The pilot 1000 Genomes "rollout" from the Gerstein Lab includes:
(i) the "main" paper in Nature, which was the most highly cited paper of 2010 in Nature;
(ii) the high-level companions for SVs and LOF variants (both of which the Gerstein Lab made senior-author level contributions to); and
(iii) the other companions (relating variation to non-coding annotation, discovering SVs, and looking at allelic effects).

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.

Landscape and variation of novel retroduplications in 26 human populations.
Y Zhang, S Li, A Abyzov, MB Gerstein (2017). PLoS Comput Biol 13: e1005567.

A global reference for human genetic variation.
1000 Genomes Project Consortium, A Auton, LD Brooks, RM Durbin, EP Garrison, HM Kang, JO Korbel, JL Marchini, S McCarthy, GA McVean, GR Abecasis (2015). Nature 526: 68-74.

An integrated map of structural variation in 2,504 human genomes.
PH Sudmant, T Rausch, EJ Gardner, RE Handsaker, A Abyzov, J Huddleston, Y Zhang, K Ye, G Jun, MH Fritz, MK Konkel, A Malhotra, AM Stutz, X Shi, FP Casale, J Chen, F Hormozdiari, G Dayama, K Chen, M Malig, MJP Chaisson, K Walter, S Meiers, S Kashin, E Garrison, A Auton, HYK Lam, XJ Mu, C Alkan, D Antaki, T Bae, E Cerveira, P Chines, Z Chong, L Clarke, E Dal, L Ding, S Emery, X Fan, M Gujral, F Kahveci, JM Kidd, Y Kong, EW Lameijer, S McCarthy, P Flicek, RA Gibbs, G Marth, CE Mason, A Menelaou, DM Muzny, BJ Nelson, A Noor, NF Parrish, M Pendleton, A Quitadamo, B Raeder, EE Schadt, M Romanovitch, A Schlattl, R Sebra, AA Shabalin, A Untergasser, JA Walker, M Wang, F Yu, C Zhang, J Zhang, X Zheng-Bradley, W Zhou, T Zichner, J Sebat, MA Batzer, SA McCarroll, 1000 Genomes Project Consortium, RE Mills, MB Gerstein, A Bashir, O Stegle, SE Devine, C Lee, EE Eichler, JO Korbel (2015). Nature 526: 75-81.

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.
A Abyzov, S Li, DR Kim, M Mohiyuddin, AM Stutz, NF Parrish, XJ Mu, W Clark, K Chen, M Hurles, JO Korbel, HY Lam, C Lee, MB Gerstein (2015). Nat Commun 6: 7256.

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, GRS 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.

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.
A Abyzov, R Iskow, O Gokcumen, DW Radke, S Balasubramanian, B Pei, L Habegger, 1000 Genomes Project Consortium, C Lee, M Gerstein (2013). Genome Res 23: 2042-52.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
SB Montgomery, DL Goode, E Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter (2013). Genome Res 23: 749-61.

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, GR Abecasis, A Auton, LD Brooks, MA DePristo, RM Durbin, RE Handsaker, HM Kang, GT Marth, GA McVean (2012). Nature 491: 56-65.

A systematic survey of loss-of-function variants in human protein-coding genes.
DG MacArthur, S Balasubramanian, A Frankish, N Huang, J Morris, K Walter, L Jostins, L Habegger, JK Pickrell, SB Montgomery, CA Albers, ZD Zhang, DF Conrad, G Lunter, H Zheng, Q Ayub, MA DePristo, E Banks, M Hu, RE Handsaker, JA Rosenfeld, M Fromer, M Jin, XJ Mu, E Khurana, K Ye, M Kay, GI Saunders, MM Suner, T Hunt, IH Barnes, C Amid, DR Carvalho-Silva, AH Bignell, C Snow, B Yngvadottir, S Bumpstead, DN Cooper, Y Xue, IG Romero, 1000 Genomes Project Consortium, J Wang, Y Li, RA Gibbs, SA McCarroll, ET Dermitzakis, JK Pritchard, JC Barrett, J Harrow, ME Hurles, MB Gerstein, C Tyler-Smith (2012). Science 335: 823-8.

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.
RR Haraksingh, A Abyzov, M Gerstein, AE Urban, M Snyder (2011). PLoS One 6: e27859.

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.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.
XJ Mu, ZJ Lu, Y Kong, HY Lam, MB Gerstein (2011). Nucleic Acids Res 39: 7058-76.

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.

Mapping copy number variation by population-scale genome sequencing.
RE Mills, K Walter, C Stewart, RE Handsaker, K Chen, C Alkan, A Abyzov, SC Yoon, K Ye, RK Cheetham, A Chinwalla, DF Conrad, Y Fu, F Grubert, I Hajirasouliha, F Hormozdiari, LM Iakoucheva, Z Iqbal, S Kang, JM Kidd, MK Konkel, J Korn, E Khurana, D Kural, HY Lam, J Leng, R Li, Y Li, CY Lin, R Luo, XJ Mu, J Nemesh, HE Peckham, T Rausch, A Scally, X Shi, MP Stromberg, AM Stutz, AE Urban, JA Walker, J Wu, Y Zhang, ZD Zhang, MA Batzer, L Ding, GT Marth, G McVean, J Sebat, M Snyder, J Wang, K Ye, EE Eichler, MB Gerstein, ME Hurles, C Lee, SA McCarroll, JO Korbel, 1000 Genomes Project (2011). Nature 470: 59-65.

A map of human genome variation from population-scale sequencing
1000 Genomes Project Consortium, GR Abecasis, D Altshuler, A Auton, LD Brooks, RM Durbin, RA Gibbs, ME Hurles, GA McVean (2010). Nature 467: 1061-73.

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