Tools listed below are actively maintained by the lab

MOAT: Efficient Detection of Highly Mutated Regions with the Mutations Overburdening Annotations Tool.
L Lochovsky, J Zhang, M Gerstein (2017). Bioinformatics.

Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.
S Balasubramanian, Y Fu, M Pawashe, P McGillivray, M Jin, J Liu, KJ Karczewski, DG MacArthur, M Gerstein (2017). Nat Commun 8: 382.

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.
KK Yan, GG Yardimci, C Yan, WS Noble, M Gerstein (2017). Bioinformatics 33: 2199-2201.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.
J Chen, J Rozowsky, TR Galeev, A Harmanci, R Kitchen, J Bedford, A Abyzov, Y Kong, L Regan, M Gerstein (2016). Nat Commun 7: 11101.

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.
D Clarke, A Sethi, S Li, S Kumar, RWF Chang, J Chen, M Gerstein (2016). Structure 24: 826-837.

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.
L Lochovsky, J Zhang, Y Fu, E Khurana, M Gerstein (2015). Nucleic Acids Res 43: 8123-34.

Loregic: a method to characterize the cooperative logic of regulatory factors.
D Wang, KK Yan, C Sisu, C Cheng, J Rozowsky, W Meyerson, MB Gerstein (2015). PLoS Comput Biol 11: e1004132.

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.
A Harmanci, J Rozowsky, M Gerstein (2014). Genome Biol 15: 474.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Y Fu, Z Liu, S Lou, J Bedford, XJ Mu, KY Yip, E Khurana, M Gerstein (2014). Genome Biol 15: 480.

Integrative annotation of variants from 1092 humans: application to cancer genomics.
E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, L Lochovsky, J Chen, A Harmanci, J Das, A Abyzov, S Balasubramanian, K Beal, D Chakravarty, D Challis, Y Chen, D Clarke, L Clarke, F Cunningham, US Evani, P Flicek, R Fragoza, E Garrison, R Gibbs, ZH Gumus, J Herrero, N Kitabayashi, Y Kong, K Lage, V Liluashvili, SM Lipkin, DG MacArthur, G Marth, D Muzny, TH Pers, GR Ritchie, JA Rosenfeld, C Sisu, X Wei, M Wilson, Y Xue, F Yu, 1000 Genomes Project Consortium, ET Dermitzakis, H Yu, MA Rubin, C Tyler-Smith, M Gerstein (2013). Science 342: 1235587

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
L Habegger, S Balasubramanian, DZ Chen, E Khurana, A Sboner, A Harmanci, J Rozowsky, D Clarke, M Snyder, M Gerstein (2012). Bioinformatics 28: 2267-9.

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.
J Du, J Leng, L Habegger, A Sboner, D McDermott, M Gerstein (2012). PLoS One 7: e29175.

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.
N Bhardwaj, A Abyzov, D Clarke, C Shou, MB Gerstein (2011). Protein Sci 20: 1745-54.

AlleleSeq: analysis of allele-specific expression and binding in a network framework.
J Rozowsky, A Abyzov, J Wang, P Alves, D Raha, A Harmanci, J Leng, R Bjornson, Y Kong, N Kitabayashi, N Bhardwaj, M Rubin, M Snyder, M Gerstein (2011). Mol Syst Biol 7: 522.

ACT: aggregation and correlation toolbox for analyses of genome tracks.
J Jee, J Rozowsky, KY Yip, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein (2011). Bioinformatics 27: 1152-4.

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
A Abyzov, AE Urban, M Snyder, M Gerstein (2011). Genome Res 21: 974-84.

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
A Abyzov, M Gerstein (2011). Bioinformatics 27: 595-603.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
L Habegger, A Sboner, TA Gianoulis, J Rozowsky, A Agarwal, M Snyder, M Gerstein (2011). Bioinformatics 27: 281-3.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
A Sboner, L Habegger, D Pflueger, S Terry, DZ Chen, JS Rozowsky, AK Tewari, N Kitabayashi, BJ Moss, MS Chee, F Demichelis, MA Rubin, MB Gerstein (2010). Genome Biol 11: R104.

3V: cavity, channel and cleft volume calculator and extractor.
NR Voss, M Gerstein (2010). Nucleic Acids Res 38: W555-62.

MOTIPS: automated motif analysis for predicting targets of modular protein domains.
HY Lam, PM Kim, J Mok, R Tonikian, SS Sidhu, BE Turk, M Snyder, MB Gerstein (2010). BMC Bioinformatics 11: 243.

Relating protein conformational changes to packing efficiency and disorder.
N Bhardwaj, M Gerstein (2009). Protein Sci 18: 1230-40.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009). Genome Biol 10: R23.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009). Nat Biotechnol 27: 66-75.

An integrated system for studying residue coevolution in proteins.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008). Bioinformatics 24: 290-2.

PARE: a tool for comparing protein abundance and mRNA expression data.
EZ Yu, AE Burba, M Gerstein (2007). BMC Bioinformatics 8: 309. a comprehensive database and comparison platform for pseudogene annotation.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein (2007). Nucleic Acids Res 35: D55-60.

Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
AE Burba, U Lehnert, EZ Yu, M Gerstein (2006). Bioinformatics 22: 2735-8.

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22: 2968-70.

The Database of Macromolecular Motions: new features added at the decade mark.
S Flores, N Echols, D Milburn, B Hespenheide, K Keating, J Lu, S Wells, EZ Yu, M Thorpe, M Gerstein (2006). Nucleic Acids Res 34: D296-301.

PubNet: a flexible system for visualizing literature derived networks.
SM Douglas, GT Montelione, M Gerstein (2005). Genome Biol 6: R80.

Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.
NR Voss, M Gerstein (2005). J Mol Biol 346: 477-92.

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.
H Yu, X Zhu, D Greenbaum, J Karro, M Gerstein (2004). Nucleic Acids Res 32: 328-37.

MolMovDB: analysis and visualization of conformational change and structural flexibility.
N Echols, D Milburn, M Gerstein (2003). Nucleic Acids Res 31: 478-82.

Calculations of protein volumes: sensitivity analysis and parameter database.
J Tsai, M Gerstein (2002). Bioinformatics 18: 985-95.

Determining the minimum number of types necessary to represent the sizes of protein atoms.
J Tsai, N Voss, M Gerstein (2001). Bioinformatics 17: 949-56.

Protein Geometry: Distances, Areas, and Volumes
M Gerstein, F M Richards (2001). International Tables for Crystallography (Volume F, Chapter 22.1.1, pages 531-539; M Rossmann & E Arnold, editors; Dordrecht: Kluwer)

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
WG Krebs, M Gerstein (2000). Nucleic Acids Res 28: 1665-75.

A database of macromolecular motions.
M Gerstein, W Krebs (1998). Nucleic Acids Res 26: 4280-90.

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