Genome-scale Disk-based Suffix Tree Indexing
Summary: Genome-scale disk-based suffix tree: Trellis preserves suffix links and enables external indexing for DNA sequences. Index the human genome in ~4h with 2GB RAM and ~2h suffix-link recovery, outpacing prior methods on index and query performance. (summarized by gpt-5-nano on Feb 09 2026)
Incoming Non-self Citations Over Time
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Incoming Citations (Sorted by Pagerank)
Showing 4 of 4 citing papers.
| Rank | Citing Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 4,550 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.0866239e-05 |
| 6,319 | ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings | 2012 | VLDB | 5.1083749e-05 |
| 12,108 | RACE: A Scalable and Elastic Parallel System for Discovering Repeats in Very Long Sequences | 2013 | VLDB | 4.1905499e-05 |
| 12,373 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD | 4.1905499e-05 |
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Outgoing Citations (Sorted by Pagerank)
Showing 2 of 2 cited papers.
Citations counted here include only citations to other VLDB/SIGMOD/CIDR/PODS papers in this database.
| Rank | Cited Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 1,115 | A Database Index to Large Biological Sequences | 2001 | VLDB | 0.00013865352 |
| 2,586 | Practical Suffix Tree Construction | 2004 | VLDB | 8.4894627e-05 |
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Semantically Similar Papers
| Overall Rank | Paper | Year | Venue | Pagerank |
|---|---|---|---|---|
| 5,624 | A Scalable Index for Top-k Subtree Similarity Queries | 2019 | SIGMOD | 5.4049016e-05 |
| 12,094 | RCSI: Scalable similarity search in thousand(s) of genomes | 2013 | VLDB | 4.1905499e-05 |
| 13,468 | Memory Efficient Minimum Substring Partitioning | 2013 | VLDB | - |
| 6,458 | Reference-Based Indexing of Sequence Databases | 2006 | VLDB | 5.0484248e-05 |
| 4,375 | Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO) | 2021 | SIGMOD | 6.2345844e-05 |
| 12,373 | Improving Suffix Array Locality for Fast Pattern Matching on Disk | 2008 | SIGMOD | 4.1905499e-05 |
| 2,586 | Practical Suffix Tree Construction | 2004 | VLDB | 8.4894627e-05 |
| 6,319 | ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings | 2012 | VLDB | 5.1083749e-05 |
| 1,115 | A Database Index to Large Biological Sequences | 2001 | VLDB | 0.00013865352 |
| 4,550 | Serial and Parallel Methods for I/O Efficient Suffix Tree Construction | 2009 | SIGMOD | 6.0866239e-05 |