2019

• Capa, Maria; Nygren, Arne; Parapar, Julio; Bakken, Torkild; Meissner, Karin; Moreira, Juan. (2019) Systematic re-structure and new species of Sphaerodoridae (Annelida) after morphological revision and molecular phylogenetic analyses of the North East Atlantic fauna. ZooKeys. vol. 845.
• Ekrem, Torbjørn; Stur, Elisabeth; Bakken, Torkild; Martin, Michael David; Adamowicz, Sarah J.. (2019) Abstracts from the 8th International Barcode of Life Conference in Trondheim, Norway. Genome. vol. 62 (6).

2018

• Bakken, Torkild; Glasby, Christopher J.; Santos, Cinthya S. G.; Wilson, Robin S.. (2018) Nereididae Blainville, 1818. Handbook of Zoology Online.
• Bolotov, Ivan N.; Aksenova, Olga V.; Bakken, Torkild; Glasby, Christopher J.; Gofarov, Mikhail Yu.; Kondakov, Alexander V.; Konopleva, Ekaterina S.; Lopes-Lima, Manuel; Lyubas, Artyom A.; Wang, Yu; Bychkov, Andrey Yu.; Sokolova, Agniya M.; Tanmuangpak, Kitti; Tumpeesuwan, Sakboworn; Vikhrev, Ilya V.; Shyu, J. Bruce H.; Win, Than; Pokrovsky, Oleg S.. (2018) Discovery of a silicate rock-boring organism and macrobioerosion in fresh water. Nature Communications. vol. 9 (1).
• Capa, Maria; Bakken, Torkild; Meissner, Karin; Nygren, Arne. (2018) Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization of Ephesiella, Ephesiopsis and Sphaerodorum. PeerJ. vol. 6.
• Davidsen, Jan Grimsrud; Thingstad, Per Gustav; Øien, Dag-Inge; Bakken, Torkild; Eidnes, Grim; Kjærstad, Gaute. (2018) Utfylling av områder på og rundt Langøra sør, Stjørdal. Konsekvenser for naturverdier og vurdering av restaurerende og kompenserende tiltak. 2018. ISBN 978-82-8322-132-9. NTNU Vitenskapsmuseet naturhistorisk rapport (3).
• Nygren, Arne; Parapar, Julio; Pons, Joan; Meißner, Karin; Bakken, Torkild; Kongsrud, Jon Anders; Oug, Eivind; Gaeva, Daria; Sikorski, Andrey; Johansen, Robert André; Hutchings, Pat Ann; Lavasque, Nicolas; Capa Corrales, Maria. (2018) A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic. PLOS ONE. vol. 13 (6).
• Villalobos-Guerrero, Tulio F.; Bakken, Torkild. (2018) Revision of the Alitta virens species complex (Annelida: Nereididae) from the North Pacific Ocean. Zootaxa. vol. 4483 (2).

2017

• Frafjord, Karl; Bakken, Torkild; Kubicek, Lukas; Rønning, Ann-Helen; Syvertsen, Per Ole. (2017) Records of ocean sunfish Mola mola along the Norwegian coast spanning two centuries, 1801-2015. Journal of Fish Biology. vol. 91 (5).
• Korshunova, Tatiana; Martynov, Alexander; Bakken, Torkild; Evertsen, Jussi; Fletcher, Karin; Mudianta, I Wayan; Saito, Hiroshi; Lundin, Kennet; Schrödl, Michael; Picton, Bernard. (2017) Polyphyly of the traditional family Flabellinidae affects a major group of Nudibranchia: aeolidacean taxonomic reassessment with descriptions of several new families, genera, and species (Mollusca, Gastropoda). ZooKeys. vol. 717.
• Korshunova, Tatiana; Martynov, Alexander; Bakken, Torkild; Picton, Bernard. (2017) External diversity is restrained by internal conservatism: New nudibranch mollusc contributes to the cryptic species problem. Zoologica Scripta. vol. 46 (6).
• Sneli, Jon-Arne; Bakken, Torkild. (2017) New records of the rare gastropods Erato voluta and Simnia patula, and first record of Simnia hiscocki from Norway. Fauna Norvegica. vol. 37.

