A citation-based method for searching scientific literature

Thomas Willems, Dina Zielinski, Jie Yuan, Assaf Gordon, Melissa Gymrek, Yaniv Erlich. Nat Methods 2017
Times Cited: 79







List of co-cited articles
549 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


lobSTR: A short tandem repeat profiler for personal genomes.
Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich. Genome Res 2012
177
43

The landscape of human STR variation.
Thomas Willems, Melissa Gymrek, Gareth Highnam, David Mittelman, Yaniv Erlich. Genome Res 2014
123
31

Abundant contribution of short tandem repeats to gene expression variation in humans.
Melissa Gymrek, Thomas Willems, Audrey Guilmatre, Haoyang Zeng, Barak Markus, Stoyan Georgiev, Mark J Daly, Alkes L Price, Jonathan K Pritchard, Andrew J Sharp,[...]. Nat Genet 2016
151
30

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
27


Detection of long repeat expansions from PCR-free whole-genome sequence data.
Egor Dolzhenko, Joke J F A van Vugt, Richard J Shaw, Mitchell A Bekritsky, Marka van Blitterswijk, Giuseppe Narzisi, Subramanian S Ajay, Vani Rajan, Bryan R Lajoie, Nathan H Johnson,[...]. Genome Res 2017
139
25

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.
Gareth Highnam, Christopher Franck, Andy Martin, Calvin Stephens, Ashwin Puthige, David Mittelman. Nucleic Acids Res 2013
87
24

Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes.
Haibao Tang, Ewen F Kirkness, Christoph Lippert, William H Biggs, Martin Fabani, Ernesto Guzman, Smriti Ramakrishnan, Victor Lavrenko, Boyko Kakaradov, Claire Hou,[...]. Am J Hum Genet 2017
57
33

A genomic view of short tandem repeats.
Melissa Gymrek. Curr Opin Genet Dev 2017
35
51



STRetch: detecting and discovering pathogenic short tandem repeat expansions.
Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua S Clayton, Nigel G Laing,[...]. Genome Biol 2018
54
29


Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.
Javier Quilez, Audrey Guilmatre, Paras Garg, Gareth Highnam, Melissa Gymrek, Yaniv Erlich, Ricky S Joshi, David Mittelman, Andrew J Sharp. Nucleic Acids Res 2016
53
24

Interpreting short tandem repeat variations in humans using mutational constraint.
Melissa Gymrek, Thomas Willems, David Reich, Yaniv Erlich. Nat Genet 2017
27
44

Profiling the genome-wide landscape of tandem repeat expansions.
Nima Mousavi, Sharona Shleizer-Burko, Richard Yanicky, Melissa Gymrek. Nucleic Acids Res 2019
44
27

The impact of short tandem repeat variation on gene expression.
Stephanie Feupe Fotsing, Jonathan Margoliash, Catherine Wang, Shubham Saini, Richard Yanicky, Sharona Shleizer-Burko, Alon Goren, Melissa Gymrek. Nat Genet 2019
37
32

A direct characterization of human mutation based on microsatellites.
James X Sun, Agnar Helgason, Gisli Masson, Sigríður Sunna Ebenesersdóttir, Heng Li, Swapan Mallick, Sante Gnerre, Nick Patterson, Augustine Kong, David Reich,[...]. Nat Genet 2012
178
13

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
13

Inferring short tandem repeat variation from paired-end short reads.
Minh Duc Cao, Edward Tasker, Kai Willadsen, Michael Imelfort, Sailaja Vishwanathan, Sridevi Sureshkumar, Sureshkumar Balasubramanian, Mikael Bodén. Nucleic Acids Res 2014
34
32

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
13

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
13


popSTR: population-scale detection of STR variants.
Snædís Kristmundsdóttir, Brynja D Sigurpálsdóttir, Birte Kehr, Bjarni V Halldórsson. Bioinformatics 2017
15
66

Variable tandem repeats accelerate evolution of coding and regulatory sequences.
Rita Gemayel, Marcelo D Vinces, Matthieu Legendre, Kevin J Verstrepen. Annu Rev Genet 2010
329
12

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
12


The overdue promise of short tandem repeat variation for heritability.
Maximilian O Press, Keisha D Carlson, Christine Queitsch. Trends Genet 2014
51
17

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
620
11

An integrated map of structural variation in 2,504 human genomes.
Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz,[...]. Nature 2015
11

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.
Arkarachai Fungtammasan, Guruprasad Ananda, Suzanne E Hile, Marcia Shu-Wei Su, Chen Sun, Robert Harris, Paul Medvedev, Kristin Eckert, Kateryna D Makova. Genome Res 2015
47
19

Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data.
Rick M Tankard, Mark F Bennett, Peter Degorski, Martin B Delatycki, Paul J Lockhart, Melanie Bahlo. Am J Hum Genet 2018
42
21

Repeat expansion disease: progress and puzzles in disease pathogenesis.
Albert R La Spada, J Paul Taylor. Nat Rev Genet 2010
296
10

Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates.
Thomas Willems, Melissa Gymrek, G David Poznik, Chris Tyler-Smith, Yaniv Erlich. Am J Hum Genet 2016
41
19

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon,[...]. Nature 2016
555
10

Analysis of protein-coding genetic variation in 60,706 humans.
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O'Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings,[...]. Nature 2016
10

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna,[...]. Nat Genet 2011
10

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
10

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J Cox, Semyon Kruglyak, Christopher T Saunders. Bioinformatics 2016
593
8



Large-scale analysis of tandem repeat variability in the human genome.
Jorge Duitama, Alena Zablotskaya, Rita Gemayel, An Jansen, Stefanie Belet, Joris R Vermeesch, Kevin J Verstrepen, Guy Froyen. Nucleic Acids Res 2014
38
18

Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements.
Sterling Sawaya, Andrew Bagshaw, Emmanuel Buschiazzo, Pankaj Kumar, Shantanu Chowdhury, Michael A Black, Neil Gemmell. PLoS One 2013
90
8

Unstable tandem repeats in promoters confer transcriptional evolvability.
Marcelo D Vinces, Matthieu Legendre, Marina Caldara, Masaki Hagihara, Kevin J Verstrepen. Science 2009
215
8

The impact of structural variation on human gene expression.
Colby Chiang, Alexandra J Scott, Joe R Davis, Emily K Tsang, Xin Li, Yungil Kim, Tarik Hadzic, Farhan N Damani, Liron Ganel, Stephen B Montgomery,[...]. Nat Genet 2017
139
8

Fast STR allele identification with STRait Razor 3.0.
August E Woerner, Jonathan L King, Bruce Budowle. Forensic Sci Int Genet 2017
45
13

Characterization of genetic sequence variation of 58 STR loci in four major population groups.
Nicole M M Novroski, Jonathan L King, Jennifer D Churchill, Lay Hong Seah, Bruce Budowle. Forensic Sci Int Genet 2016
90
7

Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Justin M Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E Mason, Noah Alexander,[...]. Sci Data 2016
270
7

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.
Tugce Bilgin Sonay, Tiago Carvalho, Mark D Robinson, Maja P Greminger, Michael Krützen, David Comas, Gareth Highnam, David Mittelman, Andrew Sharp, Tomàs Marques-Bonet,[...]. Genome Res 2015
38
15

Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n.
E J Kremer, M Pritchard, M Lynch, S Yu, K Holman, E Baker, S T Warren, D Schlessinger, G R Sutherland, R I Richards. Science 1991
813
7


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.