinform. 25(10): 1259-1263 (2009) - [j27]Yong Wang, Ruslan Sadreyev, Nick V. Grishin:
PROCAIN server for remote protein sequence similarity search. Bioinform. 25(16): 2076-2077 (2009) - [j26]Ruslan Sadreyev, Jamison D. Feramisco, Hensin Tsao, Nick V. Grishin:
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways. Bioinform. 25(22): 2891-2896 (2009) - [j25]Ruslan Sadreyev, Yong Wang, Nick V. Grishin:
Considering scores between unrelated proteins in the search database improves profile comparison. BMC Bioinform. 10: 399 (2009) - [j24]Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res. 37(Web-Server-Issue): 90-94 (2009) - [j23]Shuoyong Shi, Bhadrachalam Chitturi, Nick V. Grishin:
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. Nucleic Acids Res. 37(Web-Server-Issue): 526-531 (2009) - [j22]Bong-Hyun Kim, Hua Cheng, Nick V. Grishin:
HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web-Server-Issue): 532-538 (2009) - 2008
- [j21]James O. Wrabl, Nick V. Grishin:
Statistics of Random Protein Superpositions: p-Values for Pairwise Structure Alignment. J. Comput. Biol. 15(3): 317-355 (2008) - [j20]Hua Cheng, Bong-Hyun Kim, Nick V. Grishin:
MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res. 36(Database-Issue): 211-217 (2008) - [j19]Jimin Pei, Ming Tang, Nick V. Grishin:
PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res. 36(Web-Server-Issue): 30-34 (2008) - 2007
- [j18]Jimin Pei, Nick V. Grishin:
PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinform. 23(7): 802-808 (2007) - [j17]Shuoyong Shi, Yi Zhong, Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin:
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinform. 23(11): 1331-1338 (2007) - [j16]Yuan Qi, Ruslan Sadreyev, Yong Wang, Bong-Hyun Kim, Nick V. Grishin:
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinform. 8 (2007) - [j15]Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grishin:
PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res. 35(Web-Server-Issue): 649-652 (2007) - [j14]Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
COMPASS server for remote homology inference. Nucleic Acids Res. 35(Web-Server-Issue): 653-658 (2007) - 2006
- [j13]Jimin Pei, Wei Cai, Lisa N. Kinch, Nick V. Grishin:
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinform. 22(2): 164-171 (2006) - [j12]Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin:
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinform. 22(21): 2581-2584 (2006) - 2005
- [j11]S. Sri Krishna, Nick V. Grishin:
Structural drift: a possible path to protein fold change. Bioinform. 21(8): 1308-1310 (2005) - [j10]Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin:
PALSSE: A program to delineate linear secondary structural elements from protein structures. BMC Bioinform. 6: 202 (2005) - 2004
- [j9]Ruslan Sadreyev, Nick V. Grishin:
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinform. 20(6): 818-828 (2004) - [j8]Yuan Qi, Nick V. Grishin:
PCOAT: positional correlation analysis using multiple methods. Bioinform. 20(18): 3697-3699 (2004) - [j7]Ruslan Sadreyev, Nick V. Grishin:
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. BMC Bioinform. 5: 106 (2004) - [j6]Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin:
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies. BMC Bioinform. 5: 197 (2004) - [j5]Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, Leszek Rychlewski:
Detecting distant homology with Meta-BASIC. Nucleic Acids Res. 32(Web-Server-Issue): 576-581 (2004) - 2003
- [j4]Jimin Pei, Ruslan Sadreyev, Nick V. Grishin:
PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinform. 19(3): 427-428 (2003) - [j3]David Mittelman, Ruslan Sadreyev, Nick V. Grishin:
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinform. 19(12): 1531-1539 (2003) - 2002
- [j2]Vyacheslav N. Grishin, Nick V. Grishin:
Euclidian space and grouping of biological objects. Bioinform. 18(11): 1523-1534 (2002) - 2001
- [j1]Jimin Pei, Nick V. Grishin:
AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinform. 17(8): 700-712 (2001)
Coauthor Index
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