2016

• Capa, Maria; Osborn, Karen J; Bakken, Torkild. (2016) Sphaerodoridae (Annelida) of the deep northwestern Atlantic, including remarkable new species of Euritmia and sphaerephesia. ZooKeys. vol. 2016 (615).
• Oug, Eivind; Bakken, Torkild; Kongsrud, Jon Anders; Alvestad, Tom. (2016) Polychaetous annelids in the deep Nordic Seas: Strong bathymetric gradients, low diversity and underdeveloped taxonomy. Deep-sea research. Part II, Topical studies in oceanography. vol. 137.

2015

• Altin, Dag; Bakken, Torkild; Rapp, Hans Tore; Kaltenborn, Anita; Sandlund, Vera. (2015) Systematisk oversikt i faunistikk. BI1002 Faunistikk og floristikk. Utgave 3.0. 2015.
• Bakken, Torkild; Oug, Eivind; Haraldsen, Trond Knapp; Sloreid, Svein Erik; Bremnes, Trond; Dolmen, Dag. (2015) Leddormer - Annelida. Norsk rødliste for arter 2015. Versjon 1.2.
• Capa, Maria; Aguado, Maria Teresa; Bakken, Torkild. (2015) Phylogenetic hypothesis of Sphaerodoridae Malmgren, 1867 (Annelida) and its position within Phyllodocida. Cladistics.
• Capa, Maria; Bakken, Torkild. (2015) Revision of the Australian Sphaerodoridae (Annelida) including the description of four new species. Zootaxa. vol. 4000 (2).
• Oug, Eivind; Christiansen, Marit Ellen; Dobbe, Kristine; Rønning, Ann-Helen; Bakken, Torkild; Kongsrud, Jon Anders. (2015) Mapping of marine benthic invertebrates in the Oslofjord and the Skagerrak: sampling data of museum collections from 1950–1955 and from recent investigations. Fauna Norvegica. vol. 35.
• Thingstad, Per Gustav; Bakken, Torkild; Stokland, Øystein. (2015) Ramsarområdet Tautra med Svaet: Respons hos vannfugl og bunndyrfauna på bruåpningen i veimoloen ut til Tautra. 2015. ISBN 978-82-8322-048-3. NTNU Vitenskapsmuseet naturhistorisk notat (7).

2014

• Lynghammar, Arve; Christiansen, Jørgen Schou; Griffiths, Andrew M.; Fevolden, Svein-Erik; Hop, Haakon; Bakken, Torkild. (2014) DNA barcoding of the northern Northeast Atlantic skates (Chondrichthyes, Rajiformes), with remarks on the widely distributed starry ray. Zoologica Scripta. vol. 43 (5).
• Bakken, Torkild. (2014) Svaets bunndyrfauna. Tautra - den mangfoldige fugleøya i Trondheimsfjorden.
• Bakken, Torkild; Oug, Eivind; Kongsrud, Jon Anders. (2014) Occurrence and distribution of Pseudoscalibregma and Scalibregma (Annelida, Scalibregmatidae) in the deep Nordic Seas, with the description of Scalibregma hanseni n. sp. Zootaxa. vol. 3753 (2).
• Capa, Maria; Bakken, Torkild; Purschke, Günter. (2014) Sphaerodoridae Malmgren, 1867. Handbook of Zoology Online.
• Oug, Eivind; Bakken, Torkild; Kongsrud, Jon Anders. (2014) Original specimens and type localities of early described polychaete species (Annelida) from Norway, with particular attention to species described by O.F. Müller and M. Sars. Memoirs of Museum Victoria. vol. 71.

