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Method

Optimal marker genes for c-separated cell types with SepSolve

  • Bartol Borozan
  • Tomislav Prusina
  • Luka Borozan
  • Domagoj Ševerdija
  • Francisca Rojas Ringeling
  • Domagoj Matijević
  • Stefan Canzar
  • First Published October 9, 2025
Method

Partial alignment of multislice spatially resolved transcriptomics data

  • Xinhao Liu
  • Ron Zeira
  • Benjamin J. Raphael
  • First Published August 8, 2023
Method

Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data

  • Van Hoan Do
  • Francisca Rojas Ringeling
  • Stefan Canzar
  • First Published February 24, 2021
Corrigendum

Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping

  • Jordan A. Ramilowski
  • Chi Wai Yip
  • Saumya Agrawal
  • Jen-Chien Chang
  • Yari Ciani
  • Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
  • ... [+107 authors] ...,
  • Ken Yagi
  • Michiel J.L. de Hoon
  • Jay W. Shin
  • Piero Carninci
  • First Published September 14, 2020
Method

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

  • Sergey Aganezov
  • Benjamin J. Raphael
  • First Published September 4, 2020
Resource

Functional annotation of human long noncoding RNAs via molecular phenotyping

  • Jordan A. Ramilowski
  • Chi Wai Yip
  • Saumya Agrawal
  • Jen-Chien Chang
  • Yari Ciani
  • Ivan V. Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F. Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V. Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher J.F. Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L. Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S. Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J. Makeev Luigi Marchionni Yulia A. Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R. Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J.C. Parr Owen J.L. Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A.M. Semple Youtaro Shibayama Divya M. Sivaraman Takahiro Suzuki Suzannah C. Szumowski Michihira Tagami Martin S. Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E. Vorontsov Chinatsu Yamamoto Robert S. Young J. Kenneth Baillie Alistair R.R. Forrest Roderic Guigó Michael M. Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki
  • ... [+107 authors] ...,
  • Ken Yagi
  • Michiel J.L. de Hoon
  • Jay W. Shin
  • Piero Carninci
  • First Published July 27, 2020
Method

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

  • Jack Kuipers
  • Katharina Jahn
  • Benjamin J. Raphael
  • Niko Beerenwinkel
  • First Published October 13, 2017
Resource

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

  • R. Jay Mashl
  • Adam D. Scott
  • Kuan-lin Huang
  • Matthew A. Wyczalkowski
  • Christopher J. Yoon
  • Beifang Niu Erin DeNardo Venkata D. Yellapantula Robert E. Handsaker Ken Chen Daniel C. Koboldt Kai Ye
  • ... [+7 authors] ...,
  • David Fenyö
  • Benjamin J. Raphael
  • Michael C. Wendl
  • Li Ding
  • First Published May 18, 2017
Method

De novo discovery of mutated driver pathways in cancer

  • Fabio Vandin
  • Eli Upfal
  • Benjamin J. Raphael
  • First Published June 7, 2011
Methods

Decoding the fine-scale structure of a breast cancer genome and transcriptome

  • Stanislav Volik
  • Benjamin J. Raphael
  • Guiqing Huang
  • Michael R. Stratton
  • Graham Bignel
  • John Murnane John H. Brebner Krystyna Bajsarowicz Pamela L. Paris Quanzhou Tao David Kowbel Anna Lapuk Dmitri A. Shagin Irina A. Shagina Joe W. Gray
  • ... [+10 authors] ...,
  • Jan-Fang Cheng
  • Pieter J. de Jong
  • Pavel Pevzner
  • Colin Collins
  • First Published February 3, 2006
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