The Gerstein lab has made it a priority to develop its cutting edge algorithms into tools in the form of downloadable programs, webservers, and databases. These tools are the heart of our work in transforming the big data of genomes into knowledge. For a full list of tools, with links to download, see the lab tools page. The source code of many of our tools in avalable on our lab Github page
Z Bai, D Zhang, Y Gao, B Tao, D Zhang, S Bao, A Enninful, Y Wang, H Li, G Su, X Tian, N Zhang, Y Xiao, Y Liu, M Gerstein, M Li, Y Xing, J Lu, ML Xu, R Fan (2024). Cell 187: 6760-6779e24.
J Du, J Leng, L Habegger, A Sboner, D McDermott, M Gerstein (2012). PLoS One 7: e29175.
HY Lam, MJ Clark, R Chen, R Chen, G Natsoulis, M O'Huallachain, FE Dewey, L Habegger, EA Ashley, MB Gerstein, AJ Butte, HP Ji, M Snyder (2011). Nat Biotechnol 30: 78-82.
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.
ZD Zhang, J Du, H Lam, A Abyzov, AE Urban, M Snyder, M Gerstein (2011). BMC Genomics 12: 375.
XJ Mu, ZJ Lu, Y Kong, HY Lam, MB Gerstein (2011). Nucleic Acids Res 39: 7058-76.
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.
A Abyzov, AE Urban, M Snyder, M Gerstein (2011). Genome Res 21: 974-84.
A Abyzov, M Gerstein (2011). Bioinformatics 27: 595-603.
ZJ Lu, KY Yip, G Wang, C Shou, LW Hillier, E Khurana, A Agarwal, R Auerbach, J Rozowsky, C Cheng, M Kato, DM Miller, F Slack, M Snyder, RH Waterston, V Reinke, MB Gerstein (2011). Genome Res 21: 276-85.
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.
HY Lam, XJ Mu, AM Stutz, A Tanzer, PD Cayting, M Snyder, PM Kim, JO Korbel, MB Gerstein (2010). Nat Biotechnol 28: 47-55.
J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, MB Gerstein (2009). PLoS Comput Biol 5: e1000432.
JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009). Genome Biol 10: R23.
J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009). Nat Biotechnol 27: 66-75.
LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009). Genome Res 19: 106-17.
ZD Zhang, J Rozowsky, M Snyder, J Chang, M Gerstein (2008). PLoS Comput Biol 4: e1000158.
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