2013

• Evertsen, Jussi; Bakken, Torkild. (2013) Diversity of Norwegian sea slugs (Nudibranchia): new species to Norwegian coastal waters and new data on distribution of rare species. Fauna Norvegica. vol. 32.
• Kongsrud, Jon Anders; Budaeva, Nataliya; Barnich, Ruth; Oug, Eivind; Bakken, Torkild. (2013) Benthic polychaetes from the northern Mid-Atlantic Ridge between the Azores and the Reykjanes Ridge. Marine Biology Research. vol. 9 (5-6).
• Nygren, Arne; Bakken, Torkild. (2013) Familj Nereididae – rovmaskar. Bestämningsnyckel till och presentation av svenska familjer av havsborstmaskar.
• Nygren, Arne; Bakken, Torkild. (2013) Familj Sphaerodoridae – bollhudingar. Bestämningsnyckel till och presentation av svenska familjer av havsborstmaskar.
• Søreide, Fredrik; Bakken, Torkild; Jasinski, Marek E.. (2013) Archaeology and biology in the deep sea: The Ormen Lange marine archaeology project. OCEANS - Bergen, 2013 MTS/IEEE - Bergen, 10-14 June.

2012

• Bakken, Torkild; Fremstad, Eli; Aagaard, Kaare. (2012) Bishop Gunnerus as a naturalist: His impact on biodiversity research today. Aspects of Johan Ernst Gunnerus' life and work.

2011

• Glasby, Christopher J.; Wilson, Robin S.; Bakken, Torkild. (2011) Redescription of the Indo-Pacific polychaete Neanthes pachychaeta (Fauvel, 1918) n. comb. (Annelida, Phyllodocida, Nereididae) and its synonyms. Zoosystema. vol. 33 (3).
• Griffiths, Andrew M.; Sims, David W.; Johnson, Andrew; Lynghammar, Arve; McHugh, Matthew; Bakken, Torkild; Genner, Martin J.. (2011) Levels of connectivity between longnose skate (Dipturus oxyrinchus) in the Mediterranean Sea and the north-eastern Atlantic Ocean. Conservation Genetics. vol. 12 (2).
• Kongsrud, Jon Anders; Bakken, Torkild; Oug, Eivind. (2011) Deep-water species of the genus Ophelina (Annelida, Opheliidae) in the Nordic Seas, with the description of Ophelina brattegardi sp. nov. The Italian journal of zoology. vol. 78.

2010

• Oug, Eivind; Gjøsæter, Jakob; Anker-Nilssen, Tycho; Bakken, Torkild; Sneli, Jon-Arne; Rueness, Jan. (2010) Marine environments. Environmental conditions and impacts for red list species.
• Bakken, Torkild; Kongsrud, Jon Anders; Oug, Eivind; Cochrane, Sabine; Moen, Toril Loennechen; Solbakken, Beata Elisabeth Borowiec. (2010) Polychaetes from Jan Mayen (Annelida, Polychaeta). Polar Research. vol. 29 (1).
• Schander, Christoffer; Rapp, Hans Tore; Kongsrud, Jon Anders; Bakken, Torkild; Berge, Jørgen; Cochrane, Sabine; Oug, Eivind; Byrkjedal, Ingvar; Todt, Christiane; Cedhagen, Tomas; Fosshagen, Audun; Gebruk, Andrey; Larsen, Kim; Levin, Lisa; Obst, Matthias; Pleijel, Fredrik; Stöhr, Sabine; Warén, Anders; Mikkelsen, Nina Therese; Hadler-Jacobsen, Silje Hope; Keuning, Rozemarijn; Petersen, Kristin Heggøy; Thorseth, Ingunn Hindenes; Pedersen, Rolf-Birger. (2010) The fauna of hydrothermal vents on the Mohn Ridge (North Atlantic). Marine Biology Research. vol. 6 (2).

