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Sequence alignment

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

James A. Stapleton, Jeongwoon Kim, [ ... ], Timothy A. Whitehead

On the Evolutionary History of Uleiella chilensis, a Smut Fungus Parasite of Araucaria araucana in South America: Uleiellales ord. nov. in Ustilaginomycetes

Kai Riess, Max E. Schön, [ ... ], Sigisfredo Garnica

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

Lei Hua, Yang Song, [ ... ], Tamar Schlick

A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing

Elizabeth P. St. John, Birgitte B. Simen, [ ... ], 454 HIV-1 Alpha Study Group

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline

Mark Davids, Floor Hugenholtz, [ ... ], Peter J. Schaap

Identification and Functional Analysis of the Mycophenolic Acid Gene Cluster of Penicillium roqueforti

Abdiel Del-Cid, Carlos Gil-Durán, [ ... ], Renato Chávez

DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes

Romana Iftikhar, Muhammad Ashfaq, Akhtar Rasool, Paul D. N. Hebert

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

Deanne W. Sammond, Noah Kastelowitz, [ ... ], Yannick J. Bomble

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

Michael J. Ford, Jennifer Hempelmann, [ ... ], Linda K. Park

SeqFeatR for the Discovery of Feature-Sequence Associations

Bettina Budeus, Jörg Timm, Daniel Hoffmann

Decoding Biomass-Sensing Regulons of Clostridium thermocellum Alternative Sigma-I Factors in a Heterologous Bacillus subtilis Host System

Iván Muñoz-Gutiérrez, Lizett Ortiz de Ora, [ ... ], Ilya Borovok

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

Loren A. Honaas, Eric K. Wafula, [ ... ], Claude W. dePamphilis

“Candidatus Fokinia solitaria”, a Novel “Stand-Alone” Symbiotic Lineage of Midichloriaceae (Rickettsiales)

Franziska Szokoli, Elena Sabaneyeva, [ ... ], Giulio Petroni

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