2009

• Bakken, Torkild; Glasby, Christopher J.; Wilson, Robin S.. (2009) A review of paragnath morphology in Nereididae (Polychaeta). Zoosymposia. vol. 2.
• Bakken, Torkild; Stenøien, Hans K.. (2009) Systematikk, systembiologi, biosystematikk, taksonomi, floristikk og faunistikk: en storrengjøring. Biolog. vol. 2.

2007

• Bakken, Torkild. (2007) Revision of Pseudonereis (Polychaeta, Nereididae). Zoological Journal of the Linnean Society. vol. 150.

2006

• Kålås, John Atle; Viken, Åslaug; Bakken, Torkild. (2006) Norsk Rødliste 2006 - 2006 Norwegian Red List. 2006. ISBN 82-92838-00-7.

2005

• Evertsen, Jussi; Bakken, Torkild. (2005) Nudibranch diversity (Heterobranchia, Gastropoda) along the coast of Norway. Fauna Norvegica. vol. 25.
• Bakken, Torkild; Wilson, Robin S.. (2005) Phylogeny of nereidids (Polychaeta, Nereididae) with paragnaths. Zoologica Scripta. vol. 34.

2004

• Bakken, Torkild. (2004) A revision of Nereidinae (Polychaeta, Nereididae). 2004. ISBN 82-471-6205-9.

2003

• Bakken, Torkild. (2003) Redescription and resurrection of Typhlonereis gracilis Hansen, 1879 (Polychaeta, Nereididae). Sarsia. vol. 88 (5).
• Wilson, Robin S.; Bakken, Torkild. (2003) Sphaerodoridae (Polychaeta)�A DELTA database of genera, and Australian species. In RS Wilson, PA Hutchings & GJ Glasby (eds) Polychaetes: Interactive identification and information retrieval.
• Wilson, Robin S.; Bakken, Torkild; Glasby, Christopher J.. (2003) Nereididae (Polychaeta)�A DELTA database of genera, and Australian species. In RS Wilson, PA Hutchings & CJ Glasby (eds) Polychaetes: Interactive identification and information retrieval.

2002

• Bakken, Torkild. (2002) A new species of Neanthes (Polychaeta: Nereididae) from southern Australia. Memoirs of Museum Victoria (Nedlagt 1998). vol. 59 (2).
• Bakken, Torkild; Holthe, Torleif. (2002) Haliphron atlanticum (Cephalopoda, Alloposidae) caught in Skjørafjorden (64°N), Norway. Fauna Norvegica. vol. 22.
• Evertsen, Jussi; Bakken, Torkild. (2002) Heterobranchia (Mollusca, Gastropoda) from northern Norway, with notes on ecology and distribution. Fauna Norvegica. vol. 22.

2001

• Bakken, Torkild. (2001) Sjøstjernen Brisinga endecacnemos i Norge, og dens oppdager - P. Chr. Asbjørnsen. Fauna. vol. 54 (1).
• Bakken, Torkild; Moen, Toril Loennechen. (2001) Er scalpellidene (Cirripedia, Scalpellidae) i de Nordiske hav en biogeografisk avgrenset gruppe?. Norske havforskeres forening, årsmøte . [Mangler data]; Bodø. 2001-11-25.

1999

• Bakken, Torkild. (1999) A catalogue of the type specimens of protozoans, invertebrates and fish in the Museum of Natural History and Archaeology, NTNU. Gunneria. vol. 74.
• Mancini, Ines; Guerriero, Antonio; Guella, Graziano; Bakken, Torkild; Zibrowius, Helmut; Pietra, Francesco. (1999) Novel 10-hydroxydocosapolyenoic acids from deep-water scleractinian corals. Helvetica Chimica Acta. vol. 82.

1997

• Bakken, Torkild. (1997) Systematikken til Nereididae og Sphaerodoridae (Polychaeta: Annelida) og deres geografiske utbredelse i norske og tilstøtende arktiske farvann. 1997.